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API Reference

cosmolkit.bio_from_mmcif(text) → BioStructure

Parse mmCIF text into a BioStructure using the native structural reader, retaining supported hierarchy, coordinates and metadata.

cosmolkit.bio_from_pdb(text: str, *, max_line_length: SupportsIndex | None = None, check_non_ascii: bool | None = None, ignore_ter: bool | None = None, split_chain_on_ter: bool | None = None, skip_remarks: bool | None = None) → BioStructure
cosmolkit.bio_from_pdb(text: str, params: BioPdbReadParams | None = None) → BioStructure

Parse PDB text into a BioStructure, retaining hierarchy, coordinates and supported structural metadata under the selected reader options.

cosmolkit.canonical_tautomer_from_molecules(molecules, params=None) → Molecule

Select the canonical tautomer from supplied molecular candidates using the native scoring policy.

cosmolkit.canonical_tautomer_from_molecules_with_params(molecules, params) → Molecule

Select the canonical tautomer from supplied candidates using the explicit native scoring parameters.

cosmolkit.compile_query(query) → CompiledQuery

Compile a QueryGraph into a reusable native query; invalid query state produces a structured error.

cosmolkit.default_tautomer_score_terms() → list[TautomerScoreTerm]

Return independent values for the canonical default tautomer-scoring terms.

cosmolkit.element_info(element) → ElementInfo

Return periodic-table metadata for the supplied Element from the canonical native table.

cosmolkit.expand_one_letter(code, kind) → str | None

Expand a one-letter residue code in the selected residue category; return None when the native table has no expansion.

cosmolkit.expand_one_letter_sequence(sequence, kind) → list[str]

Expand one-letter sequence codes using the selected residue category and native sequence expansion rules.

cosmolkit.explain_path_score(score, size=4) → list[tuple[str, int, int]]

Decode a topological-torsion path score into the canonical atom-code components for the specified path size.

cosmolkit.feature_spec(name) → FeatureSpec | None

Look up a public feature declaration by its exact name; return None for an unknown feature.

cosmolkit.feature_specs() → FeatureSpecIter

Iterate the canonical public feature declarations compiled into this library.

cosmolkit.find_residue_info(name) → ResidueInfo

Look up canonical residue information by name, returning the native unknown-residue entry when unrecognized.

cosmolkit.find_residue_info_index(name) → int

Look up a residue name in the canonical table, preserving the native unknown-name sentinel.

cosmolkit.fingerprint_layered_query_with_output_with_params(query, params) → LayeredFingerprintResult

Calculate a QueryGraph layered fingerprint with native additional output.

cosmolkit.fingerprint_layered_query_with_params(query, params) → Fingerprint

Calculate a layered path fingerprint for a QueryGraph using explicit LayeredFingerprintParams.

cosmolkit.fingerprint_pattern_query(query: QueryGraph, *, n_bits: SupportsIndex | None = None, tautomeric: bool | None = None) → Fingerprint
cosmolkit.fingerprint_pattern_query(query: QueryGraph, params: PatternFingerprintParams | None = None) → Fingerprint

Calculate the native pattern fingerprint for a QueryGraph with the selected bit width and query options.

cosmolkit.fingerprint_pattern_query_with_params(query, params) → Fingerprint

Calculate a QueryGraph pattern fingerprint with explicit PatternFingerprintParams.

cosmolkit.fingerprint_topological_query_with_output_with_params(query, params, request) → TopologicalFingerprintResult

Calculate a QueryGraph topological fingerprint together with the requested atom/bit provenance.

cosmolkit.fingerprint_topological_query_with_params(query, params) → Fingerprint

Calculate a path-based topological fingerprint for a QueryGraph using explicit parameters.

cosmolkit.inchi_to_key(inchi) → str

Convert an InChI string to its InChIKey; invalid input retains the native structured error.

cosmolkit.maximum_common_substructure(inputs: _typeshed.SupportsGetItem[int, Molecule], *, store_all: bool | None = None, maximize_bonds: bool | None = None, threshold: SupportsFloat | SupportsIndex | None = None, timeout: SupportsIndex | None = None, verbose: bool | None = None, atom_compare_parameters: McsAtomCompareParameters | None = None, bond_compare_parameters: McsBondCompareParameters | None = None, atom_comparator: McsAtomComparator | str | None = None, bond_comparator: McsBondComparator | str | None = None, initial_seed: str | None = None) → McsResult
cosmolkit.maximum_common_substructure(inputs: _typeshed.SupportsGetItem[int, Molecule], params: McsParameters | None = None) → McsResult

Search for the maximum common substructure of the supplied molecules using the selected matching, timeout and callback policy.

cosmolkit.maximum_common_substructure_with_params(inputs, params) → McsResult

Search for the maximum common substructure with explicit McsParameters, retaining native completion status and diagnostics.

cosmolkit.mol_from_binary(data) → Molecule

Decode COSMolKit molecular archive bytes through the canonical binary reader.

cosmolkit.mol_from_inchi(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None) → Molecule
cosmolkit.mol_from_inchi(text: str, params: InchiReadParams | None = None) → Molecule

Parse an InChI string into a molecular value with the selected sanitization and hydrogen-removal policy.

cosmolkit.mol_from_mmcif(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, flavor: PdbReadFlags | None = None, proximity_bonding: bool | None = None) → Molecule
cosmolkit.mol_from_mmcif(text: str, params: BioMoleculeParams | None = None) → Molecule

Parse mmCIF text into a molecular value using the selected structural and chemical conversion policy. This accepts content, not a path.

cosmolkit.mol_from_mol(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → Molecule
cosmolkit.mol_from_mol(text: str, params: SdfReadParams | None = None) → Molecule

Parse an MDL MolBlock into a molecular value using SdfReadParams or keyword options, not both.

cosmolkit.mol_from_mol2(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, variant: Mol2Type | str | None = None, cleanup_substructures: bool | None = None) → Molecule
cosmolkit.mol_from_mol2(text: str, params: Mol2ReadParams | None = None) → Molecule

Parse Tripos MOL2 text into a molecular value with the selected reader parameters.

cosmolkit.mol_from_pdb(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, flavor: PdbReadFlags | None = None, proximity_bonding: bool | None = None) → Molecule
cosmolkit.mol_from_pdb(text: str, params: BioMoleculeParams | None = None) → Molecule

Parse PDB text into a molecular value using the selected model, connectivity and sanitization policy. This accepts file content, not a path.

cosmolkit.mol_from_rdkit(rdmol, sanitize=None) → Molecule

Import an RDKit molecule through the native adapter, preserving the selected sanitization policy.

cosmolkit.mol_from_sdf(input: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → Molecule
cosmolkit.mol_from_sdf(input: str, params: SdfReadParams | None = None) → Molecule

Parse SDF text into a molecular value using SdfReadParams or keyword options, not both.

cosmolkit.mol_from_smiles(text: str, *, sanitize: bool | None = None, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None, parse_name: bool | None = None, remove_hs: bool | None = None, skip_cleanup: bool | None = None, debug_parse: bool | None = None, replacements: dict[str, str] | None = None) → Molecule
cosmolkit.mol_from_smiles(text: str, params: SmilesParseParams | None = None) → Molecule

Parse SMILES into a new Molecule. Supply SmilesParseParams or keyword options, not both; the native parsing and sanitization defaults are preserved.

cosmolkit.mol_from_xyz_block(text) → Molecule

Parse XYZ text into a molecular value with atom identities and coordinates; XYZ does not encode chemical bonds.

cosmolkit.mols_from_records(records, errors=None) → MoleculeBatch

Construct an ordered MoleculeBatch from the supplied native batch records, preserving missing records and their errors.

cosmolkit.mols_from_sdf_records(text: str, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → MoleculeBatch
cosmolkit.mols_from_sdf_records(text: str, read: SdfReadParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch

Convert SDF records into an ordered MoleculeBatch using the selected native record-conversion policy.

cosmolkit.mols_from_smiles_list(smiles: _typeshed.SupportsGetItem[int, str], *, params: BatchParams | None = None, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, sanitize: bool | None = None, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None, parse_name: bool | None = None, remove_hs: bool | None = None, skip_cleanup: bool | None = None, debug_parse: bool | None = None, replacements: dict[str, str] | None = None) → MoleculeBatch
cosmolkit.mols_from_smiles_list(smiles: _typeshed.SupportsGetItem[int, str], parse: SmilesParseParams | None = None, params: BatchParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch

Parse SMILES strings into an ordered MoleculeBatch. Parsing failures follow the selected errors policy; n_jobs controls native parallel work.

cosmolkit.operation_invariant(method) → OperationInvariantEntry | None

Look up invariant requirements for an exact operation method name, or None when unregistered.

cosmolkit.operation_invariant_matrix() → list[OperationInvariantEntry]

Return declared operation invariant requirements, generated from canonical operation declarations.

cosmolkit.operation_parity(method) → ParityMatrixEntry | None

Look up declared parity metadata for an exact operation method name, or None when unregistered.

cosmolkit.operation_spec(method) → MoleculeOpSpec | None

Look up the operation specification for an exact method name, or None if it is unregistered.

cosmolkit.operation_specs() → list[MoleculeOpSpec]

Return the molecule-operation specifications generated from the canonical operation declarations.

cosmolkit.parity_matrix() → list[ParityMatrixEntry]

Return declared operation parity metadata; this is not a report of a newly executed comparison.

cosmolkit.parse_smarts(text: str, *, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None, parse_name: bool | None = None, merge_hs: bool | None = None, skip_cleanup: bool | None = None, debug_parse: bool | None = None, replacements: dict[str, str] | None = None) → QueryGraph
cosmolkit.parse_smarts(text: str, params: SmartsParseParams | None = None) → QueryGraph

Parse SMARTS into a QueryGraph. Supply SmartsParseParams or keyword options, not both; syntax failures retain structured diagnostics.

cosmolkit.parse_smarts_with_params(text, params) → QueryGraph

Parse SMARTS into a QueryGraph with explicit SmartsParseParams.

cosmolkit.parse_smirks(text: str, *, use_smiles: bool | None = None, sanitize: bool | None = None, replacements: dict[str, str] | None = None, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None) → Reaction
cosmolkit.parse_smirks(text: str, params: ReactionParseParams | None = None) → Reaction

Parse reaction SMIRKS into a Reaction using the selected native parsing parameters.

cosmolkit.parse_smirks_with_params(text, params) → Reaction

Parse reaction SMIRKS into a Reaction with explicit ReactionParseParams.

cosmolkit.property_value_to_text(value) → str

Convert a typed PropertyValue to text using the canonical native conversion; conversion errors propagate.

cosmolkit.protein_from_mmcif(text) → Protein

Parse mmCIF text and construct the canonical Protein projection.

cosmolkit.protein_from_pdb(text: str, *, max_line_length: SupportsIndex | None = None, check_non_ascii: bool | None = None, ignore_ter: bool | None = None, split_chain_on_ter: bool | None = None, skip_remarks: bool | None = None) → Protein
cosmolkit.protein_from_pdb(text: str, params: BioPdbReadParams | None = None) → Protein

Parse PDB text and construct the canonical Protein projection under the supplied reader parameters.

cosmolkit.reaction_from_smirks(text: str, *, use_smiles: bool | None = None, sanitize: bool | None = None, replacements: dict[str, str] | None = None, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None) → Reaction
cosmolkit.reaction_from_smirks(text: str, params: ReactionParseParams | None = None) → Reaction

Construct a Reaction from SMIRKS using the same canonical parser as parse_smirks.

cosmolkit.residue_code(name) → ResidueCode

Convert a residue name to the canonical ResidueCode, preserving the native unknown-name value.

cosmolkit.residue_info(index) → ResidueInfo

Return residue-table information at the given index; invalid indices raise IndexError.

cosmolkit.residue_info_checked(index) → ResidueInfo | None

Return residue-table information at the given index, or None when out of bounds.

cosmolkit.support_matrix() → list[SupportMatrixEntry]

Return the declared language/feature support matrix generated from canonical operations; registration alone is not a parity result.

cosmolkit.version() → str

Return the COSMolKit package version compiled into this extension.

cosmolkit.write_cx_smarts(query: QueryGraph, *, include_atom_maps: bool | None = None, isomeric_smiles: bool | None = None, include_dative_bonds: bool | None = None, rooted_at_atom: SupportsIndex | None = None) → str
cosmolkit.write_cx_smarts(query: QueryGraph, params: SmartsWriteParams | None = None) → str

Serialize a QueryGraph as SMARTS with the selected CX extensions; returns text.

cosmolkit.write_smarts(query: QueryGraph, *, include_atom_maps: bool | None = None, isomeric_smiles: bool | None = None, include_dative_bonds: bool | None = None, rooted_at_atom: SupportsIndex | None = None) → str
cosmolkit.write_smarts(query: QueryGraph, params: SmartsWriteParams | None = None) → str

Serialize a QueryGraph as SMARTS using the selected writer parameters; returns text.

class cosmolkit.Molecule

Molecular graph, properties and independently selected 2D/3D coordinates. Value-returning operations leave their source unchanged; methods ending in an underscore modify this value in place. copy() initially shares molecular storage, with changes isolated by copy-on-write.

Members (434)
add_2d_coordinates_(*, coordinate_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, canonical_orientation: bool | None = None, clear_existing_2d: bool | None = None, flips_per_sample: SupportsIndex | None = None, samples: SupportsIndex | None = None, sample_seed: SupportsIndex | None = None, permute_degree_four: bool | None = None, force_rdkit: bool | None = None, use_ring_templates: bool | None = None, use_path_angle_expansion: bool | None = None) → None
add_2d_coordinates_(params: Coordinate2DParams | None = None) → None

Generate and install a 2D depiction layout in place. Supply Coordinate2DParams or keyword layout options, not both.

add_2d_coordinates_with_params_(params) → None

Generate and install a 2D depiction layout in place using Coordinate2DParams.

add_3d_conformer_(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], *, is_3d: bool | None = None) → int
add_3d_conformer_(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], params: Coordinate3DInputParams | None = None) → int

Add a 3D conformer from supplied coordinates in place; existing conformers are retained.

add_3d_conformer_with_params_(coordinates, params) → int

Add a 3D conformer from supplied coordinates in place; existing conformers are retained. Uses the explicit configuration argument.

add_hydrogens_(*, explicit_only: bool | None = None, add_coords: bool | None = None, add_residue_info: bool | None = None, skip_queries: bool | None = None, only_on_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → None
add_hydrogens_(params: AddHsParams | None = None) → None

In place, add explicit hydrogen atoms using AddHsParams or keyword options. Copy-on-write isolates molecular values sharing the original storage. Returns None; use with_hydrogens to obtain a new molecule instead.

add_hydrogens_with_params_(params) → None

Add hydrogen atoms in place using AddHsParams and copy-on-write isolation from other molecule values.

align_conformers_(*, atom_indices: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, conformer_ids: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, reflect: bool | None = None, max_iterations: SupportsIndex | None = None) → ConformerAlignmentReport
align_conformers_(params: ConformerAlignmentParameters | None = None) → ConformerAlignmentReport

Align the stored conformers in place according to the supplied parameters.

align_conformers_with_params_(params) → ConformerAlignmentReport

Align this molecule’s conformers in place using explicit alignment parameters.

align_to_(reference: Molecule, *, probe_conformer_id: SupportsIndex | None = None, reference_conformer_id: SupportsIndex | None = None, atom_map: _typeshed.SupportsGetItem[int, AlignmentAtomMap] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, reflect: bool | None = None, max_iterations: SupportsIndex | None = None) → AlignmentResult
align_to_(reference: Molecule, params: AlignmentParameters | None = None) → AlignmentResult

Align this molecule to the reference coordinates in place; COW isolates other molecular values.

align_to_with_params_(reference, params) → AlignmentResult

Align this molecule’s selected conformer to a reference in place using explicit alignment parameters.

alignment_transform_to(reference: Molecule, *, probe_conformer_id: SupportsIndex | None = None, reference_conformer_id: SupportsIndex | None = None, atom_map: _typeshed.SupportsGetItem[int, AlignmentAtomMap] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, reflect: bool | None = None, max_iterations: SupportsIndex | None = None) → AlignmentResult
alignment_transform_to(reference: Molecule, params: AlignmentParameters | None = None) → AlignmentResult

Calculate a coordinate alignment transform to a reference without applying it. Parameters select conformers, atom correspondences, weights and reflection.

alignment_transform_to_with_params(reference, params) → AlignmentResult

Calculate a coordinate alignment transform to a reference without applying it. Parameters select conformers, atom correspondences, weights and reflection. This entry accepts the explicit native parameter form.

all_conformer_best_rmsds(*, atom_maps: _typeshed.SupportsGetItem[int, _typeshed.SupportsGetItem[int, AlignmentAtomMap]] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, max_matches: SupportsIndex | None = None, symmetrize_conjugated_terminal_groups: bool | None = None, ignore_hydrogens: bool | None = None, num_threads: SupportsIndex | None = None) → list[ConformerRmsd]
all_conformer_best_rmsds(params: AllConformerRmsdParameters | None = None) → list[ConformerRmsd]

Calculate symmetry-aware best RMSDs between this molecule’s conformers using the selected matching and alignment parameters.

all_conformer_best_rmsds_with_params(params) → list[ConformerRmsd]

Calculate symmetry-aware best RMSDs between this molecule’s conformers using the selected matching and alignment parameters. This entry accepts the explicit native parameter form.

apply_reaction(reaction: Reaction, *, remove_unmatched_atoms: bool | None = None) → ReactionApplyResult
apply_reaction(reaction: Reaction, params: ReactionApplyParams | None = None) → ReactionApplyResult

Return the native single-reactant application result as a new molecular value, leaving this molecule unchanged.

apply_reaction_(reaction: Reaction, *, remove_unmatched_atoms: bool | None = None) → bool
apply_reaction_(reaction: Reaction, params: ReactionApplyParams | None = None) → bool

Apply a single-reactant reaction in place and return whether it changed the molecule. COW isolates other molecular values.

apply_reaction_with_params(reaction, params) → ReactionApplyResult

Return the native single-reactant application result as a new molecular value, leaving this molecule unchanged. Uses the explicit configuration argument.

apply_reaction_with_params_(reaction, params) → bool

Apply a single-reactant reaction in place and return whether it changed the molecule. COW isolates other molecular values. Uses the explicit configuration argument.

assign_aromaticity_(*, model: AromaticityModel | str | None = None) → None
assign_aromaticity_(params: AromaticityParams | None = None) → None

Assign aromaticity in place using the selected aromaticity model.

assign_aromaticity_with_params_(params) → None

Assign aromaticity in place using the selected aromaticity model. Uses the explicit configuration argument.

assign_chiral_tags_from_structure_(*, conformer_id: SupportsIndex | None = None, replace_existing_tags: bool | None = None) → None
assign_chiral_tags_from_structure_(params: StructureTagParams | None = None) → None

Assign chiral tags in place from the selected coordinate structure.

assign_chiral_tags_from_structure_with_params_(params) → None

Assign chiral tags in place from the selected coordinate structure. Uses the explicit configuration argument.

assign_cip_labels_(*, atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, bonds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, max_recursive_iterations: SupportsIndex | None = None) → None
assign_cip_labels_(options: CipLabelOptions | None = None) → None

Assign CIP labels in place under the selected complete or partial assignment options.

assign_cip_labels_with_options_(options) → None

Assign CIP labels in place under the selected complete or partial assignment options. Uses the explicit configuration argument.

assign_radicals_() → None

Assign radical-electron counts in place using the native radical assignment.

assign_ring_families_(*, include_dative_bonds: bool | None = None, include_hydrogen_bonds: bool | None = None) → None
assign_ring_families_(params: RingSearchParams | None = None) → None

Calculate and install ring families in place using the selected ring-search policy.

assign_ring_families_with_params_(params) → None

Calculate and install ring families in place using the selected ring-search policy. Uses the explicit configuration argument.

assign_rings_() → None

Calculate and install ordinary ring information in place.

assign_valence_(*, model: ValenceModel | str | None = None, strict: bool | None = None) → None
assign_valence_(params: ValenceParams | None = None) → None

Assign valence information in place under the selected valence model and strictness.

assign_valence_with_params_(params) → None

Assign valence information in place under the selected valence model and strictness. Uses the explicit configuration argument.

atom(atom_id) → MoleculeAtom | None

Return the atom at a zero-based index, or None when the index is absent. The returned atom retains this molecular version; later edits to the source molecule do not change its topology or contextual properties.

atom_metadata(recalculate=True) → list[AtomMetadata]

Return per-atom degree, valence and hydrogen information in atom-index order. recalculate explicitly requests rebuilding the required information.

atom_property_bool(atom, key) → bool | None

Read the atom’s boolean property. A missing key returns None; an incompatible stored type or invalid atom index raises a structured error.

atom_property_double(atom, key) → float | None

Read the atom’s 64-bit floating-point property. A missing key returns None; an incompatible stored type or invalid atom index raises a structured error.

atom_property_int(atom, key) → int | None

Read the atom’s signed 32-bit integer property. A missing key returns None; an incompatible stored type or invalid atom index raises a structured error.

atom_property_int_vector(atom, key) → list[int] | None

Read the atom’s signed-integer vector property. A missing key returns None; an incompatible stored type or invalid atom index raises a structured error.

atom_property_string(atom, key) → str | None

Read the atom’s text property. A missing key returns None; an incompatible stored type or invalid atom index raises a structured error.

atom_property_string_vector(atom, key) → list[str] | None

Read the atom’s text-vector property. A missing key returns None; an incompatible stored type or invalid atom index raises a structured error.

atom_property_uint(atom, key) → int | None

Read the atom’s unsigned 32-bit integer property. A missing key returns None; an incompatible stored type or invalid atom index raises a structured error.

atomic_numbers() → list[int]

Return an independent list of atomic numbers in atom-index order, without creating atom handles. Dummy atoms are zero.

atoms: list[MoleculeAtom]

Atoms in index order, each retaining this molecular version for contextual reads.

best_alignment_to(reference: Molecule, *, probe_conformer_id: SupportsIndex | None = None, reference_conformer_id: SupportsIndex | None = None, atom_maps: _typeshed.SupportsGetItem[int, _typeshed.SupportsGetItem[int, AlignmentAtomMap]] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, reflect: bool | None = None, max_iterations: SupportsIndex | None = None, max_matches: SupportsIndex | None = None, symmetrize_conjugated_terminal_groups: bool | None = None, ignore_hydrogens: bool | None = None, num_threads: SupportsIndex | None = None) → AlignmentResult
best_alignment_to(reference: Molecule, params: BestAlignmentParameters | None = None) → AlignmentResult

Find the best alignment to a reference across allowed atom mappings, returning its transform and RMSD without changing either molecule.

best_alignment_to_with_params(reference, params) → AlignmentResult

Find the best alignment to a reference across allowed atom mappings, returning its transform and RMSD without changing either molecule. This entry accepts the explicit native parameter form.

best_rmsd_to(reference: Molecule, *, probe_conformer_id: SupportsIndex | None = None, reference_conformer_id: SupportsIndex | None = None, atom_maps: _typeshed.SupportsGetItem[int, _typeshed.SupportsGetItem[int, AlignmentAtomMap]] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, reflect: bool | None = None, max_iterations: SupportsIndex | None = None, max_matches: SupportsIndex | None = None, symmetrize_conjugated_terminal_groups: bool | None = None, ignore_hydrogens: bool | None = None, num_threads: SupportsIndex | None = None) → float
best_rmsd_to(reference: Molecule, params: BestAlignmentParameters | None = None) → float

Calculate the best alignment RMSD to a reference across allowed atom mappings without changing either molecule.

best_rmsd_to_with_params(reference, params) → float

Calculate the best alignment RMSD to a reference across allowed atom mappings without changing either molecule. This entry accepts the explicit native parameter form.

bond(bond_id) → Bond | None

Return a detached bond value at a zero-based index, or None when the index is absent.

bond_property_string(id, key) → str | None

Read the selected bond’s text property, returning None for an absent key and a structured error for an incompatible value.

bonds: list[Bond]

Detached bond values in bond-index order.

canonical_tautomer(*, max_tautomers: SupportsIndex | None = None, max_transforms: SupportsIndex | None = None, remove_sp3_stereo: bool | None = None, remove_bond_stereo: bool | None = None, remove_isotopic_hydrogens: bool | None = None, reassign_stereo: bool | None = None, callback: collections.abc.Callable[[TautomerMoleculeView, TautomerProgress], bool] | None = None, scorer: collections.abc.Callable[[TautomerMoleculeView], int] | None = None, score_params: TautomerScoreParams | None = None) → Molecule
canonical_tautomer(params: TautomerParams | None = None) → Molecule

Select the canonical tautomer using the supplied enumeration and scoring policy.

canonical_tautomer_with_params(params) → Molecule

Select the canonical tautomer using the supplied enumeration and scoring policy. Uses the explicitly supplied parameter form.

chi_0() → float

Calculate the zeroth-order connectivity index from atomic degrees.

chi_0_n(*, force=None) → float

Calculate the order-0 normalized connectivity index. force requests recalculation.

chi_0_n_with_params(force) → float

Calculate the order-0 normalized connectivity index. force requests recalculation.

chi_0_v(*, force=None) → float

Calculate the order-0 valence connectivity index. force requests recalculation.

chi_0_v_with_params(force) → float

Calculate the order-0 valence connectivity index. force requests recalculation.

chi_1() → float

Calculate the first-order connectivity index from bonded atomic degrees.

chi_1_n(*, force=None) → float

Calculate the order-1 normalized connectivity index. force requests recalculation.

chi_1_n_with_params(force) → float

Calculate the order-1 normalized connectivity index. force requests recalculation.

chi_1_v(*, force=None) → float

Calculate the order-1 valence connectivity index. force requests recalculation.

chi_1_v_with_params(force) → float

Calculate the order-1 valence connectivity index. force requests recalculation.

chi_2_n(*, force=None) → float

Calculate the order-2 normalized connectivity index. force requests recalculation.

chi_2_n_with_params(force) → float

Calculate the order-2 normalized connectivity index. force requests recalculation.

chi_2_v(*, force=None) → float

Calculate the order-2 valence connectivity index. force requests recalculation.

chi_2_v_with_params(force) → float

Calculate the order-2 valence connectivity index. force requests recalculation.

chi_3_n(*, force=None) → float

Calculate the order-3 normalized connectivity index. force requests recalculation.

chi_3_n_with_params(force) → float

Calculate the order-3 normalized connectivity index. force requests recalculation.

chi_3_v(*, force=None) → float

Calculate the order-3 valence connectivity index. force requests recalculation.

chi_3_v_with_params(force) → float

Calculate the order-3 valence connectivity index. force requests recalculation.

chi_4_n(*, force=None) → float

Calculate the order-4 normalized connectivity index. force requests recalculation.

chi_4_n_with_params(force) → float

Calculate the order-4 normalized connectivity index. force requests recalculation.

chi_4_v(*, force=None) → float

Calculate the order-4 valence connectivity index. force requests recalculation.

chi_4_v_with_params(force) → float

Calculate the order-4 valence connectivity index. force requests recalculation.

chi_n_n(order, *, force=None) → float

Calculate the normalized connectivity index at the requested path order. force requests recalculation.

chi_n_n_with_params(order, force) → float

Calculate the normalized connectivity index at the requested path order. force requests recalculation. Uses the explicitly supplied parameter form.

chi_n_v(order, *, force=None) → float

Calculate the valence connectivity index at the requested path order. force requests recalculation.

chi_n_v_with_params(order, force) → float

Calculate the valence connectivity index at the requested path order. force requests recalculation. Uses the explicitly supplied parameter form.

cip_computed: bool

Whether a complete molecular CIP assignment is recorded. A partial assignment does not imply this flag.

clear_3d_conformers_() → None

Remove all 3D conformers in place. The 2D coordinate block is unchanged; returns None.

conformers_3d: list[Conformer3D]

Return stored 3D conformer values in native storage order.

coordinate_rmsd_to(reference: Molecule, *, probe_conformer_id: SupportsIndex | None = None, reference_conformer_id: SupportsIndex | None = None, atom_maps: _typeshed.SupportsGetItem[int, _typeshed.SupportsGetItem[int, AlignmentAtomMap]] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, max_matches: SupportsIndex | None = None, symmetrize_conjugated_terminal_groups: bool | None = None) → float
coordinate_rmsd_to(reference: Molecule, params: CoordinateRmsdParameters | None = None) → float

Calculate coordinate RMSD to the reference without first aligning the coordinates.

coordinate_rmsd_to_with_params(reference, params) → float

Calculate coordinate RMSD to the reference without first aligning the coordinates. This entry accepts the explicit native parameter form.

coordinates_2d: numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]] | None

[“numpy”], “type”: “numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]] | None”} Independent float64 array of shape (num_atoms, 2), in atom-index order, or None when no 2D coordinate block is stored. Does not generate a layout.

Type:

{“role”

Type:

“return_type”, “imports”

coordinates_3d(conformer_id=0) → numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]

Return an independent float64 array of shape (num_atoms, 3) for conformer_id. An absent conformer raises Coordinate3DReadError.

copy() → Molecule

Return an independent molecule value using copy-on-write. Molecular storage is initially shared, not eagerly deep-copied. Subsequent modifications to either molecule do not affect the other.

crippen_descriptors(*, include_hydrogens=None, force=None) → CrippenTotals

Calculate the Wildman-Crippen logP and molar-refractivity descriptors. include_hydrogens controls hydrogen contributions; force requests recalculation.

crippen_descriptors_with_params(include_hydrogens, force) → CrippenTotals

Calculate the Wildman-Crippen logP and molar-refractivity descriptors. include_hydrogens controls hydrogen contributions; force requests recalculation. This entry accepts the explicit native parameter form.

detect_chemistry_problems(*, operations: SanitizeOperations | str | None = None) → ChemistryProblemReport
detect_chemistry_problems(params: SanitizeParams | None = None) → ChemistryProblemReport

Inspect the molecule under the selected sanitization checks and return structured chemical-problem diagnostics.

detect_chemistry_problems_with_params(params) → ChemistryProblemReport

Inspect the molecule under the selected sanitization checks and return structured chemical-problem diagnostics. This entry accepts the explicit native parameter form.

dg_bounds_matrix() → numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]

Return an independent NumPy distance-geometry bounds matrix in atom-index order.

distance_matrix(*, use_bond_order: bool | None = None, use_atom_weights: bool | None = None) → DenseMatrix
distance_matrix(params: DistanceMatrixParams | None = None) → DenseMatrix

Return the topological atom-distance matrix, with rows and columns in atom-index order.

distance_matrix_3d(*, conformer_id: SupportsIndex | None = None, use_atom_weights: bool | None = None) → DenseMatrix
distance_matrix_3d(params: DistanceMatrix3dParams | None = None) → DenseMatrix

Return the coordinate-distance matrix for the selected 3D conformer, in atom-index order.

distance_matrix_3d_with_params(params) → DenseMatrix

Return the coordinate-distance matrix for the selected 3D conformer, in atom-index order. Uses the explicitly supplied parameter form.

distance_matrix_with_params(params) → DenseMatrix

Return the topological atom-distance matrix, with rows and columns in atom-index order. Uses the explicitly supplied parameter form.

embed_3d_conformer_(*, max_iterations: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, random_seed: SupportsIndex | None = None, clear_conformers: bool | None = None, use_random_coords: bool | None = None, box_size_mult: SupportsFloat | SupportsIndex | None = None, rand_neg_eig: bool | None = None, num_zero_fail: SupportsIndex | None = None, coord_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, optimizer_force_tol: SupportsFloat | SupportsIndex | None = None, ignore_smoothing_failures: bool | None = None, enforce_chirality: bool | None = None, use_exp_torsion_angle_prefs: bool | None = None, use_basic_knowledge: bool | None = None, verbose: bool | None = None, basin_thresh: SupportsFloat | SupportsIndex | None = None, prune_rms_thresh: SupportsFloat | SupportsIndex | None = None, only_heavy_atoms_for_rms: bool | None = None, et_version: SupportsIndex | None = None, embed_fragments_separately: bool | None = None, use_small_ring_torsions: bool | None = None, use_macrocycle_torsions: bool | None = None, use_macrocycle14config: bool | None = None, timeout: SupportsIndex | None = None, cpci: dict[tuple[SupportsIndex, SupportsIndex], SupportsFloat | SupportsIndex] | None = None, force_trans_amides: bool | None = None, use_symmetry_for_pruning: bool | None = None, bounds_mat_force_scaling: SupportsFloat | SupportsIndex | None = None, track_failures: bool | None = None, enable_sequential_random_seeds: bool | None = None, symmetrize_conjugated_terminal_groups_for_pruning: bool | None = None) → None
embed_3d_conformer_(params: EmbedParams | None = None) → None

Embed a 3D conformer in place using the selected distance-geometry parameters.

embed_3d_conformer_result_(*, max_iterations: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, random_seed: SupportsIndex | None = None, clear_conformers: bool | None = None, use_random_coords: bool | None = None, box_size_mult: SupportsFloat | SupportsIndex | None = None, rand_neg_eig: bool | None = None, num_zero_fail: SupportsIndex | None = None, coord_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, optimizer_force_tol: SupportsFloat | SupportsIndex | None = None, ignore_smoothing_failures: bool | None = None, enforce_chirality: bool | None = None, use_exp_torsion_angle_prefs: bool | None = None, use_basic_knowledge: bool | None = None, verbose: bool | None = None, basin_thresh: SupportsFloat | SupportsIndex | None = None, prune_rms_thresh: SupportsFloat | SupportsIndex | None = None, only_heavy_atoms_for_rms: bool | None = None, et_version: SupportsIndex | None = None, embed_fragments_separately: bool | None = None, use_small_ring_torsions: bool | None = None, use_macrocycle_torsions: bool | None = None, use_macrocycle14config: bool | None = None, timeout: SupportsIndex | None = None, cpci: dict[tuple[SupportsIndex, SupportsIndex], SupportsFloat | SupportsIndex] | None = None, force_trans_amides: bool | None = None, use_symmetry_for_pruning: bool | None = None, bounds_mat_force_scaling: SupportsFloat | SupportsIndex | None = None, track_failures: bool | None = None, enable_sequential_random_seeds: bool | None = None, symmetrize_conjugated_terminal_groups_for_pruning: bool | None = None) → EmbedMoleculeResult
embed_3d_conformer_result_(params: EmbedParams | None = None) → EmbedMoleculeResult

Embed a 3D conformer in place and return the native generation outcome and diagnostics.

embed_3d_conformer_result_with_params_(params) → EmbedMoleculeResult

Embed a 3D conformer in place and return the native generation outcome and diagnostics. Uses the explicit configuration argument.

embed_3d_conformer_with_params_(params) → None

Embed a 3D conformer in place using the selected distance-geometry parameters. Uses the explicit configuration argument.

embed_3d_conformers_(num_confs: SupportsIndex, *, max_iterations: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, random_seed: SupportsIndex | None = None, clear_conformers: bool | None = None, use_random_coords: bool | None = None, box_size_mult: SupportsFloat | SupportsIndex | None = None, rand_neg_eig: bool | None = None, num_zero_fail: SupportsIndex | None = None, coord_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, optimizer_force_tol: SupportsFloat | SupportsIndex | None = None, ignore_smoothing_failures: bool | None = None, enforce_chirality: bool | None = None, use_exp_torsion_angle_prefs: bool | None = None, use_basic_knowledge: bool | None = None, verbose: bool | None = None, basin_thresh: SupportsFloat | SupportsIndex | None = None, prune_rms_thresh: SupportsFloat | SupportsIndex | None = None, only_heavy_atoms_for_rms: bool | None = None, et_version: SupportsIndex | None = None, embed_fragments_separately: bool | None = None, use_small_ring_torsions: bool | None = None, use_macrocycle_torsions: bool | None = None, use_macrocycle14config: bool | None = None, timeout: SupportsIndex | None = None, cpci: dict[tuple[SupportsIndex, SupportsIndex], SupportsFloat | SupportsIndex] | None = None, force_trans_amides: bool | None = None, use_symmetry_for_pruning: bool | None = None, bounds_mat_force_scaling: SupportsFloat | SupportsIndex | None = None, track_failures: bool | None = None, enable_sequential_random_seeds: bool | None = None, symmetrize_conjugated_terminal_groups_for_pruning: bool | None = None) → None
embed_3d_conformers_(num_confs: SupportsIndex, params: EmbedParams | None = None) → None

Embed the requested number of 3D conformers in place under the selected sampling and pruning policy.

embed_3d_conformers_result_(num_confs: SupportsIndex, *, max_iterations: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, random_seed: SupportsIndex | None = None, clear_conformers: bool | None = None, use_random_coords: bool | None = None, box_size_mult: SupportsFloat | SupportsIndex | None = None, rand_neg_eig: bool | None = None, num_zero_fail: SupportsIndex | None = None, coord_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, optimizer_force_tol: SupportsFloat | SupportsIndex | None = None, ignore_smoothing_failures: bool | None = None, enforce_chirality: bool | None = None, use_exp_torsion_angle_prefs: bool | None = None, use_basic_knowledge: bool | None = None, verbose: bool | None = None, basin_thresh: SupportsFloat | SupportsIndex | None = None, prune_rms_thresh: SupportsFloat | SupportsIndex | None = None, only_heavy_atoms_for_rms: bool | None = None, et_version: SupportsIndex | None = None, embed_fragments_separately: bool | None = None, use_small_ring_torsions: bool | None = None, use_macrocycle_torsions: bool | None = None, use_macrocycle14config: bool | None = None, timeout: SupportsIndex | None = None, cpci: dict[tuple[SupportsIndex, SupportsIndex], SupportsFloat | SupportsIndex] | None = None, force_trans_amides: bool | None = None, use_symmetry_for_pruning: bool | None = None, bounds_mat_force_scaling: SupportsFloat | SupportsIndex | None = None, track_failures: bool | None = None, enable_sequential_random_seeds: bool | None = None, symmetrize_conjugated_terminal_groups_for_pruning: bool | None = None) → EmbedMultipleConfsResult
embed_3d_conformers_result_(num_confs: SupportsIndex, params: EmbedParams | None = None) → EmbedMultipleConfsResult

Embed multiple conformers in place and return native generation results and diagnostics.

embed_3d_conformers_result_with_params_(num_confs, params) → EmbedMultipleConfsResult

Embed multiple conformers in place and return native generation results and diagnostics. Uses the explicit configuration argument.

embed_3d_conformers_with_params_(num_confs, params) → None

Embed the requested number of 3D conformers in place under the selected sampling and pruning policy. Uses the explicit configuration argument.

enumerate_stereoisomers(*, try_embedding: bool | None = None, only_unassigned: bool | None = None, max_isomers: SupportsIndex | None = None, random_source: StereoisomerRandomSource | None = None, unique: bool | None = None, only_stereo_groups: bool | None = None) → StereoisomerIterator
enumerate_stereoisomers(options: StereoisomerOptions | None = None) → StereoisomerIterator

Enumerate stereoisomer molecules under the configured assignment, uniqueness and sampling policy.

enumerate_stereoisomers_with_options(options) → StereoisomerIterator

Enumerate stereoisomer molecules under the configured assignment, uniqueness and sampling policy. Uses the explicitly supplied options.

enumerate_stereoisomers_with_random_bits(options, callback) → StereoisomerIterator

Enumerate stereoisomers with the explicitly supplied random-bit source, preserving its native state and sampling behavior.

enumerate_tautomers(*, max_tautomers: SupportsIndex | None = None, max_transforms: SupportsIndex | None = None, remove_sp3_stereo: bool | None = None, remove_bond_stereo: bool | None = None, remove_isotopic_hydrogens: bool | None = None, reassign_stereo: bool | None = None, callback: collections.abc.Callable[[TautomerMoleculeView, TautomerProgress], bool] | None = None, scorer: collections.abc.Callable[[TautomerMoleculeView], int] | None = None, score_params: TautomerScoreParams | None = None) → TautomerEnumeration
enumerate_tautomers(params: TautomerParams | None = None) → TautomerEnumeration

Enumerate tautomers using the supplied transformation, limit and callback policy; return the native result and enumeration status.

enumerate_tautomers_with_params(params) → TautomerEnumeration

Enumerate tautomers using the supplied transformation, limit and callback policy; return the native result and enumeration status. Uses the explicitly supplied parameter form.

exact_molecular_weight(*, only_heavy=None) → float

Calculate exact molecular weight using isotopic masses. only_heavy excludes hydrogens.

exact_molecular_weight_with_params(only_heavy) → float

Calculate exact molecular weight using isotopic masses. only_heavy excludes hydrogens. This entry accepts the explicit native parameter form.

find_chiral_centers(include_unassigned=False) → list[tuple[int, str]]

Return pairs of atom indices and chiral labels; include_unassigned controls inclusion of unassigned centers.

fingerprint_atom_pair(additional_output: FingerprintAdditionalOutput | None = None, *, min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → Fingerprint
fingerprint_atom_pair(params: AtomPairFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → Fingerprint

Calculate a fixed-width bit fingerprint from atom-pair atom types and distances. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_atom_pair_count(additional_output: FingerprintAdditionalOutput | None = None, *, min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → SparseCountFingerprint32
fingerprint_atom_pair_count(params: AtomPairFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint32

Calculate a fixed-width count fingerprint from atom-pair atom types and distances. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_atom_pair_count_with_params(params, additional_output=None) → SparseCountFingerprint32

Calculate a fixed-width count fingerprint from atom-pair atom types and distances using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_atom_pair_sparse(additional_output: FingerprintAdditionalOutput | None = None, *, min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → SparseBitFingerprint
fingerprint_atom_pair_sparse(params: AtomPairFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseBitFingerprint

Calculate a sparse bit fingerprint from atom-pair atom types and distances. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_atom_pair_sparse_count(additional_output: FingerprintAdditionalOutput | None = None, *, min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → SparseCountFingerprint
fingerprint_atom_pair_sparse_count(params: AtomPairFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint

Calculate a sparse count fingerprint from atom-pair atom types and distances. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_atom_pair_sparse_count_with_params(params, additional_output=None) → SparseCountFingerprint

Calculate a sparse count fingerprint from atom-pair atom types and distances using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_atom_pair_sparse_with_params(params, additional_output=None) → SparseBitFingerprint

Calculate a sparse bit fingerprint from atom-pair atom types and distances using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_atom_pair_with_params(params, additional_output=None) → Fingerprint

Calculate a fixed-width bit fingerprint from atom-pair atom types and distances using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_avalon(*, n_bits: SupportsIndex | None = None, is_query: bool | None = None, bit_flags: SupportsIndex | None = None) → Fingerprint
fingerprint_avalon(params: AvalonFingerprintParams | None = None) → Fingerprint

Calculate the Avalon fingerprint using the selected native Avalon options.

fingerprint_avalon_with_params(params) → Fingerprint

Calculate the Avalon fingerprint using the selected native Avalon options. Uses the explicit configuration argument.

fingerprint_layered(*, layers: SupportsIndex | None = None, min_path: SupportsIndex | None = None, max_path: SupportsIndex | None = None, fp_size: SupportsIndex | None = None, atom_counts: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, set_only_bits: Fingerprint | None = None, branched_paths: bool | None = None, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → Fingerprint
fingerprint_layered(params: LayeredFingerprintParams | None = None) → Fingerprint

Calculate a layered path fingerprint using the selected layer flags, path bounds and bit width.

fingerprint_layered_with_output(*, layers: SupportsIndex | None = None, min_path: SupportsIndex | None = None, max_path: SupportsIndex | None = None, fp_size: SupportsIndex | None = None, atom_counts: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, set_only_bits: Fingerprint | None = None, branched_paths: bool | None = None, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → LayeredFingerprintResult
fingerprint_layered_with_output(params: LayeredFingerprintParams | None = None) → LayeredFingerprintResult

Calculate a layered path fingerprint together with its native additional output.

fingerprint_layered_with_output_with_params(params) → LayeredFingerprintResult

Calculate a layered path fingerprint together with its native additional output. Uses the explicit configuration argument.

fingerprint_layered_with_params(params) → Fingerprint

Calculate a layered path fingerprint using the selected layer flags, path bounds and bit width. Uses the explicit configuration argument.

fingerprint_maccs(*, n_bits: SupportsIndex | None = None) → Fingerprint
fingerprint_maccs(params: MaccsFingerprintParams | None = None) → Fingerprint

Calculate MACCS keys using MaccsFingerprintParams or the n_bits keyword, not both.

fingerprint_maccs_raw() → Fingerprint

Return the raw 167-bit MACCS fingerprint with bit zero unused. The ordinary fingerprint_maccs entry projects keys 1..166 to 166 bits.

fingerprint_maccs_with_params(params) → Fingerprint

Calculate MACCS keys using MaccsFingerprintParams or the n_bits keyword, not both. Uses the explicitly supplied parameter form.

fingerprint_morgan(additional_output: FingerprintAdditionalOutput | None = None, *, radius: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_bond_types: bool | None = ..., include_ring_membership: bool | None = ..., only_nonzero_invariants: bool | None = ..., include_redundant_environments: bool | None = ..., fp_size: SupportsIndex | None = ..., count_simulation: bool | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., invariants: MorganInvariants | None = ...) → Fingerprint
fingerprint_morgan(params: MorganFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → Fingerprint

Calculate a fixed-width bit fingerprint from Morgan circular atom environments. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_morgan_count(additional_output: FingerprintAdditionalOutput | None = None, *, radius: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_bond_types: bool | None = ..., include_ring_membership: bool | None = ..., only_nonzero_invariants: bool | None = ..., include_redundant_environments: bool | None = ..., fp_size: SupportsIndex | None = ..., count_simulation: bool | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., invariants: MorganInvariants | None = ...) → SparseCountFingerprint32
fingerprint_morgan_count(params: MorganFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint32

Calculate a fixed-width count fingerprint from Morgan circular atom environments. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_morgan_count_with_generator(generator: MorganFingerprintGenerator, additional_output: FingerprintAdditionalOutput | None = None, *, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → SparseCountFingerprint32
fingerprint_morgan_count_with_generator(generator: MorganFingerprintGenerator, params: MorganCallParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint32

Calculate a fixed-width count fingerprint from Morgan circular atom environments with a reusable generator. The generator supplies algorithm settings; per-call parameters select atoms and custom invariants. Supply per-call Params or keywords, not both.

fingerprint_morgan_count_with_params(params, additional_output=None) → SparseCountFingerprint32

Calculate a fixed-width count fingerprint from Morgan circular atom environments using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_morgan_sparse(additional_output: FingerprintAdditionalOutput | None = None, *, radius: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_bond_types: bool | None = ..., include_ring_membership: bool | None = ..., only_nonzero_invariants: bool | None = ..., include_redundant_environments: bool | None = ..., fp_size: SupportsIndex | None = ..., count_simulation: bool | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., invariants: MorganInvariants | None = ...) → SparseBitFingerprint
fingerprint_morgan_sparse(params: MorganFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseBitFingerprint

Calculate a sparse bit fingerprint from Morgan circular atom environments. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_morgan_sparse_count(additional_output: FingerprintAdditionalOutput | None = None, *, radius: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_bond_types: bool | None = ..., include_ring_membership: bool | None = ..., only_nonzero_invariants: bool | None = ..., include_redundant_environments: bool | None = ..., fp_size: SupportsIndex | None = ..., count_simulation: bool | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., invariants: MorganInvariants | None = ...) → SparseCountFingerprint
fingerprint_morgan_sparse_count(params: MorganFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint

Calculate a sparse count fingerprint from Morgan circular atom environments. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_morgan_sparse_count_with_generator(generator: MorganFingerprintGenerator, additional_output: FingerprintAdditionalOutput | None = None, *, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → SparseCountFingerprint
fingerprint_morgan_sparse_count_with_generator(generator: MorganFingerprintGenerator, params: MorganCallParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint

Calculate a sparse count fingerprint from Morgan circular atom environments with a reusable generator. The generator supplies algorithm settings; per-call parameters select atoms and custom invariants. Supply per-call Params or keywords, not both.

fingerprint_morgan_sparse_count_with_params(params, additional_output=None) → SparseCountFingerprint

Calculate a sparse count fingerprint from Morgan circular atom environments using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_morgan_sparse_with_generator(generator: MorganFingerprintGenerator, additional_output: FingerprintAdditionalOutput | None = None, *, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → SparseBitFingerprint
fingerprint_morgan_sparse_with_generator(generator: MorganFingerprintGenerator, params: MorganCallParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseBitFingerprint

Calculate a sparse bit fingerprint from Morgan circular atom environments with a reusable generator. The generator supplies algorithm settings; per-call parameters select atoms and custom invariants. Supply per-call Params or keywords, not both.

fingerprint_morgan_sparse_with_params(params, additional_output=None) → SparseBitFingerprint

Calculate a sparse bit fingerprint from Morgan circular atom environments using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_morgan_with_generator(generator: MorganFingerprintGenerator, additional_output: FingerprintAdditionalOutput | None = None, *, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → Fingerprint
fingerprint_morgan_with_generator(generator: MorganFingerprintGenerator, params: MorganCallParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → Fingerprint

Calculate a fixed-width bit fingerprint from Morgan circular atom environments with a reusable generator. The generator supplies algorithm settings; per-call parameters select atoms and custom invariants. Supply per-call Params or keywords, not both.

fingerprint_morgan_with_params(params, additional_output=None) → Fingerprint

Calculate a fixed-width bit fingerprint from Morgan circular atom environments using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_pattern(*, n_bits: SupportsIndex | None = None, tautomeric: bool | None = None) → Fingerprint
fingerprint_pattern(params: PatternFingerprintParams | None = None) → Fingerprint

Calculate the canonical pattern fingerprint using the requested bit width and pattern options.

fingerprint_pattern_with_params(params) → Fingerprint

Calculate the canonical pattern fingerprint using the requested bit width and pattern options. Uses the explicit configuration argument.

fingerprint_topological(*, min_path: SupportsIndex | None = None, max_path: SupportsIndex | None = None, fp_size: SupportsIndex | None = None, num_bits_per_feature: SupportsIndex | None = None, use_hs: bool | None = None, target_density: SupportsFloat | SupportsIndex | None = None, min_size: SupportsIndex | None = None, branched_paths: bool | None = None, use_bond_order: bool | None = None, atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → Fingerprint
fingerprint_topological(params: TopologicalFingerprintParams | None = None) → Fingerprint

Calculate the RDKit-style path-based topological bit fingerprint with the supplied path and folding settings.

fingerprint_topological_torsion(additional_output: FingerprintAdditionalOutput | None = None, *, torsion_atom_count: SupportsIndex | None = ..., only_shortest_paths: bool | None = ..., include_chirality: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → Fingerprint
fingerprint_topological_torsion(params: TopologicalTorsionFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → Fingerprint

Calculate a fixed-width bit fingerprint from topological torsion paths. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_topological_torsion_count(additional_output: FingerprintAdditionalOutput | None = None, *, torsion_atom_count: SupportsIndex | None = ..., only_shortest_paths: bool | None = ..., include_chirality: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → SparseCountFingerprint32
fingerprint_topological_torsion_count(params: TopologicalTorsionFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint32

Calculate a fixed-width count fingerprint from topological torsion paths. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_topological_torsion_count_legacy(*, torsion_atom_count: SupportsIndex | None = None, include_chirality: bool | None = None, fp_size: SupportsIndex | None = None, bits_per_entry: SupportsIndex | None = None, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → SparseCountFingerprint
fingerprint_topological_torsion_count_legacy(params: LegacyTopologicalTorsionParams | None = None) → SparseCountFingerprint

Calculate the legacy topological-torsion count fingerprint with the selected encoding policy.

fingerprint_topological_torsion_count_legacy_with_params(params) → SparseCountFingerprint

Calculate the legacy topological-torsion count fingerprint with the selected encoding policy. Uses the explicit configuration argument.

fingerprint_topological_torsion_count_with_generator(generator: TopologicalTorsionFingerprintGenerator, additional_output: FingerprintAdditionalOutput | None = None, *, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, use_legacy_stereo_perception: bool | None = None) → SparseCountFingerprint32
fingerprint_topological_torsion_count_with_generator(generator: TopologicalTorsionFingerprintGenerator, params: TopologicalTorsionCallParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint32

Calculate a fixed-width count fingerprint from topological torsion paths with a reusable generator. The generator supplies algorithm settings; per-call parameters select atoms and custom invariants. Supply per-call Params or keywords, not both.

fingerprint_topological_torsion_count_with_params(params, additional_output=None) → SparseCountFingerprint32

Calculate a fixed-width count fingerprint from topological torsion paths using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_topological_torsion_legacy(*, torsion_atom_count: SupportsIndex | None = None, include_chirality: bool | None = None, fp_size: SupportsIndex | None = None, bits_per_entry: SupportsIndex | None = None, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → Fingerprint
fingerprint_topological_torsion_legacy(params: LegacyTopologicalTorsionParams | None = None) → Fingerprint

Calculate the legacy topological-torsion bit fingerprint with the selected torsion length and chirality policy.

fingerprint_topological_torsion_legacy_with_params(params) → Fingerprint

Calculate the legacy topological-torsion bit fingerprint with the selected torsion length and chirality policy. Uses the explicit configuration argument.

fingerprint_topological_torsion_sparse(additional_output: FingerprintAdditionalOutput | None = None, *, torsion_atom_count: SupportsIndex | None = ..., only_shortest_paths: bool | None = ..., include_chirality: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → SparseBitFingerprint
fingerprint_topological_torsion_sparse(params: TopologicalTorsionFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseBitFingerprint

Calculate a sparse bit fingerprint from topological torsion paths. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_topological_torsion_sparse_count(additional_output: FingerprintAdditionalOutput | None = None, *, torsion_atom_count: SupportsIndex | None = ..., only_shortest_paths: bool | None = ..., include_chirality: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → SparseCountFingerprint
fingerprint_topological_torsion_sparse_count(params: TopologicalTorsionFingerprintParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint

Calculate a sparse count fingerprint from topological torsion paths. Supply a parameter object or keyword options, not both. additional_output, when supplied, collects the requested provenance in that output object.

fingerprint_topological_torsion_sparse_count_legacy(*, torsion_atom_count: SupportsIndex | None = None, include_chirality: bool | None = None, fp_size: SupportsIndex | None = None, bits_per_entry: SupportsIndex | None = None, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → SparseCountFingerprint
fingerprint_topological_torsion_sparse_count_legacy(params: LegacyTopologicalTorsionParams | None = None) → SparseCountFingerprint

Calculate sparse legacy topological-torsion counts keyed by torsion identifiers.

fingerprint_topological_torsion_sparse_count_legacy_with_params(params) → SparseCountFingerprint

Calculate sparse legacy topological-torsion counts keyed by torsion identifiers. Uses the explicit configuration argument.

fingerprint_topological_torsion_sparse_count_with_generator(generator: TopologicalTorsionFingerprintGenerator, additional_output: FingerprintAdditionalOutput | None = None, *, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, use_legacy_stereo_perception: bool | None = None) → SparseCountFingerprint
fingerprint_topological_torsion_sparse_count_with_generator(generator: TopologicalTorsionFingerprintGenerator, params: TopologicalTorsionCallParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseCountFingerprint

Calculate a sparse count fingerprint from topological torsion paths with a reusable generator. The generator supplies algorithm settings; per-call parameters select atoms and custom invariants. Supply per-call Params or keywords, not both.

fingerprint_topological_torsion_sparse_count_with_params(params, additional_output=None) → SparseCountFingerprint

Calculate a sparse count fingerprint from topological torsion paths using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_topological_torsion_sparse_with_generator(generator: TopologicalTorsionFingerprintGenerator, additional_output: FingerprintAdditionalOutput | None = None, *, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, use_legacy_stereo_perception: bool | None = None) → SparseBitFingerprint
fingerprint_topological_torsion_sparse_with_generator(generator: TopologicalTorsionFingerprintGenerator, params: TopologicalTorsionCallParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → SparseBitFingerprint

Calculate a sparse bit fingerprint from topological torsion paths with a reusable generator. The generator supplies algorithm settings; per-call parameters select atoms and custom invariants. Supply per-call Params or keywords, not both.

fingerprint_topological_torsion_sparse_with_params(params, additional_output=None) → SparseBitFingerprint

Calculate a sparse bit fingerprint from topological torsion paths using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_topological_torsion_with_generator(generator: TopologicalTorsionFingerprintGenerator, additional_output: FingerprintAdditionalOutput | None = None, *, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, use_legacy_stereo_perception: bool | None = None) → Fingerprint
fingerprint_topological_torsion_with_generator(generator: TopologicalTorsionFingerprintGenerator, params: TopologicalTorsionCallParams | None = None, additional_output: FingerprintAdditionalOutput | None = None) → Fingerprint

Calculate a fixed-width bit fingerprint from topological torsion paths with a reusable generator. The generator supplies algorithm settings; per-call parameters select atoms and custom invariants. Supply per-call Params or keywords, not both.

fingerprint_topological_torsion_with_params(params, additional_output=None) → Fingerprint

Calculate a fixed-width bit fingerprint from topological torsion paths using the supplied parameter object. The input molecule is unchanged; additional_output collects requested provenance.

fingerprint_topological_with_output(*, request: TopologicalFingerprintOutputRequest | None = None, min_path: SupportsIndex | None = None, max_path: SupportsIndex | None = None, fp_size: SupportsIndex | None = None, num_bits_per_feature: SupportsIndex | None = None, use_hs: bool | None = None, target_density: SupportsFloat | SupportsIndex | None = None, min_size: SupportsIndex | None = None, branched_paths: bool | None = None, use_bond_order: bool | None = None, atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → TopologicalFingerprintResult
fingerprint_topological_with_output(*, atom_bits: bool | None = None, bit_info: bool | None = None, min_path: SupportsIndex | None = None, max_path: SupportsIndex | None = None, fp_size: SupportsIndex | None = None, num_bits_per_feature: SupportsIndex | None = None, use_hs: bool | None = None, target_density: SupportsFloat | SupportsIndex | None = None, min_size: SupportsIndex | None = None, branched_paths: bool | None = None, use_bond_order: bool | None = None, atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → TopologicalFingerprintResult
fingerprint_topological_with_output(params: TopologicalFingerprintParams | None = None, request: TopologicalFingerprintOutputRequest | None = None) → TopologicalFingerprintResult
fingerprint_topological_with_output(params: TopologicalFingerprintParams | None = None, *, atom_bits: bool | None = None, bit_info: bool | None = None) → TopologicalFingerprintResult

Calculate the path-based topological fingerprint and requested atom/bit provenance.

fingerprint_topological_with_output_with_params(params, request) → TopologicalFingerprintResult

Calculate the path-based topological fingerprint and requested atom/bit provenance. Uses the explicit configuration argument.

fingerprint_topological_with_params(params) → Fingerprint

Calculate the RDKit-style path-based topological bit fingerprint with the supplied path and folding settings. Uses the explicit configuration argument.

fraction_csp3() → float

Return the fraction of carbon atoms with sp3 hybridization.

fragments() → list[Molecule]

Split disconnected components into new molecular values in native component order.

static from_binary(data) → Molecule

Decode a COSMolKit molecular archive, preserving the serialized molecular state. Malformed or unsupported data raises its native archive error.

static from_inchi(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None) → Molecule
static from_inchi(text: str, params: InchiReadParams | None = None) → Molecule

Parse InChI into a new molecular value using the selected sanitization and hydrogen-removal policy.

static from_inchi_with_params(text, params) → Molecule

Parse InChI into a new molecular value using the selected sanitization and hydrogen-removal policy. Uses the explicitly supplied parameter form.

static from_mmcif(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, flavor: PdbReadFlags | None = None, proximity_bonding: bool | None = None) → Molecule
static from_mmcif(text: str, params: BioMoleculeParams | None = None) → Molecule

Parse mmCIF text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path.

static from_mmcif_with_params(text, params) → Molecule

Parse mmCIF text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path. Uses the explicit reader parameters.

static from_mol(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → Molecule
static from_mol(text: str, params: SdfReadParams | None = None) → Molecule

Parse MDL MolBlock text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path.

static from_mol2(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, variant: Mol2Type | str | None = None, cleanup_substructures: bool | None = None) → Molecule
static from_mol2(text: str, params: Mol2ReadParams | None = None) → Molecule

Parse Tripos MOL2 text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path.

static from_mol2_with_params(text, params) → Molecule

Parse Tripos MOL2 text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path. Uses the explicit reader parameters.

static from_mol_with_params(text, params) → Molecule

Parse MDL MolBlock text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path. Uses the explicit reader parameters.

static from_parts(topology, coordinates, properties) → Molecule

Construct a molecule from explicit topology, coordinates and molecular properties using the canonical validation boundary.

static from_pdb(text: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, flavor: PdbReadFlags | None = None, proximity_bonding: bool | None = None) → Molecule
static from_pdb(text: str, params: BioMoleculeParams | None = None) → Molecule

Parse PDB text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path.

static from_pdb_with_params(text, params) → Molecule

Parse PDB text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path. Uses the explicit reader parameters.

static from_rdkit(rdmol, sanitize=None) → Molecule

Import an RDKit molecule through the canonical adapter; sanitize selects whether to sanitize the imported molecular value.

static from_sdf(input: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → Molecule
static from_sdf(input: str, params: SdfReadParams | None = None) → Molecule

Parse SDF text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path.

static from_sdf_with_params(input, params) → Molecule

Parse SDF text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path. Uses the explicit reader parameters.

static from_smiles(text: str, *, sanitize: bool | None = None, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None, parse_name: bool | None = None, remove_hs: bool | None = None, skip_cleanup: bool | None = None, debug_parse: bool | None = None, replacements: dict[str, str] | None = None) → Molecule
static from_smiles(text: str, params: SmilesParseParams | None = None) → Molecule

Parse SMILES into a new molecule. Supply SmilesParseParams or keyword options, not both; sanitization follows the selected parsing policy.

static from_smiles_with_params(text, params) → Molecule

Parse SMILES into a new molecule. Supply SmilesParseParams or keyword options, not both; sanitization follows the selected parsing policy. Uses the explicitly supplied parameter form.

static from_xyz_block(text) → Molecule

Parse XYZ text into a new molecule using the canonical reader and selected input policy. This accepts content, not a filesystem path.

hall_kier_alpha() → float

Calculate the Hall-Kier alpha correction used by molecular shape descriptors.

hall_kier_alpha_with_contributions() → tuple[float, list[float]]

Return Hall-Kier alpha and its per-atom contributions in atom-index order.

has_2d_coordinates: bool

Whether a 2D coordinate block is stored; does not generate coordinates.

has_substruct_match(query: QueryGraph, *, max_matches: SupportsIndex | None = None, uniquify: bool | None = None, use_chirality: bool | None = None, use_enhanced_stereo: bool | None = None, specified_stereo_query_matches_unspecified: bool | None = None, use_query_query_matches: bool | None = None, recursion_possible: bool | None = None, max_recursive_matches: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, aromatic_matches_conjugated: bool | None = None, aromatic_matches_single_or_double: bool | None = None, extra_atom_check_overrides_default_check: bool | None = None, extra_bond_check_overrides_default_check: bool | None = None, use_generic_matchers: bool | None = None, atom_properties: _typeshed.SupportsGetItem[int, str] | None = None, bond_properties: _typeshed.SupportsGetItem[int, str] | None = None, final_match: collections.abc.Callable[[Molecule, collections.abc.Sequence[int]], bool] | None = None, atom_match: collections.abc.Callable[[QueryGraph, QueryAtom, Molecule, Atom], bool] | None = None, bond_match: collections.abc.Callable[[Bond, Bond], bool] | None = None, extra_final_check: collections.abc.Callable[[Molecule, collections.abc.Sequence[int]], bool] | None = None, extra_atom_check: collections.abc.Callable[[QueryGraph, QueryAtom, Molecule, Atom], bool] | None = None, extra_bond_check: collections.abc.Callable[[Bond, Bond], bool] | None = None) → bool
has_substruct_match(query: QueryGraph, params: SubstructMatchParams | None = None) → bool

Return whether the query has an accepted match. Supply SubstructMatchParams or keyword options, not both.

has_substruct_match_with_params(query, params) → bool

Return whether the query has an accepted match. Supply SubstructMatchParams or keyword options, not both. Uses the explicitly supplied parameter form.

has_valence_violation(atom_id) → bool

Check whether the selected atom violates the canonical valence rules.

kappa_1() → float

Calculate the first-order Kier kappa molecular shape index.

kappa_2() → float

Calculate the second-order Kier kappa molecular shape index.

kappa_3() → float

Calculate the third-order Kier kappa molecular shape index.

kekulize_bonds_(*, mark_atoms_bonds: bool | None = None, canonical: bool | None = None, max_backtracks: SupportsIndex | None = None) → None
kekulize_bonds_(params: KekulizeParams | None = None) → None

Assign Kekule bond orders in place under the selected aromatic-flag policy.

kekulize_bonds_with_params_(params) → None

Assign Kekule bond orders in place under the selected aromatic-flag policy. Uses the explicit configuration argument.

labute_asa(*, include_hydrogens=None, force=None) → float

Calculate Labute’s approximate molecular surface area. include_hydrogens controls hydrogen contributions; force requests recalculation.

labute_asa_contributions(*, include_hydrogens=None, force=None) → LabuteAsaContributions

Return per-atom Labute surface contributions and the hydrogen contribution, preserving atom-index order.

labute_asa_contributions_with_params(include_hydrogens, force) → LabuteAsaContributions

Return per-atom Labute surface contributions and the hydrogen contribution, preserving atom-index order. This entry accepts the explicit native parameter form.

labute_asa_with_params(include_hydrogens, force) → float

Calculate Labute’s approximate molecular surface area. include_hydrogens controls hydrogen contributions; force requests recalculation. This entry accepts the explicit native parameter form.

largest_fragment() → Molecule

Return the fragment selected by the native largest-fragment policy; the source is unchanged.

lipinski_hba() → int

Return the Lipinski nitrogen/oxygen acceptor count, not the SMARTS-based num_hba definition.

lipinski_hbd() → int

Return the Lipinski donor-hydrogen count, not the SMARTS-based donor-atom count num_hbd.

mmff_energy_gradient(*, mmff_variant: MmffVariant | str | None = None, non_bonded_threshold: SupportsFloat | SupportsIndex | None = None, conformer_id: SupportsIndex | None = None, ignore_interfragment_interactions: bool | None = None) → MmffEnergyGradient | None
mmff_energy_gradient(params: MmffEvaluationParams | None = None) → MmffEnergyGradient | None

Evaluate MMFF energy and coordinate gradients for the selected conformer and MMFF variant without minimizing it.

mmff_energy_gradient_with_params(params) → MmffEnergyGradient | None

Evaluate MMFF energy and coordinate gradients for the selected conformer and MMFF variant without minimizing it. Uses the explicitly supplied parameter form.

mmff_force_field(*, conformer_id: SupportsIndex | None = None, mmff_variant: MmffVariant | str | None = None, non_bonded_threshold: SupportsFloat | SupportsIndex | None = None, ignore_interfragment_interactions: bool | None = None) → MolecularForceField
mmff_force_field(params: MmffForceFieldParams | None = None) → MolecularForceField

Construct a persistent MMFF force field for the selected conformer and MMFF variant, for evaluation, constraints and minimization without rebuilding the field.

mmff_has_all_molecule_params() → bool

Return whether MMFF parameters are available for every required atom in the molecule.

mmff_properties(*, mmff_variant: MmffVariant | str | None = None) → MmffProperties
mmff_properties(params: MmffPropertiesParams | None = None) → MmffProperties

Prepare MMFF atom typing and molecular properties with the selected MMFF variant.

mmff_properties_with_params(params) → MmffProperties

Prepare MMFF atom typing and molecular properties with the selected MMFF variant. Uses the explicitly supplied parameter form.

molecular_formula(*, separate_isotopes=None, abbreviate_h_isotopes=None) → str

Return the molecular formula, with optional isotope separation and hydrogen-isotope abbreviations.

molecular_formula_with_params(separate_isotopes, abbreviate_h_isotopes) → str

Return the molecular formula, with optional isotope separation and hydrogen-isotope abbreviations. This entry accepts the explicit native parameter form.

molecular_hash() → int

Calculate the canonical molecular graph hash.

molecular_hash_with_ranks(ranks) → int

Calculate the molecular graph hash using the supplied per-atom ranks.

molecular_weight(*, only_heavy=None) → float

Calculate molecular weight using average atomic masses. only_heavy excludes hydrogens.

molecular_weight_with_params(only_heavy) → float

Calculate molecular weight using average atomic masses. only_heavy excludes hydrogens. This entry accepts the explicit native parameter form.

mqns(force=False) → list[int]

Return the 42 molecular quantum numbers in their canonical feature order. force requests recalculation.

murcko_decompose() → Molecule

Return the native Murcko decomposition as a new molecular value.

murcko_scaffold() → Molecule

Return the Bemis-Murcko ring-and-linker scaffold as a new molecule.

net_scaffold() → Molecule

Return the native net scaffold as a new molecule, leaving the source unchanged.

static new() → Molecule

Construct an empty molecular value.

num_3d_conformers: int

Number of stored 3D conformers, not the count of attempted embeddings.

num_aliphatic_carbocycles() → int

Count non-aromatic all-carbon rings in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_aliphatic_heterocycles() → int

Count non-aromatic rings containing a non-carbon atom in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_aliphatic_rings() → int

Count non-aromatic rings in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_amide_bonds() → int

Count amide bonds using the canonical amide pattern.

num_aromatic_carbocycles() → int

Count aromatic all-carbon rings in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_aromatic_heterocycles() → int

Count aromatic rings containing a non-carbon atom in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_aromatic_rings() → int

Count aromatic rings in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_atom_stereo_centers() → int

Count assigned and unassigned atom stereocenters recognized by the canonical stereo analysis.

num_atoms: int

Number of stored atom rows. Implicit hydrogens are not separate rows.

num_bonds: int

Number of stored bond rows.

num_bridgehead_atoms() → int

Count bridgehead atoms from the molecule’s ring information.

num_hba() → int

Count hydrogen-bond acceptor atoms using the canonical SMARTS definitions. Requires prepared valence and ring information.

num_hbd() → int

Count hydrogen-bond donor atoms using the canonical SMARTS definitions. Requires prepared valence information.

num_heavy_atoms() → int

Count atoms other than hydrogen.

num_heteroatoms() → int

Count atoms other than carbon and hydrogen using the canonical heteroatom query.

num_heterocycles() → int

Count rings containing a non-carbon atom in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_rings() → int

Read the initialized ring count. Does not calculate rings; missing initialized ring information raises DescriptorReadError.

num_rotatable_bonds(params=None) → int

Count rotatable bonds under the selected strictness definition; None uses the native default.

num_rotatable_bonds_with_params(params) → int

Count rotatable bonds under the explicitly selected strictness definition.

num_saturated_carbocycles() → int

Count saturated all-carbon rings in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_saturated_heterocycles() → int

Count saturated rings containing a non-carbon atom in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_saturated_rings() → int

Count saturated rings in the stored ring information. Does not calculate rings; an empty or absent ring assignment yields zero.

num_spiro_atoms() → int

Count spiro atoms from the molecule’s ring information.

num_unspecified_atom_stereo_centers() → int

Count recognized atom stereocenters without a specified stereochemical assignment.

perceive_stereochemistry() → None

Run the native stereochemistry perception query and propagate any error.

phi() → float

Calculate the molecular flexibility index from the canonical kappa descriptors.

potential_stereo(*, clean: bool | None = None, flag_possible: bool | None = None, allow_nontetrahedral: bool | None = None) → PotentialStereoResult
potential_stereo(params: PotentialStereoParams | None = None) → PotentialStereoResult

Return the native potential-stereo information for atoms and bonds under the selected options.

potential_stereo_with_params(params) → PotentialStereoResult

Return the native potential-stereo information for atoms and bonds under the selected options. Uses the explicitly supplied parameter form.

properties: MoleculeProperties

Return the molecule-level property value collection.

property(key) → PropertyValue | None

Read a molecule-level property as a typed PropertyValue, or None when the key is absent.

qed() → float

Calculate the quantitative estimate of drug-likeness with the canonical default weights.

reaction_products(reaction: Reaction, reactant_template: SupportsIndex, *, coordinate_selection: ReactionCoordinateSelection | None = None) → list[list[Molecule]]
reaction_products(reaction: Reaction, reactant_template: SupportsIndex, params: ReactionSingleRunParams | None = None) → list[list[Molecule]]

Apply this molecule to the selected reactant template and return product sets. Matching callbacks and coordinate selection follow the supplied reaction policy.

reaction_products_from_inputs(reaction: Reaction, reactants: _typeshed.SupportsGetItem[int, Molecule], *, max_products: SupportsIndex | None = None, coordinate_selections: _typeshed.SupportsGetItem[int, ReactionCoordinateSelection] | None = None, copy_atom_properties: bool | None = None) → list[list[Molecule]]
reaction_products_from_inputs(reaction: Reaction, reactants: _typeshed.SupportsGetItem[int, Molecule], params: ReactionRunParams | None = None) → list[list[Molecule]]

Run the reaction with this molecule and the supplied additional reactant inputs, returning product sets in native order.

reaction_products_with_params(reaction, reactant_template, params) → list[list[Molecule]]

Apply this molecule to the selected reactant template and return product sets. Matching callbacks and coordinate selection follow the supplied reaction policy. Uses the explicit configuration argument.

static read_mol(path: str | os.PathLike[str], *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → Molecule
static read_mol(path: str | os.PathLike[str], params: SdfReadParams | None = None) → Molecule

Read a molecule from a MDL MolBlock file at the supplied path using the canonical reader. IO and parsing errors propagate.

static read_mol2(path: str | os.PathLike[str], *, sanitize: bool | None = None, remove_hs: bool | None = None, variant: Mol2Type | str | None = None, cleanup_substructures: bool | None = None) → Molecule
static read_mol2(path: str | os.PathLike[str], params: Mol2ReadParams | None = None) → Molecule

Read a molecule from a Tripos MOL2 file at the supplied path using the canonical reader. IO and parsing errors propagate.

static read_mol2_with_params(path, params) → Molecule

Read a molecule from a Tripos MOL2 file at the supplied path using the canonical reader. IO and parsing errors propagate. Uses explicit reader parameters.

static read_mol_with_params(path, params) → Molecule

Read a molecule from a MDL MolBlock file at the supplied path using the canonical reader. IO and parsing errors propagate. Uses explicit reader parameters.

static read_sdf(path: str | os.PathLike[str], *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → Molecule
static read_sdf(path: str | os.PathLike[str], params: SdfReadParams | None = None) → Molecule

Read a molecule from a SDF file at the supplied path using the canonical reader. IO and parsing errors propagate.

static read_sdf_with_params(path, params) → Molecule

Read a molecule from a SDF file at the supplied path using the canonical reader. IO and parsing errors propagate. Uses explicit reader parameters.

static read_xyz(path) → Molecule

Read a molecule from a XYZ file at the supplied path using the canonical reader. IO and parsing errors propagate.

remove_hydrogens_(*, remove_degree_zero: bool | None = None, remove_higher_degrees: bool | None = None, remove_only_h_neighbors: bool | None = None, remove_isotopes: bool | None = None, remove_and_track_isotopes: bool | None = None, remove_dummy_neighbors: bool | None = None, remove_defining_bond_stereo: bool | None = None, remove_with_wedged_bond: bool | None = None, remove_with_query: bool | None = None, remove_mapped: bool | None = None, remove_in_sgroups: bool | None = None, show_warnings: bool | None = None, remove_nonimplicit: bool | None = None, update_explicit_count: bool | None = None, remove_hydrides: bool | None = None, remove_nontetrahedral_neighbors: bool | None = None, sanitize: bool | None = None) → None
remove_hydrogens_(params: RemoveHsParams | None = None) → None

Remove eligible hydrogen atoms in place under RemoveHsParams. The removal policy determines which isotopic, mapped and stereochemistry-defining hydrogens remain.

remove_hydrogens_with_params_(params) → None

Remove eligible hydrogen atoms in place under RemoveHsParams. The removal policy determines which isotopic, mapped and stereochemistry-defining hydrogens remain. Uses the explicit configuration argument.

sanitize(*, operations: SanitizeOperations | str | None = None) → Molecule
sanitize(params: SanitizeParams | None = None) → Molecule

Return a sanitized molecular value using the requested sanitization stages. The source is unchanged; errors retain their native type and cause.

sanitize_(*, operations: SanitizeOperations | str | None = None) → None
sanitize_(params: SanitizeParams | None = None) → None

Run the requested sanitization stages in place. Errors retain their native type and cause.

sanitize_with_params(params) → Molecule

Return a sanitized molecular value using the requested sanitization stages. The source is unchanged; errors retain their native type and cause. Uses the explicit configuration argument.

sanitize_with_params_(params) → None

Run the requested sanitization stages in place. Errors retain their native type and cause. Uses the explicit configuration argument.

set_2d_coordinates_(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex]], *, z_policy: CoordinateZPolicy | str | None = None) → None
set_2d_coordinates_(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex]], params: Coordinate2DInputParams | None = None) → None

Install the supplied 2D coordinates in place. Coordinate rows must match the atom count and the declared coordinate-input policy.

set_2d_coordinates_with_params_(coordinates, params) → None

Install the supplied 2D coordinates in place. Coordinate rows must match the atom count and the declared coordinate-input policy. Uses the explicit configuration argument.

set_3d_coordinates_(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], *, conformer_id: SupportsIndex | None = None) → None
set_3d_coordinates_(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], params: Replace3DCoordinatesParams | None = None) → None

Install supplied 3D coordinate rows in place under the selected input policy. Does not run conformer embedding.

set_3d_coordinates_with_params_(coordinates, params) → None

Install supplied 3D coordinate rows in place under the selected input policy. Does not run conformer embedding. Uses the explicit configuration argument.

set_atom_position_(atom: SupportsIndex, position: _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex], *, conformer_id: SupportsIndex | None = None) → None
set_atom_position_(atom: SupportsIndex, position: _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex], params: AtomPositionParams | None = None) → None

Replace one atom position in place under the selected coordinate and Z policy.

set_atom_position_with_params_(atom, position, params) → None

Replace one atom position in place under the selected coordinate and Z policy. Uses the explicit configuration argument.

set_atom_property_bool_(atom, key, value) → None

Set the atom’s boolean property in place. atom is a zero-based index; COW isolates other molecular values sharing the original storage.

set_atom_property_double_(atom, key, value) → None

Set the atom’s 64-bit floating-point property in place. atom is a zero-based index; COW isolates other molecular values sharing the original storage.

set_atom_property_int_(atom, key, value) → None

Set the atom’s signed 32-bit integer property in place. atom is a zero-based index; COW isolates other molecular values sharing the original storage.

set_atom_property_int_vector_(atom, key, value) → None

Set the atom’s signed-integer vector property in place. atom is a zero-based index; COW isolates other molecular values sharing the original storage.

set_atom_property_string_(atom, key, value) → None

Set the atom’s text property in place. atom is a zero-based index; COW isolates other molecular values sharing the original storage.

set_atom_property_string_vector_(atom, key, value) → None

Set the atom’s text-vector property in place. atom is a zero-based index; COW isolates other molecular values sharing the original storage.

set_atom_property_uint_(atom, key, value) → None

Set the atom’s unsigned 32-bit integer property in place. atom is a zero-based index; COW isolates other molecular values sharing the original storage.

set_only_3d_conformer_(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], *, is_3d: bool | None = None) → int
set_only_3d_conformer_(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], params: Coordinate3DInputParams | None = None) → int

Replace all 3D conformers with one containing the supplied coordinates. Each row contains exactly three numeric components.

set_only_3d_conformer_with_params_(coordinates, params) → int

Replace all 3D conformers with one containing the supplied coordinates. Each row contains exactly three numeric components. Uses the explicit configuration argument.

slogp_vsa(*, bins=None, force=None) → list[float]

Return surface-area bins classified by atomic Crippen logP contributions. bins supplies ordered cut points; None uses native default bins.

slogp_vsa_1() → float

Return bin 1 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_10() → float

Return bin 10 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_11() → float

Return bin 11 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_12() → float

Return bin 12 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_2() → float

Return bin 2 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_3() → float

Return bin 3 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_4() → float

Return bin 4 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_5() → float

Return bin 5 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_6() → float

Return bin 6 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_7() → float

Return bin 7 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_8() → float

Return bin 8 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_9() → float

Return bin 9 of the default surface-area descriptor classified by atomic Crippen logP.

slogp_vsa_with_params(bins, force) → list[float]

Return surface-area bins classified by atomic Crippen logP contributions. bins supplies ordered cut points; None uses native default bins. This entry accepts the explicit native parameter form.

smr_vsa(*, bins=None, force=None) → list[float]

Return surface-area bins classified by atomic Crippen molar-refractivity contributions. bins supplies ordered cut points; None uses native defaults.

smr_vsa_1() → float

Return bin 1 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_10() → float

Return bin 10 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_2() → float

Return bin 2 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_3() → float

Return bin 3 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_4() → float

Return bin 4 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_5() → float

Return bin 5 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_6() → float

Return bin 6 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_7() → float

Return bin 7 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_8() → float

Return bin 8 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_9() → float

Return bin 9 of the default surface-area descriptor classified by atomic Crippen molar refractivity.

smr_vsa_with_params(bins, force) → list[float]

Return surface-area bins classified by atomic Crippen molar-refractivity contributions. bins supplies ordered cut points; None uses native defaults. This entry accepts the explicit native parameter form.

stereoisomer_count(*, try_embedding: bool | None = None, only_unassigned: bool | None = None, max_isomers: SupportsIndex | None = None, random_source: StereoisomerRandomSource | None = None, unique: bool | None = None, only_stereo_groups: bool | None = None) → int
stereoisomer_count(options: StereoisomerOptions | None = None) → int

Return the arbitrary-precision count from the native stereoisomer enumeration policy.

stereoisomer_count_with_options(options) → int

Return the arbitrary-precision count from the native stereoisomer enumeration policy. Uses the explicitly supplied options.

substruct_match(query: QueryGraph, *, max_matches: SupportsIndex | None = None, uniquify: bool | None = None, use_chirality: bool | None = None, use_enhanced_stereo: bool | None = None, specified_stereo_query_matches_unspecified: bool | None = None, use_query_query_matches: bool | None = None, recursion_possible: bool | None = None, max_recursive_matches: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, aromatic_matches_conjugated: bool | None = None, aromatic_matches_single_or_double: bool | None = None, extra_atom_check_overrides_default_check: bool | None = None, extra_bond_check_overrides_default_check: bool | None = None, use_generic_matchers: bool | None = None, atom_properties: _typeshed.SupportsGetItem[int, str] | None = None, bond_properties: _typeshed.SupportsGetItem[int, str] | None = None, final_match: collections.abc.Callable[[Molecule, collections.abc.Sequence[int]], bool] | None = None, atom_match: collections.abc.Callable[[QueryGraph, QueryAtom, Molecule, Atom], bool] | None = None, bond_match: collections.abc.Callable[[Bond, Bond], bool] | None = None, extra_final_check: collections.abc.Callable[[Molecule, collections.abc.Sequence[int]], bool] | None = None, extra_atom_check: collections.abc.Callable[[QueryGraph, QueryAtom, Molecule, Atom], bool] | None = None, extra_bond_check: collections.abc.Callable[[Bond, Bond], bool] | None = None) → MatchResult | None
substruct_match(query: QueryGraph, params: SubstructMatchParams | None = None) → MatchResult | None

Find the first query match, returning its atom mapping or None. Supply SubstructMatchParams or keyword options, not both.

substruct_match_with_params(query, params) → MatchResult | None

Find the first query match, returning its atom mapping or None. Supply SubstructMatchParams or keyword options, not both. Uses the explicitly supplied parameter form.

substruct_matches(query: QueryGraph, *, max_matches: SupportsIndex | None = None, uniquify: bool | None = None, use_chirality: bool | None = None, use_enhanced_stereo: bool | None = None, specified_stereo_query_matches_unspecified: bool | None = None, use_query_query_matches: bool | None = None, recursion_possible: bool | None = None, max_recursive_matches: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, aromatic_matches_conjugated: bool | None = None, aromatic_matches_single_or_double: bool | None = None, extra_atom_check_overrides_default_check: bool | None = None, extra_bond_check_overrides_default_check: bool | None = None, use_generic_matchers: bool | None = None, atom_properties: _typeshed.SupportsGetItem[int, str] | None = None, bond_properties: _typeshed.SupportsGetItem[int, str] | None = None, final_match: collections.abc.Callable[[Molecule, collections.abc.Sequence[int]], bool] | None = None, atom_match: collections.abc.Callable[[QueryGraph, QueryAtom, Molecule, Atom], bool] | None = None, bond_match: collections.abc.Callable[[Bond, Bond], bool] | None = None, extra_final_check: collections.abc.Callable[[Molecule, collections.abc.Sequence[int]], bool] | None = None, extra_atom_check: collections.abc.Callable[[QueryGraph, QueryAtom, Molecule, Atom], bool] | None = None, extra_bond_check: collections.abc.Callable[[Bond, Bond], bool] | None = None) → list[MatchResult]
substruct_matches(query: QueryGraph, params: SubstructMatchParams | None = None) → list[MatchResult]

Return query matches in native order under the selected uniqueness, chirality and match-limit settings. Supply Params or keywords, not both.

substruct_matches_compiled(query) → list[MatchResult]

Match an already compiled query without recompiling its query representation.

substruct_matches_with_params(query, params) → list[MatchResult]

Return query matches in native order under the selected uniqueness, chirality and match-limit settings. Supply Params or keywords, not both. Uses the explicitly supplied parameter form.

symmetrized_sssr(*, include_dative_bonds: bool | None = None, include_hydrogen_bonds: bool | None = None) → RingSearchResult
symmetrized_sssr(params: RingSearchParams | None = None) → RingSearchResult

Calculate the complete symmetrized SSSR ring collection without modifying the source molecule.

symmetrized_sssr_with_params(params) → RingSearchResult

Calculate the complete symmetrized SSSR ring collection without modifying the source molecule. Uses the explicitly supplied parameter form.

tautomer_score(*, terms: _typeshed.SupportsGetItem[int, TautomerScoreTerm] | None = None) → TautomerScore
tautomer_score(params: TautomerScoreParams | None = None) → TautomerScore

Calculate the tautomer score using the supplied scoring terms and options.

tautomer_score_with_params(params) → TautomerScore

Calculate the tautomer score using the supplied scoring terms and options. Uses the explicitly supplied parameter form.

tetrahedral_stereo(include_unassigned=True) → list[tuple[int, list[int | None] | None]]

Return (center, configuration) pairs. An undetermined configuration is None; within an ordered configuration, None denotes hydrogen or a lone pair.

to_binary() → bytes

Serialize the molecular value to COSMolKit archive bytes for later from_binary or pickle reconstruction.

to_builder() → MoleculeBuilder

Create a molecule builder initialized from this molecular value.

to_cx_smarts(*, include_atom_maps: bool | None = None, isomeric_smiles: bool | None = None, include_dative_bonds: bool | None = None, rooted_at_atom: SupportsIndex | None = None) → str
to_cx_smarts(params: SmartsWriteParams | None = None) → str

Serialize SMARTS with CX extensions without changing the molecule. Supply SmartsWriteParams or keyword options, not both.

to_cx_smarts_with_params(params) → str

Serialize SMARTS with CX extensions without changing the molecule. Supply SmartsWriteParams or keyword options, not both. This entry accepts the explicit native parameter form.

to_cx_smiles(*, smiles: SmilesWriteParams | None = None, fields: CxSmilesFields | str | None = None, coordinate_selection: CxCoordinateSelection | str | None = None) → str
to_cx_smiles(params: CxSmilesWriteParams | None = None) → str

Serialize SMILES with the selected CX extensions. Supply CxSmilesWriteParams or keyword options, not both.

to_cx_smiles_with_params(params) → str

Serialize SMILES with the selected CX extensions. Supply CxSmilesWriteParams or keyword options, not both. Uses the explicitly supplied parameter form.

to_fragment_cx_smiles(atoms: _typeshed.SupportsGetItem[int, SupportsIndex], *, cx: CxSmilesWriteParams | None = None, bonds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, atom_symbols: _typeshed.SupportsGetItem[int, str] | None = None, bond_symbols: _typeshed.SupportsGetItem[int, str] | None = None) → str
to_fragment_cx_smiles(params: FragmentCxSmilesWriteParams) → str

Serialize selected atoms and bonds as fragment CXSMILES with the requested extensions.

to_fragment_cx_smiles_with_params(params) → str

Serialize selected atoms and bonds as fragment CXSMILES with the requested extensions. Uses the explicitly supplied parameter form.

to_fragment_smiles(atoms: _typeshed.SupportsGetItem[int, SupportsIndex], *, smiles: SmilesWriteParams | None = None, bonds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, atom_symbols: _typeshed.SupportsGetItem[int, str] | None = None, bond_symbols: _typeshed.SupportsGetItem[int, str] | None = None) → str
to_fragment_smiles(params: FragmentSmilesWriteParams) → str

Serialize only the selected atoms and bonds as fragment SMILES, without changing the molecule.

to_fragment_smiles_with_params(params) → str

Serialize only the selected atoms and bonds as fragment SMILES, without changing the molecule. Uses the explicitly supplied parameter form.

to_inchi(*, options: str | None = None) → str
to_inchi(params: InchiWriteParams | None = None) → str

Generate an InChI string using the selected native InChI options.

to_inchi_key(*, options: str | None = None) → str
to_inchi_key(params: InchiWriteParams | None = None) → str

Generate the InChIKey for this molecule with the selected InChI options.

to_inchi_key_with_params(params) → str

Generate the InChIKey for this molecule with the selected InChI options. Uses the explicitly supplied parameter form.

to_inchi_result(*, options: str | None = None) → InchiResult
to_inchi_result(params: InchiWriteParams | None = None) → InchiResult

Generate InChI with the native result metadata and diagnostic information.

to_inchi_result_with_params(params) → InchiResult

Generate InChI with the native result metadata and diagnostic information. Uses the explicitly supplied parameter form.

to_inchi_with_params(params) → str

Generate an InChI string using the selected native InChI options. Uses the explicitly supplied parameter form.

to_mol(*, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → str
to_mol(params: MolBlockWriteParams | None = None) → str

Serialize the molecule as MDL MolBlock text with the selected writer and coordinate options; does not write a file.

to_mol_with_params(params) → str

Serialize the molecule as MDL MolBlock text with the selected writer and coordinate options; does not write a file. Uses explicit writer parameters.

to_pdb(*, coordinate_selection: MolCoordinateSelection | str | None = None, all_conformers: bool | None = None, flavor: PdbWriteFlags | None = None) → str
to_pdb(params: PdbWriteParams | None = None) → str

Serialize the molecule as PDB text with the selected writer and coordinate options; does not write a file.

to_pdb_with_params(params) → str

Serialize the molecule as PDB text with the selected writer and coordinate options; does not write a file. Uses explicit writer parameters.

to_png(width, height) → bytes

Render a molecular PNG image at the supplied width and height, returning PNG bytes.

to_random_smiles(count: SupportsIndex, seed: SupportsIndex, *, isomeric_smiles: bool | None = None, kekule: bool | None = None, all_bonds_explicit: bool | None = None, all_hydrogens_explicit: bool | None = None) → list[str]
to_random_smiles(count: SupportsIndex, seed: SupportsIndex, params: RandomSmilesWriteParams | None = None) → list[str]

Generate randomized SMILES using the requested count and random seed; molecular chemistry is unchanged.

to_random_smiles_with_params(count, seed, params) → list[str]

Generate randomized SMILES using the requested count and random seed; molecular chemistry is unchanged. Uses the explicitly supplied parameter form.

to_sdf(*, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → str
to_sdf(params: MolBlockWriteParams | None = None) → str

Serialize the molecule as SDF text with the selected writer and coordinate options; does not write a file.

to_sdf_2d(*, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → str
to_sdf_2d(params: MolBlockWriteParams | None = None) → str

Serialize SDF using the molecule’s 2D coordinate selection and the supplied writer options. Returns text without writing a file.

to_sdf_2d_with_params(params) → str

Serialize SDF using the molecule’s 2D coordinate selection and the supplied writer options. Returns text without writing a file.

to_sdf_3d(*, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → str
to_sdf_3d(params: MolBlockWriteParams | None = None) → str

Serialize SDF using the molecule’s 3D coordinate selection and the supplied writer options. Returns text without writing a file.

to_sdf_3d_with_params(params) → str

Serialize SDF using the molecule’s 3D coordinate selection and the supplied writer options. Returns text without writing a file.

to_sdf_with_params(params) → str

Serialize the molecule as SDF text with the selected writer and coordinate options; does not write a file. Uses explicit writer parameters.

to_smarts(*, include_atom_maps: bool | None = None, isomeric_smiles: bool | None = None, include_dative_bonds: bool | None = None, rooted_at_atom: SupportsIndex | None = None) → str
to_smarts(params: SmartsWriteParams | None = None) → str

Serialize the molecule as SMARTS without changing it. Supply SmartsWriteParams or keyword options, not both.

to_smarts_with_params(params) → str

Serialize the molecule as SMARTS without changing it. Supply SmartsWriteParams or keyword options, not both. This entry accepts the explicit native parameter form.

to_smiles(*, isomeric_smiles: bool | None = None, kekule: bool | None = None, canonical: bool | None = None, clean_stereo: bool | None = None, rooted_at_atom: SupportsIndex | None = None, all_bonds_explicit: bool | None = None, all_hydrogens_explicit: bool | None = None, include_dative_bonds: bool | None = None, ignore_atom_map_numbers: bool | None = None) → str
to_smiles(params: SmilesWriteParams | None = None) → str

Serialize SMILES with the selected canonicalization, stereochemistry and atom-order options. Supply SmilesWriteParams or keywords, not both.

to_smiles_with_params(params) → str

Serialize SMILES with the selected canonicalization, stereochemistry and atom-order options. Supply SmilesWriteParams or keywords, not both. Uses the explicitly supplied parameter form.

to_svg(width, height) → str

Render a molecular SVG image at the supplied width and height, returning its XML text.

to_xyz(*, conformer_id: SupportsIndex | None = None, precision: SupportsIndex | None = None) → str
to_xyz(params: XyzWriteParams | None = None) → str

Serialize the molecule as XYZ text with the selected writer and coordinate options; does not write a file.

to_xyz_with_params(params) → str

Serialize the molecule as XYZ text with the selected writer and coordinate options; does not write a file. Uses explicit writer parameters.

topological_torsion_ids(torsion_atom_count=None) → list[int]

Return legacy topological torsion identifiers with the requested torsion and chirality settings.

topological_torsion_ids_with_params(torsion_atom_count) → list[int]

Return legacy topological torsion identifiers with the requested torsion and chirality settings. This entry accepts the explicit native parameter form.

topological_torsion_path_score(path, size, atom_codes=None) → int

Calculate the canonical topological torsion score for the supplied atom path.

topology: TopologyBlock

Return the detached topology value; modifying another molecule cannot invalidate this read.

total_atom_count() → int

Count atoms including explicit and implicit hydrogens, rather than only stored atom rows.

tpsa(*, include_sulfur_phosphorus=None, force=None) → float

Calculate topological polar surface area. include_sulfur_phosphorus includes sulfur and phosphorus fragments; force requests recalculation.

tpsa_with_params(include_sulfur_phosphorus, force) → float

Calculate topological polar surface area. include_sulfur_phosphorus includes sulfur and phosphorus fragments; force requests recalculation. This entry accepts the explicit native parameter form.

uff_energy_gradient(*, vdw_threshold: SupportsFloat | SupportsIndex | None = None, conformer_id: SupportsIndex | None = None, ignore_interfragment_interactions: bool | None = None) → UffEnergyGradient
uff_energy_gradient(params: UffEvaluationParams | None = None) → UffEnergyGradient

Evaluate UFF energy and coordinate gradients for the selected conformer without minimizing it.

uff_energy_gradient_with_params(params) → UffEnergyGradient

Evaluate UFF energy and coordinate gradients for the selected conformer without minimizing it. Uses the explicitly supplied parameter form.

uff_force_field(*, conformer_id: SupportsIndex | None = None, vdw_threshold: SupportsFloat | SupportsIndex | None = None, ignore_interfragment_interactions: bool | None = None) → MolecularForceField
uff_force_field(params: UffForceFieldParams | None = None) → MolecularForceField

Construct a persistent UFF force field for the selected conformer, for evaluation, constraints and minimization without rebuilding the field.

uff_has_all_molecule_params() → bool

Return whether UFF parameters are available for every required atom in the molecule.

with_2d_coordinate_block(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex]], *, z_policy: CoordinateZPolicy | str | None = None) → Molecule
with_2d_coordinate_block(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex]], params: Coordinate2DInputParams | None = None) → Molecule

Return a new molecule with the supplied 2D coordinate block installed. This installs coordinates rather than generating a layout.

with_2d_coordinate_block_with_params(coordinates, params) → Molecule

Return a new molecule with the supplied 2D coordinate block installed. This installs coordinates rather than generating a layout. Uses the explicit configuration argument.

with_2d_coordinates(*, coordinate_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, canonical_orientation: bool | None = None, clear_existing_2d: bool | None = None, flips_per_sample: SupportsIndex | None = None, samples: SupportsIndex | None = None, sample_seed: SupportsIndex | None = None, permute_degree_four: bool | None = None, force_rdkit: bool | None = None, use_ring_templates: bool | None = None, use_path_angle_expansion: bool | None = None) → Molecule
with_2d_coordinates(params: Coordinate2DParams | None = None) → Molecule

Generate a 2D depiction layout in a new molecule. Supply Coordinate2DParams or keyword layout options, not both; the source is unchanged.

with_2d_coordinates_with_params(params) → Molecule

Generate a 2D depiction layout in a new molecule using Coordinate2DParams; the source is unchanged.

with_3d_conformer(*, max_iterations: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, random_seed: SupportsIndex | None = None, clear_conformers: bool | None = None, use_random_coords: bool | None = None, box_size_mult: SupportsFloat | SupportsIndex | None = None, rand_neg_eig: bool | None = None, num_zero_fail: SupportsIndex | None = None, coord_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, optimizer_force_tol: SupportsFloat | SupportsIndex | None = None, ignore_smoothing_failures: bool | None = None, enforce_chirality: bool | None = None, use_exp_torsion_angle_prefs: bool | None = None, use_basic_knowledge: bool | None = None, verbose: bool | None = None, basin_thresh: SupportsFloat | SupportsIndex | None = None, prune_rms_thresh: SupportsFloat | SupportsIndex | None = None, only_heavy_atoms_for_rms: bool | None = None, et_version: SupportsIndex | None = None, embed_fragments_separately: bool | None = None, use_small_ring_torsions: bool | None = None, use_macrocycle_torsions: bool | None = None, use_macrocycle14config: bool | None = None, timeout: SupportsIndex | None = None, cpci: dict[tuple[SupportsIndex, SupportsIndex], SupportsFloat | SupportsIndex] | None = None, force_trans_amides: bool | None = None, use_symmetry_for_pruning: bool | None = None, bounds_mat_force_scaling: SupportsFloat | SupportsIndex | None = None, track_failures: bool | None = None, enable_sequential_random_seeds: bool | None = None, symmetrize_conjugated_terminal_groups_for_pruning: bool | None = None) → Molecule
with_3d_conformer(params: EmbedParams | None = None) → Molecule

Embed a 3D conformer in a new molecular value using the selected distance-geometry parameters.

with_3d_conformer_result(*, max_iterations: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, random_seed: SupportsIndex | None = None, clear_conformers: bool | None = None, use_random_coords: bool | None = None, box_size_mult: SupportsFloat | SupportsIndex | None = None, rand_neg_eig: bool | None = None, num_zero_fail: SupportsIndex | None = None, coord_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, optimizer_force_tol: SupportsFloat | SupportsIndex | None = None, ignore_smoothing_failures: bool | None = None, enforce_chirality: bool | None = None, use_exp_torsion_angle_prefs: bool | None = None, use_basic_knowledge: bool | None = None, verbose: bool | None = None, basin_thresh: SupportsFloat | SupportsIndex | None = None, prune_rms_thresh: SupportsFloat | SupportsIndex | None = None, only_heavy_atoms_for_rms: bool | None = None, et_version: SupportsIndex | None = None, embed_fragments_separately: bool | None = None, use_small_ring_torsions: bool | None = None, use_macrocycle_torsions: bool | None = None, use_macrocycle14config: bool | None = None, timeout: SupportsIndex | None = None, cpci: dict[tuple[SupportsIndex, SupportsIndex], SupportsFloat | SupportsIndex] | None = None, force_trans_amides: bool | None = None, use_symmetry_for_pruning: bool | None = None, bounds_mat_force_scaling: SupportsFloat | SupportsIndex | None = None, track_failures: bool | None = None, enable_sequential_random_seeds: bool | None = None, symmetrize_conjugated_terminal_groups_for_pruning: bool | None = None) → EmbedMoleculeResult
with_3d_conformer_result(params: EmbedParams | None = None) → EmbedMoleculeResult

Embed a 3D conformer and return a new molecule with its generation outcome and diagnostics. A failed attempt is not a valid conformer identifier.

with_3d_conformer_result_with_params(params) → EmbedMoleculeResult

Embed a 3D conformer and return a new molecule with its generation outcome and diagnostics. A failed attempt is not a valid conformer identifier. Uses the explicit configuration argument.

with_3d_conformer_with_params(params) → Molecule

Embed a 3D conformer in a new molecular value using the selected distance-geometry parameters. Uses the explicit configuration argument.

with_3d_conformers(num_confs: SupportsIndex, *, max_iterations: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, random_seed: SupportsIndex | None = None, clear_conformers: bool | None = None, use_random_coords: bool | None = None, box_size_mult: SupportsFloat | SupportsIndex | None = None, rand_neg_eig: bool | None = None, num_zero_fail: SupportsIndex | None = None, coord_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, optimizer_force_tol: SupportsFloat | SupportsIndex | None = None, ignore_smoothing_failures: bool | None = None, enforce_chirality: bool | None = None, use_exp_torsion_angle_prefs: bool | None = None, use_basic_knowledge: bool | None = None, verbose: bool | None = None, basin_thresh: SupportsFloat | SupportsIndex | None = None, prune_rms_thresh: SupportsFloat | SupportsIndex | None = None, only_heavy_atoms_for_rms: bool | None = None, et_version: SupportsIndex | None = None, embed_fragments_separately: bool | None = None, use_small_ring_torsions: bool | None = None, use_macrocycle_torsions: bool | None = None, use_macrocycle14config: bool | None = None, timeout: SupportsIndex | None = None, cpci: dict[tuple[SupportsIndex, SupportsIndex], SupportsFloat | SupportsIndex] | None = None, force_trans_amides: bool | None = None, use_symmetry_for_pruning: bool | None = None, bounds_mat_force_scaling: SupportsFloat | SupportsIndex | None = None, track_failures: bool | None = None, enable_sequential_random_seeds: bool | None = None, symmetrize_conjugated_terminal_groups_for_pruning: bool | None = None) → Molecule
with_3d_conformers(num_confs: SupportsIndex, params: EmbedParams | None = None) → Molecule

Embed the requested number of 3D conformers in a new molecular value under the selected sampling and pruning policy.

with_3d_conformers_result(num_confs: SupportsIndex, *, max_iterations: SupportsIndex | None = None, num_threads: SupportsIndex | None = None, random_seed: SupportsIndex | None = None, clear_conformers: bool | None = None, use_random_coords: bool | None = None, box_size_mult: SupportsFloat | SupportsIndex | None = None, rand_neg_eig: bool | None = None, num_zero_fail: SupportsIndex | None = None, coord_map: dict[SupportsIndex, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]] | None = None, optimizer_force_tol: SupportsFloat | SupportsIndex | None = None, ignore_smoothing_failures: bool | None = None, enforce_chirality: bool | None = None, use_exp_torsion_angle_prefs: bool | None = None, use_basic_knowledge: bool | None = None, verbose: bool | None = None, basin_thresh: SupportsFloat | SupportsIndex | None = None, prune_rms_thresh: SupportsFloat | SupportsIndex | None = None, only_heavy_atoms_for_rms: bool | None = None, et_version: SupportsIndex | None = None, embed_fragments_separately: bool | None = None, use_small_ring_torsions: bool | None = None, use_macrocycle_torsions: bool | None = None, use_macrocycle14config: bool | None = None, timeout: SupportsIndex | None = None, cpci: dict[tuple[SupportsIndex, SupportsIndex], SupportsFloat | SupportsIndex] | None = None, force_trans_amides: bool | None = None, use_symmetry_for_pruning: bool | None = None, bounds_mat_force_scaling: SupportsFloat | SupportsIndex | None = None, track_failures: bool | None = None, enable_sequential_random_seeds: bool | None = None, symmetrize_conjugated_terminal_groups_for_pruning: bool | None = None) → EmbedMultipleConfsResult
with_3d_conformers_result(num_confs: SupportsIndex, params: EmbedParams | None = None) → EmbedMultipleConfsResult

Return a new molecule with multiple-conformer generation results and diagnostics. Requested attempts and successful conformers are distinct counts.

with_3d_conformers_result_with_params(num_confs, params) → EmbedMultipleConfsResult

Return a new molecule with multiple-conformer generation results and diagnostics. Requested attempts and successful conformers are distinct counts. Uses the explicit configuration argument.

with_3d_conformers_with_params(num_confs, params) → Molecule

Embed the requested number of 3D conformers in a new molecular value under the selected sampling and pruning policy. Uses the explicit configuration argument.

with_3d_coordinates(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], *, conformer_id: SupportsIndex | None = None) → Molecule
with_3d_coordinates(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], params: Replace3DCoordinatesParams | None = None) → Molecule

Return a new molecule with supplied 3D coordinate rows installed under the selected input policy. Does not run conformer embedding.

with_3d_coordinates_with_params(coordinates, params) → Molecule

Return a new molecule with supplied 3D coordinate rows installed under the selected input policy. Does not run conformer embedding. Uses the explicit configuration argument.

with_added_3d_conformer(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], *, is_3d: bool | None = None) → Molecule
with_added_3d_conformer(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], params: Coordinate3DInputParams | None = None) → Molecule

Return a new molecule with an additional 3D conformer containing the supplied coordinates.

with_added_3d_conformer_with_params(coordinates, params) → Molecule

Return a new molecule with an additional 3D conformer containing the supplied coordinates. Uses the explicit configuration argument.

with_aligned_conformers(*, atom_indices: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, conformer_ids: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, reflect: bool | None = None, max_iterations: SupportsIndex | None = None) → tuple[Molecule, ConformerAlignmentReport]
with_aligned_conformers(params: ConformerAlignmentParameters | None = None) → tuple[Molecule, ConformerAlignmentReport]

Return a new molecule with its conformers aligned according to the supplied parameters.

with_aligned_conformers_with_params(params) → tuple[Molecule, ConformerAlignmentReport]

Return a new molecule with its conformers aligned according to the supplied parameters. Uses the explicitly supplied parameter form.

with_alignment_to(reference: Molecule, *, probe_conformer_id: SupportsIndex | None = None, reference_conformer_id: SupportsIndex | None = None, atom_map: _typeshed.SupportsGetItem[int, AlignmentAtomMap] | None = None, weights: _typeshed.SupportsGetItem[int, SupportsFloat | SupportsIndex] | None = None, reflect: bool | None = None, max_iterations: SupportsIndex | None = None) → tuple[Molecule, AlignmentResult]
with_alignment_to(reference: Molecule, params: AlignmentParameters | None = None) → tuple[Molecule, AlignmentResult]

Return a new molecule aligned to the reference coordinates, preserving the source molecule.

with_alignment_to_with_params(reference, params) → tuple[Molecule, AlignmentResult]

Return a new molecule aligned to the reference coordinates, preserving the source molecule. Uses the explicitly supplied parameter form.

with_assigned_aromaticity(*, model: AromaticityModel | str | None = None) → Molecule
with_assigned_aromaticity(params: AromaticityParams | None = None) → Molecule

Return a new molecule with aromaticity assigned by the selected aromaticity model.

with_assigned_aromaticity_with_params(params) → Molecule

Return a new molecule with aromaticity assigned by the selected aromaticity model. Uses the explicit configuration argument.

with_assigned_radicals() → Molecule

Return a new molecule with radical-electron counts assigned by the native radical assignment.

with_assigned_ring_families(*, include_dative_bonds: bool | None = None, include_hydrogen_bonds: bool | None = None) → Molecule
with_assigned_ring_families(params: RingSearchParams | None = None) → Molecule

Return a new molecule with ring families calculated using the selected ring-search policy.

with_assigned_ring_families_with_params(params) → Molecule

Return a new molecule with ring families calculated using the selected ring-search policy. Uses the explicit configuration argument.

with_assigned_rings() → Molecule

Return a new molecule with ordinary ring information assigned.

with_assigned_valence(*, model: ValenceModel | str | None = None, strict: bool | None = None) → Molecule
with_assigned_valence(params: ValenceParams | None = None) → Molecule

Return a new molecule with valence information assigned under the selected valence model and strictness.

with_assigned_valence_with_params(params) → Molecule

Return a new molecule with valence information assigned under the selected valence model and strictness. Uses the explicit configuration argument.

with_atom_pair_atom_code(atom_id, branch_subtract=0, include_chirality=False, use_legacy_stereo_perception=True) → AtomPairAtomCodeResult

Return the native atom-pair code result for the selected atom and encoding options.

with_atom_position(atom: SupportsIndex, position: _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex], *, conformer_id: SupportsIndex | None = None) → Molecule
with_atom_position(atom: SupportsIndex, position: _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex], params: AtomPositionParams | None = None) → Molecule

Return a new molecule with one atom position replaced under the selected coordinate and Z policy. The source is unchanged.

with_atom_position_with_params(atom, position, params) → Molecule

Return a new molecule with one atom position replaced under the selected coordinate and Z policy. The source is unchanged. Uses the explicit configuration argument.

with_atom_property_bool(atom, key, value) → Molecule

Return a new molecule with the atom’s boolean property set to value. The source molecule is unchanged; atom is a zero-based index.

with_atom_property_double(atom, key, value) → Molecule

Return a new molecule with the atom’s 64-bit floating-point property set to value. The source molecule is unchanged; atom is a zero-based index.

with_atom_property_int(atom, key, value) → Molecule

Return a new molecule with the atom’s signed 32-bit integer property set to value. The source molecule is unchanged; atom is a zero-based index.

with_atom_property_int_vector(atom, key, value) → Molecule

Return a new molecule with the atom’s signed-integer vector property set to value. The source molecule is unchanged; atom is a zero-based index.

with_atom_property_string(atom, key, value) → Molecule

Return a new molecule with the atom’s text property set to value. The source molecule is unchanged; atom is a zero-based index.

with_atom_property_string_vector(atom, key, value) → Molecule

Return a new molecule with the atom’s text-vector property set to value. The source molecule is unchanged; atom is a zero-based index.

with_atom_property_uint(atom, key, value) → Molecule

Return a new molecule with the atom’s unsigned 32-bit integer property set to value. The source molecule is unchanged; atom is a zero-based index.

with_chiral_tags_from_structure(*, conformer_id: SupportsIndex | None = None, replace_existing_tags: bool | None = None) → Molecule
with_chiral_tags_from_structure(params: StructureTagParams | None = None) → Molecule

Return a new molecule with chiral tags assigned from the selected coordinate structure.

with_chiral_tags_from_structure_with_params(params) → Molecule

Return a new molecule with chiral tags assigned from the selected coordinate structure. Uses the explicit configuration argument.

with_cip_labels(*, atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, bonds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None, max_recursive_iterations: SupportsIndex | None = None) → Molecule
with_cip_labels(options: CipLabelOptions | None = None) → Molecule

Return a new molecule with CIP labels assigned under the selected complete or partial assignment options.

with_cip_labels_with_options(options) → Molecule

Return a new molecule with CIP labels assigned under the selected complete or partial assignment options. Uses the explicit configuration argument.

with_cleared_3d_conformers() → Molecule

Return a new molecule with all 3D conformers removed. The source molecule and its 2D coordinate block are unchanged.

with_hydrogens(*, explicit_only: bool | None = None, add_coords: bool | None = None, add_residue_info: bool | None = None, skip_queries: bool | None = None, only_on_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = None) → Molecule
with_hydrogens(params: AddHsParams | None = None) → Molecule

Return a molecule with explicit hydrogen atoms added; the source molecule is unchanged. Supply either AddHsParams or keyword options, never both. With no options, use the Rust defaults. only_on_atoms limits addition to the selected zero-based atom indices; add_coords requests hydrogen coordinates.

with_hydrogens_with_params(params) → Molecule

Return a new molecule with explicit hydrogen atoms added using AddHsParams; the source molecule is unchanged.

with_kekulized_bonds(*, mark_atoms_bonds: bool | None = None, canonical: bool | None = None, max_backtracks: SupportsIndex | None = None) → Molecule
with_kekulized_bonds(params: KekulizeParams | None = None) → Molecule

Return a new molecule with Kekule bond orders assigned under the selected aromatic-flag policy.

with_kekulized_bonds_with_params(params) → Molecule

Return a new molecule with Kekule bond orders assigned under the selected aromatic-flag policy. Uses the explicit configuration argument.

with_mmff_optimized(*, mmff_variant: MmffVariant | str | None = None, max_iterations: SupportsIndex | None = None, non_bonded_threshold: SupportsFloat | SupportsIndex | None = None, conformer_id: SupportsIndex | None = None, ignore_interfragment_interactions: bool | None = None) → MmffOptimizeMoleculeResult
with_mmff_optimized(params: MmffOptimizationParams | None = None) → MmffOptimizeMoleculeResult

Return a new molecule and MMFF minimization outcome for the selected conformer, leaving the source unchanged.

with_mmff_optimized_conformers(*, num_threads: SupportsIndex | None = None, max_iterations: SupportsIndex | None = None, mmff_variant: MmffVariant | str | None = None, non_bonded_threshold: SupportsFloat | SupportsIndex | None = None, ignore_interfragment_interactions: bool | None = None) → MmffOptimizeMoleculeConfsResult
with_mmff_optimized_conformers(params: MmffConformerOptimizationParams | None = None) → MmffOptimizeMoleculeConfsResult

Optimize the molecule’s conformers with MMFF and return the new molecule with per-conformer outcomes.

with_mmff_optimized_conformers_with_params(params) → MmffOptimizeMoleculeConfsResult

Optimize the molecule’s conformers with MMFF and return the new molecule with per-conformer outcomes. Uses the explicitly supplied parameter form.

with_mmff_optimized_with_params(params) → MmffOptimizeMoleculeResult

Return a new molecule and MMFF minimization outcome for the selected conformer, leaving the source unchanged. Uses the explicitly supplied parameter form.

with_only_3d_conformer(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], *, is_3d: bool | None = None) → Molecule
with_only_3d_conformer(coordinates: _typeshed.SupportsGetItem[int, _typeshed.SupportsLenAndGetItem[SupportsFloat | SupportsIndex]], params: Coordinate3DInputParams | None = None) → Molecule

Return a new molecule whose only 3D conformer contains the supplied coordinates. Rows contain exactly three numeric components.

with_only_3d_conformer_with_params(coordinates, params) → Molecule

Return a new molecule whose only 3D conformer contains the supplied coordinates. Rows contain exactly three numeric components. Uses the explicit configuration argument.

with_uff_optimized(*, max_iterations: SupportsIndex | None = None, vdw_threshold: SupportsFloat | SupportsIndex | None = None, conformer_id: SupportsIndex | None = None, ignore_interfragment_interactions: bool | None = None) → UffOptimizationResult
with_uff_optimized(params: UffOptimizationParams | None = None) → UffOptimizationResult

Return a new molecule and UFF minimization outcome for the selected conformer, leaving the source unchanged.

with_uff_optimized_conformers(*, num_threads: SupportsIndex | None = None, max_iterations: SupportsIndex | None = None, vdw_threshold: SupportsFloat | SupportsIndex | None = None, ignore_interfragment_interactions: bool | None = None) → UffConformerOptimizationResult
with_uff_optimized_conformers(params: UffConformerOptimizationParams | None = None) → UffConformerOptimizationResult

Optimize the molecule’s conformers with UFF and return the new molecule with per-conformer outcomes.

with_uff_optimized_conformers_with_params(params) → UffConformerOptimizationResult

Optimize the molecule’s conformers with UFF and return the new molecule with per-conformer outcomes. Uses the explicitly supplied parameter form.

with_uff_optimized_with_params(params) → UffOptimizationResult

Return a new molecule and UFF minimization outcome for the selected conformer, leaving the source unchanged. Uses the explicitly supplied parameter form.

without_hydrogens(*, remove_degree_zero: bool | None = None, remove_higher_degrees: bool | None = None, remove_only_h_neighbors: bool | None = None, remove_isotopes: bool | None = None, remove_and_track_isotopes: bool | None = None, remove_dummy_neighbors: bool | None = None, remove_defining_bond_stereo: bool | None = None, remove_with_wedged_bond: bool | None = None, remove_with_query: bool | None = None, remove_mapped: bool | None = None, remove_in_sgroups: bool | None = None, show_warnings: bool | None = None, remove_nonimplicit: bool | None = None, update_explicit_count: bool | None = None, remove_hydrides: bool | None = None, remove_nontetrahedral_neighbors: bool | None = None, sanitize: bool | None = None) → Molecule
without_hydrogens(params: RemoveHsParams | None = None) → Molecule

Return a new molecule with eligible hydrogen atoms removed under RemoveHsParams. The removal policy determines which isotopic, mapped and stereochemistry-defining hydrogens remain.

without_hydrogens_with_params(params) → Molecule

Return a new molecule with eligible hydrogen atoms removed under RemoveHsParams. The removal policy determines which isotopic, mapped and stereochemistry-defining hydrogens remain. Uses the explicit configuration argument.

write_mol(path: str | os.PathLike[str], *, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → None
write_mol(path: str | os.PathLike[str], params: MolBlockWriteParams | None = None) → None

Write the molecule as MDL MolBlock to the supplied filesystem path with the selected writer options. IO errors propagate.

write_mol_with_params(path, params) → None

Write the molecule as MDL MolBlock to the supplied filesystem path with the selected writer options. IO errors propagate. Uses explicit writer parameters.

write_png(path, width, height) → None

Render a molecular PNG image and write it to the supplied filesystem path.

write_sdf(path: str | os.PathLike[str], *, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → None
write_sdf(path: str | os.PathLike[str], params: MolBlockWriteParams | None = None) → None

Write the molecule as SDF to the supplied filesystem path with the selected writer options. IO errors propagate.

write_sdf_files(directory: str | os.PathLike[str], file_name: str | None = None, *, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → pathlib.Path
write_sdf_files(directory: str | os.PathLike[str], file_name: str | None = None, params: MolBlockWriteParams | None = None) → pathlib.Path

Write native SDF file outputs under the requested coordinate and writer policy, preserving the canonical file naming and error behavior.

write_sdf_files_with_params(directory, file_name, params) → pathlib.Path

Write native SDF file outputs under the requested coordinate and writer policy, preserving the canonical file naming and error behavior.

write_sdf_with_params(path, params) → None

Write the molecule as SDF to the supplied filesystem path with the selected writer options. IO errors propagate. Uses explicit writer parameters.

write_svg(path, width, height) → None

Render a molecular SVG image and write it to the supplied filesystem path.

write_xyz(path: str | os.PathLike[str], *, conformer_id: SupportsIndex | None = None, precision: SupportsIndex | None = None) → None
write_xyz(path: str | os.PathLike[str], params: XyzWriteParams | None = None) → None

Write the molecule as XYZ to the supplied filesystem path with the selected writer options. IO errors propagate.

write_xyz_with_params(path, params) → None

Write the molecule as XYZ to the supplied filesystem path with the selected writer options. IO errors propagate. Uses explicit writer parameters.

class cosmolkit.BioStructure

Owned structural hierarchy, coordinates and source metadata with copy-on-write updates. Models, chains, residues and atoms retain the structure version from which they were obtained.

Members (65)
assemblies: list[BioAssembly]

Independent list of biological assembly definitions.

atom(id) → BioAtom | None

Return the atom view at a local ID, or None if the ID is outside the structure.

atom_by_altloc(residue_id, name, altloc=None) → tuple[int, BioAtom]

Resolve an atom by residue, name and alternate location; native lookup failures raise BioStructureError.

atom_position(atom) → list[float] | None

Return a Cartesian position for the local atom ID, or None if out of range.

atoms: list[BioAtom]

Atom views in stored order, each retaining this structure version.

chain(id) → BioChain | None

Return the chain view at a local ID, or None if the ID is outside the structure.

chains: list[BioChain]

Chain views in stored order, each retaining this structure version.

cispeps: list[BioCisPep]

Independent list of cis-peptide annotations.

connections: list[BioConnection]

Independent list of explicit structural connections.

coordinates: BioCoordinateBlock

Detached coordinate block in atom-row order.

crystal: BioCrystalInfo | None

Crystallographic cell and symmetry information, or None when absent.

entities: list[BioEntityRow]

Independent list of detached entity rows.

find_atom(residue_id, name, request, element=None) → tuple[int, BioAtom] | None

Find an atom by residue, name, alternate-location request and optional element; return its local ID and view, or None.

find_entity(source_id) → tuple[int, BioEntityRow] | None

Find an entity by source identifier, returning its local ID and detached row, or None.

find_entity_of_subchain(subchain) → tuple[int, BioEntityRow] | None

Find the entity assigned to a source subchain identifier, or None.

static from_mmcif(text) → BioStructure

Parse mmCIF text into a structure preserving hierarchy and source metadata.

static from_parts(parts) → BioStructure

Validate detached structure parts and construct an owned BioStructure.

static from_pdb(text: str, *, max_line_length: SupportsIndex | None = None, check_non_ascii: bool | None = None, ignore_ter: bool | None = None, split_chain_on_ter: bool | None = None, skip_remarks: bool | None = None) → BioStructure
static from_pdb(text: str, params: BioPdbReadParams | None = None) → BioStructure

Parse PDB text into a structure, preserving hierarchy and source metadata. Use a parameter object or keyword options, not both.

static from_pdb_with_params(text, params) → BioStructure

Parse PDB text with explicit native reader parameters.

static from_text(text: str, *, format: BioCoordinateFormat | str | SupportsIndex | None = None, source_name: str | None = None) → BioStructure
static from_text(text: str, params: BioReadParams | None = None) → BioStructure

Parse structural-coordinate text using native format selection and source labeling.

static from_text_with_params(text, params) → BioStructure

Parse structural-coordinate text with explicit format and source-label parameters.

has_origx: bool

Whether the source explicitly supplied an original-coordinate transform.

helices: list[BioHelix]

Independent list of helix annotations.

input_format: BioCoordinateFormat

Coordinate-file format recorded by the source reader.

into_parts() → BioStructureParts

Return detached parts without invalidating Python aliases of this value. The canonical Rust conversion operates on a COW snapshot.

metadata: BioMetadata

Detached copy of experimental, refinement and provenance metadata.

mod_residues: list[BioModRes]

Independent list of modified-residue annotations.

model(id) → BioModel | None

Return the model view at a local ID, or None if the ID is outside the structure.

models: list[BioModel]

Model views in stored order, each retaining this structure version.

name: str

Structure name retained from the input.

ncs_oper_identity_id: str | None

Identifier of the native identity NCS operator, or None when absent.

ncs_operators: list[BioNcsOperator]

Independent list of non-crystallographic symmetry operators.

num_atoms: int

Number of stored atom rows, including retained alternate locations.

num_chains: int

Number of stored chain rows.

num_entities: int

Number of stored entity rows.

num_models: int

Number of stored model rows.

num_residues: int

Number of stored residue rows.

origx: BioTransform

Original-coordinate transform retained in the source state.

protein() → Protein

Create the native protein projection of this structure; projection errors retain their structured cause.

static read(path, *, format=None) → BioStructure

Read a structure from a filesystem path with optional explicit format selection.

static read_with_format(path, format) → BioStructure

Read a structure from a filesystem path in the specified coordinate format.

residue(id) → BioResidue | None

Return the residue view at a local ID, or None if the ID is outside the structure.

residue_atoms(residue) → list[BioAtom] | None

Return atom views for the local residue ID, or None if the residue does not exist.

residues: list[BioResidue]

Residue views in stored order, each retaining this structure version.

resolution: float

Resolution value reported in the source, retaining the native missing-value convention.

retain_selection_(selection) → None

Retain the selected structure contents in place with native copy-on-write isolation.

selected_atom_ids(selection) → list[int]

Return local atom IDs matching the supplied structural selection.

sheets: list[BioSheet]

Independent list of beta-sheet annotations.

source_state: BioStructureSourceState

Detached source-format state, including retained record annotations.

ter_status: int

Native status of retained PDB TER information.

to_mmcif(*, atoms: bool | None = None, block_name: bool | None = None, entry: bool | None = None, database_status: bool | None = None, author: bool | None = None, cell: bool | None = None, symmetry: bool | None = None, entity: bool | None = None, entity_poly: bool | None = None, struct_ref: bool | None = None, chem_comp: bool | None = None, exptl: bool | None = None, diffrn: bool | None = None, reflns: bool | None = None, refine: bool | None = None, title_keywords: bool | None = None, ncs: bool | None = None, struct_asym: bool | None = None, origx: bool | None = None, struct_conf: bool | None = None, struct_sheet: bool | None = None, struct_biol: bool | None = None, assembly: bool | None = None, conn: bool | None = None, cis: bool | None = None, modres: bool | None = None, scale: bool | None = None, atom_type: bool | None = None, entity_poly_seq: bool | None = None, tls: bool | None = None, software: bool | None = None, group_pdb: bool | None = None, auth_all: bool | None = None, prefer_pairs: bool | None = None, compact: bool | None = None, misuse_hash: bool | None = None, align_pairs: SupportsIndex | None = None, align_loops: SupportsIndex | None = None) → str
to_mmcif(params: BioMmcifWriteParams | None = None) → str

Serialize this structure as mmCIF text. Supply a parameter object or category/formatting keywords, not both.

to_mmcif_with_params(params) → str

Serialize this structure as mmCIF using explicit category and formatting parameters.

to_molecule(*, sanitize: bool | None = None, remove_hs: bool | None = None, flavor: PdbReadFlags | None = None, proximity_bonding: bool | None = None) → Molecule
to_molecule(params: BioMoleculeParams | None = None) → Molecule

Convert the structure through the native molecular reader using a parameter object or mutually exclusive keyword options.

to_molecule_with_params(params) → Molecule

Convert the structure to a Molecule using explicit conversion parameters.

to_pdb(*, ter_records: bool | None = None, numbered_ter: bool | None = None, ter_ignores_type: bool | None = None, preserve_serial: bool | None = None, end_record: bool | None = None) → str
to_pdb(params: BioPdbWriteParams | None = None) → str

Serialize the structure as PDB text using a parameter object or mutually exclusive keyword options.

to_pdb_with_params(params) → str

Serialize the structure as PDB text using explicit writer parameters.

translate_(offset) → None

Translate Cartesian positions in place; other copy-on-write structure values remain unchanged.

validate() → None

Validate this structure’s native row relationships and coordinate consistency.

static validate_parts(parts) → None

Validate the relationships and dimensions of detached structure parts without constructing a structure.

with_selection(selection) → BioStructure

Return a new structure containing the selected atoms and their required hierarchy; the source is unchanged.

with_translated_coordinates(offset) → BioStructure

Return a new structure with every Cartesian position translated by the three-component offset.

write_mmcif(path: str | os.PathLike[str], *, atoms: bool | None = None, block_name: bool | None = None, entry: bool | None = None, database_status: bool | None = None, author: bool | None = None, cell: bool | None = None, symmetry: bool | None = None, entity: bool | None = None, entity_poly: bool | None = None, struct_ref: bool | None = None, chem_comp: bool | None = None, exptl: bool | None = None, diffrn: bool | None = None, reflns: bool | None = None, refine: bool | None = None, title_keywords: bool | None = None, ncs: bool | None = None, struct_asym: bool | None = None, origx: bool | None = None, struct_conf: bool | None = None, struct_sheet: bool | None = None, struct_biol: bool | None = None, assembly: bool | None = None, conn: bool | None = None, cis: bool | None = None, modres: bool | None = None, scale: bool | None = None, atom_type: bool | None = None, entity_poly_seq: bool | None = None, tls: bool | None = None, software: bool | None = None, group_pdb: bool | None = None, auth_all: bool | None = None, prefer_pairs: bool | None = None, compact: bool | None = None, misuse_hash: bool | None = None, align_pairs: SupportsIndex | None = None, align_loops: SupportsIndex | None = None) → None
write_mmcif(path: str | os.PathLike[str], params: BioMmcifWriteParams | None = None) → None

Write mmCIF to a filesystem path using a parameter object or mutually exclusive keyword options.

write_mmcif_with_params(path, params) → None

Write mmCIF to a filesystem path using explicit writer parameters.

write_pdb(path: str | os.PathLike[str], *, ter_records: bool | None = None, numbered_ter: bool | None = None, ter_ignores_type: bool | None = None, preserve_serial: bool | None = None, end_record: bool | None = None) → None
write_pdb(path: str | os.PathLike[str], params: BioPdbWriteParams | None = None) → None

Write PDB to a filesystem path using a parameter object or mutually exclusive keyword options.

write_pdb_with_params(path, params) → None

Write PDB to a filesystem path using explicit writer parameters.

class cosmolkit.Protein

Protein projection of a biological structure, with COW transforms and owner-retaining hierarchy views.

Members (26)
as_bio_structure() → BioStructure

Return a COW value of the underlying biological structure.

atoms: list[ProteinAtomRef]

Atom views retaining the protein owner, in stored order.

chain(index) → ProteinChainRef | None

Return the chain at a zero-based index, or None if out of range.

chains: list[ProteinChainRef]

Chain views retaining the protein owner, in stored order.

static from_mmcif(text) → Protein

Parse mmCIF text into the native protein projection.

static from_pdb(text: str, *, max_line_length: SupportsIndex | None = None, check_non_ascii: bool | None = None, ignore_ter: bool | None = None, split_chain_on_ter: bool | None = None, skip_remarks: bool | None = None) → Protein
static from_pdb(text: str, params: BioPdbReadParams | None = None) → Protein

Parse PDB text into the native protein projection; use either parameters or keyword parsing options.

static from_pdb_with_params(text, params) → Protein

Parse PDB text into a protein using explicit reader parameters.

static from_text(text: str, *, format: BioCoordinateFormat | str | SupportsIndex | None = None, source_name: str | None = None) → Protein
static from_text(text: str, params: BioReadParams | None = None) → Protein

Parse structural text into the native protein projection using format-aware reader options.

static from_text_with_params(text, params) → Protein

Parse structural text with explicit BIO reader parameters.

input_format: BioCoordinateFormat

Detected or selected coordinate-file format.

into_bio_structure() → BioStructure

Return a COW snapshot without invalidating aliases to the Python value.

num_atoms: int

Number of stored atoms.

num_chains: int

Number of stored chains.

num_models: int

Number of stored models.

num_residues: int

Number of stored residues.

static read(path, *, format=None) → Protein

Read a protein from a filesystem path using native format detection.

static read_with_format(path, format) → Protein

Read a protein from a filesystem path using the explicitly selected format.

residues: list[ProteinResidueRef]

Residue views retaining the protein owner, in stored order.

retain_selection_(selection) → None

Retain only the selected structure in place, preserving existing shared views through COW.

selected_atom_ids(selection) → list[int]

Return local atom identifiers matching the BIO selection.

selection_summary() → ProteinSelectionSummary

Return chain, residue and atom counts for this protein.

to_molecule(*, sanitize: bool | None = None, remove_hs: bool | None = None, flavor: PdbReadFlags | None = None, proximity_bonding: bool | None = None) → Molecule
to_molecule(params: BioMoleculeParams | None = None) → Molecule

Convert the protein structure to a molecular value using native bond construction and sanitization options.

to_molecule_with_params(params) → Molecule

Convert the protein to a molecular value with explicit BIO conversion parameters.

translate_(offset) → None

Translate this protein’s coordinates in place, isolating shared owners through COW.

with_selection(selection) → Protein

Return a new protein containing the selected structure; leave this value unchanged.

with_translated_coordinates(offset) → Protein

Return a new protein with Cartesian coordinates translated by the three-component offset; leave the source unchanged.

class cosmolkit.AddHsParams(*, explicit_only=Ellipsis, add_coords=Ellipsis, add_residue_info=Ellipsis, skip_queries=Ellipsis, only_on_atoms=Ellipsis)

Parameters corresponding to RDKit’s MolOps::AddHsParameters.

Members (5)
add_coords: bool

Generate coordinates for added hydrogens when the molecule has coordinate rows.

add_residue_info: bool

Assign residue information to added hydrogens from their neighboring heavy atoms.

explicit_only: bool

Add only hydrogens already recorded as explicit hydrogen counts; do not expand implicit counts.

only_on_atoms: tuple[int, ...] | None

Restrict hydrogen addition to these atom indices; None selects all eligible atoms.

skip_queries: bool

Skip atoms carrying queries or attached to query bonds.

exception cosmolkit.AdjacencyError(*args, **kwargs)

Failure in the model domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AdjacencyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (13)
property atom: int | None

Readonly atom payload of the BondAtomOutOfRange error variant; None for other variants.

property atom_count: int | None

Readonly atom_count payload of the BondAtomOutOfRange error variant; None for other variants.

property begin: int | None

Readonly begin payload of the DuplicateEdge error variant; None for other variants.

property bond: int | None

Bond identifier implicated in the failure. Applies to AdjacencyError.BondAtomOutOfRange, AdjacencyError.DuplicateBondId. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the DuplicateEdge error variant; None for other variants.

property endpoint: str | None

Readonly endpoint payload of the BondAtomOutOfRange error variant; None for other variants.

property first_bond: int | None

Readonly first_bond payload of the DuplicateEdge error variant; None for other variants.

property first_position: int | None

Readonly first_position payload of the DuplicateBondId error variant; None for other variants.

property second_bond: int | None

Readonly second_bond payload of the DuplicateEdge error variant; None for other variants.

property second_position: int | None

Readonly second_position payload of the DuplicateBondId error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AdjacencyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AdjacencyErrorKind(value)

Discriminants of AdjacencyErrorKind.

Members: BondAtomOutOfRange, DuplicateBondId, DuplicateEdge, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
BondAtomOutOfRange = AdjacencyErrorKind.BondAtomOutOfRange
DuplicateBondId = AdjacencyErrorKind.DuplicateBondId
DuplicateEdge = AdjacencyErrorKind.DuplicateEdge
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'BondAtomOutOfRange': AdjacencyErrorKind.BondAtomOutOfRange, 'DuplicateBondId': AdjacencyErrorKind.DuplicateBondId, 'DuplicateEdge': AdjacencyErrorKind.DuplicateEdge})
values = mappingproxy({0: AdjacencyErrorKind.BondAtomOutOfRange, 1: AdjacencyErrorKind.DuplicateBondId, 2: AdjacencyErrorKind.DuplicateEdge})
exception cosmolkit.AdjustHsError(*args, **kwargs)

Failure in the adjust_hs domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AdjustHsError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (13)
property actual: int | None

Readonly actual payload of the ValenceAssignmentLength error variant; None for other variants.

property atom: int | None

Atom identifier implicated in the failure. Applies to AdjustHsError.InvalidValenceRow, AdjustHsError.ExplicitHydrogenOverflow. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the ValenceAssignmentLength error variant; None for other variants.

property field: str | None

Field whose content or type caused the failure. Applies to AdjustHsError.ValenceAssignmentLength, AdjustHsError.InvalidValenceRow. None when this payload is absent.

property original_explicit_hydrogens: int | None

Readonly original_explicit_hydrogens payload of the ExplicitHydrogenOverflow error variant; None for other variants.

property original_implicit_valence: int | None

Readonly original_implicit_valence payload of the ExplicitHydrogenOverflow error variant; None for other variants.

property recalculated_implicit_valence: int | None

Readonly recalculated_implicit_valence payload of the ExplicitHydrogenOverflow error variant; None for other variants.

property source: TopologyValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of AdjustHsError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property value: int | None

Readonly value payload of the InvalidValenceRow error variant; None for other variants.

property variant: AdjustHsErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AdjustHsErrorKind(value)

Discriminants of AdjustHsErrorKind.

Members: InvalidTopology, ValenceAssignmentLength, InvalidValenceRow, ExplicitHydrogenOverflow, Valence, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
ExplicitHydrogenOverflow = AdjustHsErrorKind.ExplicitHydrogenOverflow
InvalidTopology = AdjustHsErrorKind.InvalidTopology
InvalidValenceRow = AdjustHsErrorKind.InvalidValenceRow
Valence = AdjustHsErrorKind.Valence
ValenceAssignmentLength = AdjustHsErrorKind.ValenceAssignmentLength
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': AdjustHsErrorKind.InvalidTopology, 'ValenceAssignmentLength': AdjustHsErrorKind.ValenceAssignmentLength, 'InvalidValenceRow': AdjustHsErrorKind.InvalidValenceRow, 'ExplicitHydrogenOverflow': AdjustHsErrorKind.ExplicitHydrogenOverflow, 'Valence': AdjustHsErrorKind.Valence})
values = mappingproxy({0: AdjustHsErrorKind.InvalidTopology, 1: AdjustHsErrorKind.ValenceAssignmentLength, 2: AdjustHsErrorKind.InvalidValenceRow, 3: AdjustHsErrorKind.ExplicitHydrogenOverflow, 4: AdjustHsErrorKind.Valence})
class cosmolkit.AlignmentAtomMap(probe_atom, reference_atom)

Explicit correspondence between one probe atom and one reference atom for alignment.

Members (3)
static new(probe_atom, reference_atom) → AlignmentAtomMap

Construct a correspondence using zero-based probe and reference atom indices.

probe_atom: int

Zero-based atom index in the probe molecule.

reference_atom: int

Zero-based atom index in the reference molecule.

exception cosmolkit.AlignmentError(*args, **kwargs)

Failure in the alignment domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AlignmentError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to AlignmentError.ProbeAtomOutOfRange, AlignmentError.ReferenceAtomOutOfRange. None when this payload is absent.

property coordinates: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of AlignmentError.InvalidCoordinates; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property id: int | None

Readonly id payload of the ConformerNotFound error variant; None for other variants.

property index: int | None

Index reported by the failing native check. Applies to AlignmentError.ProbeAtomOutOfRange, AlignmentError.ReferenceAtomOutOfRange, AlignmentError.NonPositiveWeight. None when this payload is absent.

property map_len: int | None

Readonly map_len payload of the WeightCountMismatch error variant; None for other variants.

property matching: SubstructMatchError | None

“error_payload”} Structured SubstructMatchError payload of AlignmentError.Matching; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property message: str | None

Detailed native diagnostic message. Applies to AlignmentError.TerminalGroupSymmetrization, AlignmentError.NumericalPrecondition. None when this payload is absent.

property query_graph: QueryGraphError | None

“error_payload”} Structured QueryGraphError payload of AlignmentError.QueryGraph; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property query_parse: SmartsParseError | None

“error_payload”} Structured SmartsParseError payload of AlignmentError.QueryParse; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: ThreadCountError | PropertyUIntReadError | AtomPropertyError | PropertyIntReadError | TopologyValidationError | RingFindingError | StereoGroupError | CxQueryLoweringError | QueryGraphError | ParserCarrierError | BondValueError | MoleculePropertyError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property thread_selection: ThreadSelectionError | None

“error_payload”} Structured ThreadSelectionError payload of AlignmentError.ThreadSelection; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: AlignmentErrorKind

Exact Rust error variant, independent of the human-readable message.

property weight_len: int | None

Readonly weight_len payload of the WeightCountMismatch error variant; None for other variants.

class cosmolkit.AlignmentErrorKind(value)

Discriminants of AlignmentErrorKind.

Members: InvalidCoordinates, Matching, QueryGraph, QueryParse, ThreadSelection, NoConformers, ConformerNotFound, EmptyAtomMap, ProbeAtomOutOfRange, ReferenceAtomOutOfRange, WeightCountMismatch, NonPositiveWeight, NoSubstructureMatch, TerminalGroupSymmetrization, NumericalPrecondition, WorkerTerminated, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (19)
ConformerNotFound = AlignmentErrorKind.ConformerNotFound
EmptyAtomMap = AlignmentErrorKind.EmptyAtomMap
InvalidCoordinates = AlignmentErrorKind.InvalidCoordinates
Matching = AlignmentErrorKind.Matching
NoConformers = AlignmentErrorKind.NoConformers
NoSubstructureMatch = AlignmentErrorKind.NoSubstructureMatch
NonPositiveWeight = AlignmentErrorKind.NonPositiveWeight
NumericalPrecondition = AlignmentErrorKind.NumericalPrecondition
ProbeAtomOutOfRange = AlignmentErrorKind.ProbeAtomOutOfRange
QueryGraph = AlignmentErrorKind.QueryGraph
QueryParse = AlignmentErrorKind.QueryParse
ReferenceAtomOutOfRange = AlignmentErrorKind.ReferenceAtomOutOfRange
TerminalGroupSymmetrization = AlignmentErrorKind.TerminalGroupSymmetrization
ThreadSelection = AlignmentErrorKind.ThreadSelection
WeightCountMismatch = AlignmentErrorKind.WeightCountMismatch
WorkerTerminated = AlignmentErrorKind.WorkerTerminated
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidCoordinates': AlignmentErrorKind.InvalidCoordinates, 'Matching': AlignmentErrorKind.Matching, 'QueryGraph': AlignmentErrorKind.QueryGraph, 'QueryParse': AlignmentErrorKind.QueryParse, 'ThreadSelection': AlignmentErrorKind.ThreadSelection, 'NoConformers': AlignmentErrorKind.NoConformers, 'ConformerNotFound': AlignmentErrorKind.ConformerNotFound, 'EmptyAtomMap': AlignmentErrorKind.EmptyAtomMap, 'ProbeAtomOutOfRange': AlignmentErrorKind.ProbeAtomOutOfRange, 'ReferenceAtomOutOfRange': AlignmentErrorKind.ReferenceAtomOutOfRange, 'WeightCountMismatch': AlignmentErrorKind.WeightCountMismatch, 'NonPositiveWeight': AlignmentErrorKind.NonPositiveWeight, 'NoSubstructureMatch': AlignmentErrorKind.NoSubstructureMatch, 'TerminalGroupSymmetrization': AlignmentErrorKind.TerminalGroupSymmetrization, 'NumericalPrecondition': AlignmentErrorKind.NumericalPrecondition, 'WorkerTerminated': AlignmentErrorKind.WorkerTerminated})
values = mappingproxy({0: AlignmentErrorKind.InvalidCoordinates, 1: AlignmentErrorKind.Matching, 2: AlignmentErrorKind.QueryGraph, 3: AlignmentErrorKind.QueryParse, 4: AlignmentErrorKind.ThreadSelection, 5: AlignmentErrorKind.NoConformers, 6: AlignmentErrorKind.ConformerNotFound, 7: AlignmentErrorKind.EmptyAtomMap, 8: AlignmentErrorKind.ProbeAtomOutOfRange, 9: AlignmentErrorKind.ReferenceAtomOutOfRange, 10: AlignmentErrorKind.WeightCountMismatch, 11: AlignmentErrorKind.NonPositiveWeight, 12: AlignmentErrorKind.NoSubstructureMatch, 13: AlignmentErrorKind.TerminalGroupSymmetrization, 14: AlignmentErrorKind.NumericalPrecondition, 15: AlignmentErrorKind.WorkerTerminated})
class cosmolkit.AlignmentParameters(*, probe_conformer_id=Ellipsis, reference_conformer_id=Ellipsis, atom_map=Ellipsis, weights=Ellipsis, reflect=Ellipsis, max_iterations=Ellipsis)

Conformer alignment options for a fixed or native-selected atom correspondence.

Members (7)
atom_map: tuple[AlignmentAtomMap, ...] | None

Optional explicit probe-to-reference atom pairs; None requests native match selection.

max_iterations: int

Maximum iterations for native alignment optimization.

static new(probe_conformer_id=Ellipsis, reference_conformer_id=Ellipsis, atom_map=Ellipsis, weights=Ellipsis, reflect=Ellipsis, max_iterations=Ellipsis) → AlignmentParameters

Create an independent configuration through the native constructor using the supplied field values.

probe_conformer_id: int

Probe conformer identifier; -1 selects the native default conformer.

reference_conformer_id: int

Reference conformer identifier; -1 selects the native default conformer.

reflect: bool

Allow reflection while determining the alignment transform.

weights: tuple[float, ...] | None

Optional alignment weights in atom-map order.

class cosmolkit.AlignmentResult(rmsd, transform, atom_map)

Alignment result retaining RMSD, transformation and probe/reference atom correspondence.

Members (3)
atom_map: list[AlignmentAtomMap]

Independent list of probe-to-reference atom correspondences used for alignment.

rmsd: float

Root-mean-square deviation for the associated alignment or conformer pair.

transform: AlignmentTransform

Transform determined by the alignment.

class cosmolkit.AlignmentTransform(matrix)

Readonly homogeneous 4-by-4 transform mapping aligned probe coordinates into the reference frame.

Members (1)
matrix: list[list[float]]

Homogeneous 4-by-4 transformation matrix.

class cosmolkit.AllConformerRmsdParameters(*, atom_maps=Ellipsis, weights=Ellipsis, max_matches=Ellipsis, symmetrize_conjugated_terminal_groups=Ellipsis, ignore_hydrogens=Ellipsis, num_threads=Ellipsis)

All-conformer RMSD options controlling correspondence selection and parallel execution.

Members (7)
atom_maps: tuple[tuple[AlignmentAtomMap, ...], ...]

Candidate probe-to-reference atom mappings; an empty collection requests native match enumeration.

ignore_hydrogens: bool

Ignore hydrogen atoms during native match enumeration.

max_matches: int

Maximum number of candidate atom mappings considered.

static new(atom_maps=Ellipsis, weights=Ellipsis, max_matches=Ellipsis, symmetrize_conjugated_terminal_groups=Ellipsis, ignore_hydrogens=Ellipsis, num_threads=Ellipsis) → AllConformerRmsdParameters

Create an independent configuration through the native constructor using the supplied field values.

num_threads: int

Number of native alignment worker threads.

symmetrize_conjugated_terminal_groups: bool

Treat conjugated terminal groups symmetrically when selecting matches.

weights: tuple[float, ...] | None

Optional alignment weights in atom-map order.

class cosmolkit.AltLocLabel(value)

A single native alternate-location label byte.

Members (1)
value: int

Raw alternate-location label byte.

class cosmolkit.AltLocRequest

Explicit alternate-location selection: any label or an exact optional label.

Members (2)
static any() → AltLocRequest

Select any alternate location.

static exact(label) → AltLocRequest

Select exactly the supplied alternate location; None selects the unlabelled location.

exception cosmolkit.AromaticityError(*args, **kwargs)

Failure in the aromaticity domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AromaticityError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (34)
property actual: int | None

Observed value reported by the native check. Applies to AromaticityError.ValenceAssignmentLength, AromaticityError.AromaticRingCountOutOfRange, AromaticityError.AtomIdentityChanged, AromaticityError.BondIdentityChanged. None when this payload is absent.

property atom: int | None

Atom identifier implicated in the failure. Applies to AromaticityError.RingAtomOutOfRange, AromaticityError.AtomOutOfRange, AromaticityError.InvalidValenceRow. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to AromaticityError.RingRowLengthMismatch, AromaticityError.RingAtomOutOfRange, AromaticityError.AtomOutOfRange. None when this payload is absent.

property atom_rows: int | None

Readonly atom_rows payload of the RingTableLengthMismatch error variant; None for other variants.

property begin: int | None

Readonly begin payload of the ExpectedRingBondNotFound error variant; None for other variants.

property bond: int | None

Bond identifier implicated in the failure. Applies to AromaticityError.RingBondOutOfRange, AromaticityError.BondOutOfRange. None when this payload is absent.

property bond_count: int | None

Bond count used when validating the reported bond reference. Applies to AromaticityError.RingRowLengthMismatch, AromaticityError.RingBondOutOfRange, AromaticityError.BondOutOfRange. None when this payload is absent.

property bond_rows: int | None

Readonly bond_rows payload of the RingTableLengthMismatch error variant; None for other variants.

property detail: str | None

Additional native diagnostic detail. Applies to AromaticityError.UnsupportedModel, AromaticityError.UnsupportedState. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the ExpectedRingBondNotFound error variant; None for other variants.

property expected: int | None

Required value reported by the native check. Applies to AromaticityError.ValenceAssignmentLength, AromaticityError.AtomIdentityChanged, AromaticityError.BondIdentityChanged. None when this payload is absent.

property field: str | None

Field whose content or type caused the failure. Applies to AromaticityError.ValenceAssignmentLength, AromaticityError.InvalidValenceRow, AromaticityError.UnsupportedState, AromaticityError.IntegerOverflow. None when this payload is absent.

property input_atoms: int | None

Readonly input_atoms payload of the UnexpectedTopologyShape error variant; None for other variants.

property input_bonds: int | None

Readonly input_bonds payload of the UnexpectedTopologyShape error variant; None for other variants.

property kekulize: KekulizeError | None

“error_payload”} Structured KekulizeError payload of AromaticityError.Kekulize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property maximum: int | None

Readonly maximum payload of the AromaticRingCountOutOfRange error variant; None for other variants.

property model: AromaticityModel | None

“error_payload”} Structural model involved in the failure. Applies to AromaticityError.UnsupportedModel, AromaticityError.AromaticRingCountOutOfRange. None when this payload is absent.

Type:

{“role”

property output_atoms: int | None

Readonly output_atoms payload of the UnexpectedTopologyShape error variant; None for other variants.

property output_bonds: int | None

Readonly output_bonds payload of the UnexpectedTopologyShape error variant; None for other variants.

property query_state: QueryStateError | None

“error_payload”} Structured QueryStateError payload of AromaticityError.InvalidQueryState; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property ring_atom_count: int | None

Readonly ring_atom_count payload of the RingInfoDimensionMismatch error variant; None for other variants.

property ring_bond_count: int | None

Readonly ring_bond_count payload of the RingInfoDimensionMismatch error variant; None for other variants.

property ring_finding: RingFindingError | None

“error_payload”} Structured RingFindingError payload of AromaticityError.RingFinding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property ring_index: int | None

Ring index involved in the failure. Applies to AromaticityError.RingRowLengthMismatch, AromaticityError.RingAtomOutOfRange, AromaticityError.RingBondOutOfRange. None when this payload is absent.

property row: int | None

Row reported by the native failure. Applies to AromaticityError.AtomIdentityChanged, AromaticityError.BondIdentityChanged. None when this payload is absent.

property source: TopologyValidationError | MappingValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of AromaticityError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property topology_atom_count: int | None

Readonly topology_atom_count payload of the RingInfoDimensionMismatch error variant; None for other variants.

property topology_bond_count: int | None

Readonly topology_bond_count payload of the RingInfoDimensionMismatch error variant; None for other variants.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of AromaticityError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property value: int | None

Readonly value payload of the InvalidValenceRow error variant; None for other variants.

property variant: AromaticityErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AromaticityErrorKind(value)

Discriminants of AromaticityErrorKind.

Members: InvalidTopology, InvalidQueryState, RingInfoNotInitialized, RingInfoDimensionMismatch, RingTableLengthMismatch, RingRowLengthMismatch, RingAtomOutOfRange, RingBondOutOfRange, AtomOutOfRange, BondOutOfRange, ValenceAssignmentLength, InvalidValenceRow, ExpectedRingBondNotFound, UnsupportedModel, UnsupportedState, IntegerOverflow, UnexpectedTopologyShape, AtomIdentityChanged, BondIdentityChanged, AromaticRingCountOutOfRange, RingFinding, Valence, Kekulize, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (26)
AromaticRingCountOutOfRange = AromaticityErrorKind.AromaticRingCountOutOfRange
AtomIdentityChanged = AromaticityErrorKind.AtomIdentityChanged
AtomOutOfRange = AromaticityErrorKind.AtomOutOfRange
BondIdentityChanged = AromaticityErrorKind.BondIdentityChanged
BondOutOfRange = AromaticityErrorKind.BondOutOfRange
ExpectedRingBondNotFound = AromaticityErrorKind.ExpectedRingBondNotFound
IntegerOverflow = AromaticityErrorKind.IntegerOverflow
InvalidQueryState = AromaticityErrorKind.InvalidQueryState
InvalidTopology = AromaticityErrorKind.InvalidTopology
InvalidValenceRow = AromaticityErrorKind.InvalidValenceRow
Kekulize = AromaticityErrorKind.Kekulize
RingAtomOutOfRange = AromaticityErrorKind.RingAtomOutOfRange
RingBondOutOfRange = AromaticityErrorKind.RingBondOutOfRange
RingFinding = AromaticityErrorKind.RingFinding
RingInfoDimensionMismatch = AromaticityErrorKind.RingInfoDimensionMismatch
RingInfoNotInitialized = AromaticityErrorKind.RingInfoNotInitialized
RingRowLengthMismatch = AromaticityErrorKind.RingRowLengthMismatch
RingTableLengthMismatch = AromaticityErrorKind.RingTableLengthMismatch
UnexpectedTopologyShape = AromaticityErrorKind.UnexpectedTopologyShape
UnsupportedModel = AromaticityErrorKind.UnsupportedModel
UnsupportedState = AromaticityErrorKind.UnsupportedState
Valence = AromaticityErrorKind.Valence
ValenceAssignmentLength = AromaticityErrorKind.ValenceAssignmentLength
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': AromaticityErrorKind.InvalidTopology, 'InvalidQueryState': AromaticityErrorKind.InvalidQueryState, 'RingInfoNotInitialized': AromaticityErrorKind.RingInfoNotInitialized, 'RingInfoDimensionMismatch': AromaticityErrorKind.RingInfoDimensionMismatch, 'RingTableLengthMismatch': AromaticityErrorKind.RingTableLengthMismatch, 'RingRowLengthMismatch': AromaticityErrorKind.RingRowLengthMismatch, 'RingAtomOutOfRange': AromaticityErrorKind.RingAtomOutOfRange, 'RingBondOutOfRange': AromaticityErrorKind.RingBondOutOfRange, 'AtomOutOfRange': AromaticityErrorKind.AtomOutOfRange, 'BondOutOfRange': AromaticityErrorKind.BondOutOfRange, 'ValenceAssignmentLength': AromaticityErrorKind.ValenceAssignmentLength, 'InvalidValenceRow': AromaticityErrorKind.InvalidValenceRow, 'ExpectedRingBondNotFound': AromaticityErrorKind.ExpectedRingBondNotFound, 'UnsupportedModel': AromaticityErrorKind.UnsupportedModel, 'UnsupportedState': AromaticityErrorKind.UnsupportedState, 'IntegerOverflow': AromaticityErrorKind.IntegerOverflow, 'UnexpectedTopologyShape': AromaticityErrorKind.UnexpectedTopologyShape, 'AtomIdentityChanged': AromaticityErrorKind.AtomIdentityChanged, 'BondIdentityChanged': AromaticityErrorKind.BondIdentityChanged, 'AromaticRingCountOutOfRange': AromaticityErrorKind.AromaticRingCountOutOfRange, 'RingFinding': AromaticityErrorKind.RingFinding, 'Valence': AromaticityErrorKind.Valence, 'Kekulize': AromaticityErrorKind.Kekulize})
values = mappingproxy({0: AromaticityErrorKind.InvalidTopology, 1: AromaticityErrorKind.InvalidQueryState, 2: AromaticityErrorKind.RingInfoNotInitialized, 3: AromaticityErrorKind.RingInfoDimensionMismatch, 4: AromaticityErrorKind.RingTableLengthMismatch, 5: AromaticityErrorKind.RingRowLengthMismatch, 6: AromaticityErrorKind.RingAtomOutOfRange, 7: AromaticityErrorKind.RingBondOutOfRange, 8: AromaticityErrorKind.AtomOutOfRange, 9: AromaticityErrorKind.BondOutOfRange, 10: AromaticityErrorKind.ValenceAssignmentLength, 11: AromaticityErrorKind.InvalidValenceRow, 12: AromaticityErrorKind.ExpectedRingBondNotFound, 13: AromaticityErrorKind.UnsupportedModel, 14: AromaticityErrorKind.UnsupportedState, 15: AromaticityErrorKind.IntegerOverflow, 16: AromaticityErrorKind.UnexpectedTopologyShape, 17: AromaticityErrorKind.AtomIdentityChanged, 18: AromaticityErrorKind.BondIdentityChanged, 19: AromaticityErrorKind.AromaticRingCountOutOfRange, 20: AromaticityErrorKind.RingFinding, 21: AromaticityErrorKind.Valence, 22: AromaticityErrorKind.Kekulize})
class cosmolkit.AromaticityModel(value)

Typed AromaticityModel values corresponding to the Rust enum.

Members: Rdkit, Simple, Mdl, Mmff94, Custom, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (8)
Custom = AromaticityModel.Custom
Mdl = AromaticityModel.Mdl
Mmff94 = AromaticityModel.Mmff94
Rdkit = AromaticityModel.Rdkit
Simple = AromaticityModel.Simple
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Rdkit': AromaticityModel.Rdkit, 'Simple': AromaticityModel.Simple, 'Mdl': AromaticityModel.Mdl, 'Mmff94': AromaticityModel.Mmff94, 'Custom': AromaticityModel.Custom})
values = mappingproxy({0: AromaticityModel.Rdkit, 1: AromaticityModel.Simple, 2: AromaticityModel.Mdl, 3: AromaticityModel.Mmff94, 4: AromaticityModel.Custom})
class cosmolkit.AromaticityParams(*, model=Ellipsis)

Aromaticity perception model selection.

Members (1)
model: AromaticityModel

Aromaticity model used to assign aromatic atoms and bonds.

class cosmolkit.Atom

Detached readonly atom data. Context-dependent queries are available on atoms obtained from a Molecule.

Members (18)
atom_map: int | None

Atom-mapping number, or None when no map is assigned.

atomic_number: int

Atomic number of the atom’s element.

chiral_tag: ChiralTag

Stored atom stereochemical tag; reading does not assign stereochemistry.

chiral_tag_code: int

Integer code of the stored chiral tag.

chiral_tag_name: str

Canonical name of the stored chiral tag.

cip_descriptor: CipDescriptor | None

Stored CIP descriptor, or None if absent; invalid stored values raise CipDescriptorError.

cip_neighbor_order: list[int] | None

Stored CIP neighbor ordering as atom indices, or None if absent; invalid encodings raise CipDescriptorError.

cip_rank: int | None

Stored CIP rank, or None when absent; an incorrectly typed property raises PropertyValueError.

element: Element

Chemical element stored on this atom.

explicit_hydrogens: int

Explicit hydrogen count stored on the atom, distinct from neighboring hydrogen atom rows.

formal_charge: int

Stored signed formal charge, not a partial charge.

hybridization: Hybridization

Stored hybridization assignment; reading does not recompute it.

id: int

Zero-based identifier within the originating topology.

is_aromatic: bool

Stored aromaticity flag; reading does not perform aromaticity perception.

isotope: int | None

Explicit isotope mass number, or None when no isotope is specified.

no_implicit: bool

Whether implicit hydrogens are disabled for this atom.

radical_electrons: int

Stored number of radical electrons.

template_attachment_order: TemplateAttachmentOrder | None

Template attachment ordering metadata, or None when absent.

class cosmolkit.AtomAddress(chain_name, residue, logical_atom_name, altloc=None)

Source atom address comprising chain, residue, logical atom name and alternate location.

Members (4)
altloc: int

Native alternate-location label byte.

chain_name: str

Source chain identifier.

logical_atom_name: str

Logical atom name used to resolve this address.

residue: ResidueAddress

Residue address containing the referenced atom.

exception cosmolkit.AtomCodeError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AtomCodeError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property code: int | None

Readonly code payload of the Postcondition error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: ValenceError | CipLabelerError | PropertyStringError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AtomCodeErrorKind

Exact Rust error variant, independent of the human-readable message.

property what: str | None

Native description of the failed requirement. Applies to AtomCodeError.Precondition, AtomCodeError.Postcondition. None when this payload is absent.

class cosmolkit.AtomCodeErrorKind(value)

Discriminants of AtomCodeErrorKind.

Members: Precondition, Postcondition, Valence, Cip, PropertyString, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
Cip = AtomCodeErrorKind.Cip
Postcondition = AtomCodeErrorKind.Postcondition
Precondition = AtomCodeErrorKind.Precondition
PropertyString = AtomCodeErrorKind.PropertyString
Valence = AtomCodeErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Precondition': AtomCodeErrorKind.Precondition, 'Postcondition': AtomCodeErrorKind.Postcondition, 'Valence': AtomCodeErrorKind.Valence, 'Cip': AtomCodeErrorKind.Cip, 'PropertyString': AtomCodeErrorKind.PropertyString})
values = mappingproxy({0: AtomCodeErrorKind.Precondition, 1: AtomCodeErrorKind.Postcondition, 2: AtomCodeErrorKind.Valence, 3: AtomCodeErrorKind.Cip, 4: AtomCodeErrorKind.PropertyString})
class cosmolkit.AtomCodeExplanation

Decoded element, branch, pi-electron and optional chirality components of an atom-pair atom code.

Members (5)
branch_count: int

Branch count decoded from the atom code after the requested subtraction.

chirality: str | None

Decoded chirality label, or None when chirality is not included.

static from_code(code, branch_subtract=0, include_chirality=False) → AtomCodeExplanation

Decode an atom-pair atom code, optionally adjusting branch count and interpreting chirality bits.

pi_electrons: int

Pi-electron count encoded in the atom code.

symbol: str

Element symbol decoded from the atom code.

exception cosmolkit.AtomCodeExplanationError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AtomCodeExplanationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property code: int | None

Readonly code payload of the UnknownChirality error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AtomCodeExplanationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AtomCodeExplanationErrorKind(value)

Discriminants of AtomCodeExplanationErrorKind.

Members: UnknownChirality, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
UnknownChirality = AtomCodeExplanationErrorKind.UnknownChirality
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnknownChirality': AtomCodeExplanationErrorKind.UnknownChirality})
values = mappingproxy({0: AtomCodeExplanationErrorKind.UnknownChirality})
class cosmolkit.AtomMetadata(degree, explicit_valence, implicit_hydrogens, total_hydrogens, total_valence)

Read-only atom degree, valence and hydrogen counts calculated by the native chemistry implementation.

Members (5)
degree: int

Number of bonded atom neighbors.

explicit_valence: int

Assigned explicit valence.

implicit_hydrogens: int

Assigned implicit hydrogen count.

total_hydrogens: int

Combined explicit and implicit hydrogen count reported by the native metadata calculation.

total_valence: int

Assigned total valence.

class cosmolkit.AtomName

Validated atom-name text preserving the native structural-file representation.

Members (3)
as_bytes() → bytes

Atom name as an independent bytes value.

as_str() → str

Atom name as text.

static from_ascii(bytes) → AtomName | None

Construct a validated atom name from ASCII bytes; return None if invalid.

class cosmolkit.AtomPairAtomCodeResult(code, molecule)

Atom-pair atom code together with the prepared molecule used to compute it.

Members (2)
code: int

Encoded atom-pair atom invariant.

molecule: Molecule

Prepared molecule associated with this code; returned with copy-on-write value semantics.

class cosmolkit.AtomPairAtomInvariantsGenerator(*, include_chirality=Ellipsis, topological_torsion_correction=Ellipsis)

Atom-pair invariant provider with optional chirality and torsion correction.

Members (4)
include_chirality: bool

Include chirality in generated atom-pair invariants.

info_string() → str

Return the native invariant-generator settings summary.

to_json() → str

Serialize the invariant-generator settings using the native JSON format.

topological_torsion_correction: bool

Apply the atom-degree correction used for topological torsion invariants.

exception cosmolkit.AtomPairError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AtomPairError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property atom_index: int | None

Atom index involved in the failure. Present for AtomPairError.AtomInvariantLength; None when unavailable.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property length: int | None

Length relevant to the failed bounds check. Present for AtomPairError.AtomInvariantLength; None when unavailable.

property source: FingerprintError | AtomCodeError | MatrixError | TopologyValidationError | MorganError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AtomPairErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AtomPairErrorKind(value)

Discriminants of AtomPairErrorKind.

Members: Fingerprint, AtomCode, Matrix, Topology, Preparation, AtomInvariantLength, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
AtomCode = AtomPairErrorKind.AtomCode
AtomInvariantLength = AtomPairErrorKind.AtomInvariantLength
Fingerprint = AtomPairErrorKind.Fingerprint
Matrix = AtomPairErrorKind.Matrix
Preparation = AtomPairErrorKind.Preparation
Topology = AtomPairErrorKind.Topology
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Fingerprint': AtomPairErrorKind.Fingerprint, 'AtomCode': AtomPairErrorKind.AtomCode, 'Matrix': AtomPairErrorKind.Matrix, 'Topology': AtomPairErrorKind.Topology, 'Preparation': AtomPairErrorKind.Preparation, 'AtomInvariantLength': AtomPairErrorKind.AtomInvariantLength})
values = mappingproxy({0: AtomPairErrorKind.Fingerprint, 1: AtomPairErrorKind.AtomCode, 2: AtomPairErrorKind.Matrix, 3: AtomPairErrorKind.Topology, 4: AtomPairErrorKind.Preparation, 5: AtomPairErrorKind.AtomInvariantLength})
class cosmolkit.AtomPairFingerprintParams(*, min_distance=Ellipsis, max_distance=Ellipsis, include_chirality=Ellipsis, use_2d=Ellipsis, count_simulation=Ellipsis, fp_size=Ellipsis, count_bounds=Ellipsis, bits_per_feature=Ellipsis, from_atoms=Ellipsis, ignore_atoms=Ellipsis, custom_atom_invariants=Ellipsis, custom_bond_invariants=Ellipsis, conformer_id=Ellipsis, atom_invariants_generator=Ellipsis, use_legacy_stereo_perception=Ellipsis)

Complete reusable fingerprint call configuration, including generator settings and atom selections.

Members (15)
atom_invariants_generator: AtomPairAtomInvariantsGenerator | None

Optional native atom-invariant provider; None uses the generator default.

bits_per_feature: int

Number of hash-derived positions generated for each pair feature.

conformer_id: int | None

Stored conformer ID for 3D distances; None uses the native default selection. Not used when the generator’s use_2d option is true.

count_bounds: tuple[int, ...]

Occurrence thresholds used by count simulation.

count_simulation: bool

Encode occurrence-count thresholds as bits in bit fingerprints.

custom_atom_invariants: tuple[int, ...] | None

Optional per-atom invariant overrides in atom-index order.

custom_bond_invariants: tuple[int, ...] | None

Optional per-bond invariant overrides in bond-index order.

fp_size: int

Number of positions in folded fingerprints.

from_atoms: tuple[int, ...] | None

Optional zero-based atom indices restricting fingerprint contributions.

ignore_atoms: tuple[int, ...] | None

Optional zero-based atom indices excluded from fingerprint generation.

include_chirality: bool

Include atom chirality in pair identifiers.

max_distance: int

Maximum included atom-pair distance, inclusive.

min_distance: int

Minimum included atom-pair distance, inclusive.

use_2d: bool

Use graph distances when true, otherwise distances from the selected 3D conformer.

use_legacy_stereo_perception: bool

Use legacy stereochemistry perception when preparing the fingerprint input.

class cosmolkit.AtomPairGeneratorParams(*, min_distance=Ellipsis, max_distance=Ellipsis, include_chirality=Ellipsis, use_2d=Ellipsis, count_simulation=Ellipsis, fp_size=Ellipsis, count_bounds=Ellipsis, bits_per_feature=Ellipsis)

Atom-pair fingerprint settings for distance selection, chirality and count encoding.

Members (11)
bits_per_feature: int

Number of hash-derived positions generated for each pair feature.

count_bounds: tuple[int, ...]

Occurrence thresholds used by count simulation.

count_simulation: bool

Encode occurrence-count thresholds as bits in bit fingerprints.

fp_size: int

Number of positions in folded fingerprints.

include_chirality: bool

Include atom chirality in pair identifiers.

info_string() → str

Return the native human-readable fingerprint generator settings summary.

max_distance: int

Maximum included atom-pair distance, inclusive.

min_distance: int

Minimum included atom-pair distance, inclusive.

to_json() → str

Serialize generator parameters with the native JSON format.

use_2d: bool

Use graph distances when true, otherwise distances from the selected 3D conformer.

with_json(json) → AtomPairGeneratorParams

Return an independent configuration updated by the native JSON parser.

exception cosmolkit.AtomPairReadError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AtomPairReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: FingerprintPreparationError | AtomPairError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AtomPairReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AtomPairReadErrorKind(value)

Discriminants of AtomPairReadErrorKind.

Members: Preparation, Generator, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Generator = AtomPairReadErrorKind.Generator
Preparation = AtomPairReadErrorKind.Preparation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Preparation': AtomPairReadErrorKind.Preparation, 'Generator': AtomPairReadErrorKind.Generator})
values = mappingproxy({0: AtomPairReadErrorKind.Preparation, 1: AtomPairReadErrorKind.Generator})
class cosmolkit.AtomPairsParameters

Namespace for the facade’s source-defined atom-pair encoding vocabulary.

Members (10)
static atom_types() → list[int]

Atomic numbers represented by the atom-pair type encoding, in encoding order.

static code_size() → int

Number of bits in the native atom code.

static max_path_length() → int

Largest path length representable by the atom-pair encoding.

static num_atom_pair_fingerprint_bits() → int

Size of the native atom-pair fingerprint identifier space.

static num_branch_bits() → int

Number of bits reserved for atom branching information.

static num_chiral_bits() → int

Number of bits reserved for chirality information.

static num_path_bits() → int

Number of bits reserved for pair path lengths.

static num_pi_bits() → int

Number of bits reserved for pi-electron information in an atom code.

static num_type_bits() → int

Number of bits reserved for the atom type in an atom code.

static version() → str

Version of the native atom-pair encoding scheme.

exception cosmolkit.AtomPathSubsetCopyError(*args, **kwargs)

Failure in the fragments domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AtomPathSubsetCopyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property bond_copy: SelectedBondCopyError | None

“error_payload”} Structured SelectedBondCopyError payload of AtomPathSubsetCopyError.BondCopy; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property computed_properties: TopologyEditError | None

“error_payload”} Structured TopologyEditError payload of AtomPathSubsetCopyError.ComputedProperties; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property mapping_validation: MappingValidationError | None

“error_payload”} Structured MappingValidationError payload of AtomPathSubsetCopyError.MappingValidation; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property sanitize: SanitizeError | None

“error_payload”} Structured SanitizeError payload of AtomPathSubsetCopyError.Sanitize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: MoleculePropertyError | BondValueError | AtomPropertyError | TopologyValidationError | QueryStateError | CleanupError | PropertyCacheError | RingFindingError | KekulizeError | RadicalError | AromaticityError | ConjugationError | HybridizationError | AtropisomerError | StereoError | AdjustHsError | StereoGroupError | CoordinateValidationError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property substance_group_copy: SelectedSubstanceGroupCopyError | None

“error_payload”} Structured SelectedSubstanceGroupCopyError payload of AtomPathSubsetCopyError.SubstanceGroupCopy; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property topology_validation: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of AtomPathSubsetCopyError.TopologyValidation; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: AtomPathSubsetCopyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AtomPathSubsetCopyErrorKind(value)

Discriminants of AtomPathSubsetCopyErrorKind.

Members: StereoGroup, ComputedProperties, MoleculeProperty, BondProperty, AtomProperty, BondCopy, SubstanceGroupCopy, TopologyValidation, MappingValidation, Sanitize, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (13)
AtomProperty = AtomPathSubsetCopyErrorKind.AtomProperty
BondCopy = AtomPathSubsetCopyErrorKind.BondCopy
BondProperty = AtomPathSubsetCopyErrorKind.BondProperty
ComputedProperties = AtomPathSubsetCopyErrorKind.ComputedProperties
MappingValidation = AtomPathSubsetCopyErrorKind.MappingValidation
MoleculeProperty = AtomPathSubsetCopyErrorKind.MoleculeProperty
Sanitize = AtomPathSubsetCopyErrorKind.Sanitize
StereoGroup = AtomPathSubsetCopyErrorKind.StereoGroup
SubstanceGroupCopy = AtomPathSubsetCopyErrorKind.SubstanceGroupCopy
TopologyValidation = AtomPathSubsetCopyErrorKind.TopologyValidation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': AtomPathSubsetCopyErrorKind.StereoGroup, 'ComputedProperties': AtomPathSubsetCopyErrorKind.ComputedProperties, 'MoleculeProperty': AtomPathSubsetCopyErrorKind.MoleculeProperty, 'BondProperty': AtomPathSubsetCopyErrorKind.BondProperty, 'AtomProperty': AtomPathSubsetCopyErrorKind.AtomProperty, 'BondCopy': AtomPathSubsetCopyErrorKind.BondCopy, 'SubstanceGroupCopy': AtomPathSubsetCopyErrorKind.SubstanceGroupCopy, 'TopologyValidation': AtomPathSubsetCopyErrorKind.TopologyValidation, 'MappingValidation': AtomPathSubsetCopyErrorKind.MappingValidation, 'Sanitize': AtomPathSubsetCopyErrorKind.Sanitize})
values = mappingproxy({0: AtomPathSubsetCopyErrorKind.StereoGroup, 1: AtomPathSubsetCopyErrorKind.ComputedProperties, 2: AtomPathSubsetCopyErrorKind.MoleculeProperty, 3: AtomPathSubsetCopyErrorKind.BondProperty, 4: AtomPathSubsetCopyErrorKind.AtomProperty, 5: AtomPathSubsetCopyErrorKind.BondCopy, 6: AtomPathSubsetCopyErrorKind.SubstanceGroupCopy, 7: AtomPathSubsetCopyErrorKind.TopologyValidation, 8: AtomPathSubsetCopyErrorKind.MappingValidation, 9: AtomPathSubsetCopyErrorKind.Sanitize})
class cosmolkit.AtomPositionParams(*, conformer_id=Ellipsis)

Stored-conformer selection for reading an atom position.

Members (1)
conformer_id: int | None

Stored 3D conformer identifier, or None for default selection.

exception cosmolkit.AtomPropertyError(*args, **kwargs)

Failure in the property domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AtomPropertyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property computed_list_kind: PropertyValueError | None

“error_payload”} Structured PropertyValueError payload of AtomPropertyError.ComputedListKind; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AtomPropertyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AtomPropertyErrorKind(value)

Discriminants of AtomPropertyErrorKind.

Members: EmptyKey, ComputedListKind, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
ComputedListKind = AtomPropertyErrorKind.ComputedListKind
EmptyKey = AtomPropertyErrorKind.EmptyKey
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyKey': AtomPropertyErrorKind.EmptyKey, 'ComputedListKind': AtomPropertyErrorKind.ComputedListKind})
values = mappingproxy({0: AtomPropertyErrorKind.EmptyKey, 1: AtomPropertyErrorKind.ComputedListKind})
exception cosmolkit.AtomPropertyReadError(*args, **kwargs)

Failure in the property domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AtomPropertyReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property error_len: int | None

Length of the invalid UTF-8 sequence, or None for incomplete input or a different error kind.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valid_up_to: int | None

Number of valid UTF-8 bytes before the decoding failure, or None for non-decoding errors.

property variant: AtomPropertyReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AtomPropertyReadErrorKind(value)

Discriminants of AtomPropertyReadErrorKind.

Members: Operation, Type, Utf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Operation = AtomPropertyReadErrorKind.Operation
Type = AtomPropertyReadErrorKind.Type
Utf8 = AtomPropertyReadErrorKind.Utf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Operation': AtomPropertyReadErrorKind.Operation, 'Type': AtomPropertyReadErrorKind.Type, 'Utf8': AtomPropertyReadErrorKind.Utf8})
values = mappingproxy({0: AtomPropertyReadErrorKind.Operation, 1: AtomPropertyReadErrorKind.Type, 2: AtomPropertyReadErrorKind.Utf8})
class cosmolkit.AtomQueryPredicate

Read-only native atom predicate retained by a SMARTS writer diagnostic; variant determines its payload.

Members (5)
aromatic: bool | None

Aromaticity requirement in an AtomType predicate, or None for other variants.

atomic_number: int | None

Atomic number in an AtomType predicate, or None for other variants.

name: str | None

Property name in a PropertyValue predicate, or None for other variants.

value: int | bool | bytes | str | Hybridization | ChiralTag | RecursiveStructureQuery | AtomRangeQuery | None

Typed payload of the selected predicate or one-sided bound; None for payload-free or differently structured variants.

variant: AtomQueryPredicateKind

Exact native predicate or bound variant; payload availability follows this variant.

class cosmolkit.AtomQueryPredicateKind(value)

Discriminants of AtomQueryPredicateKind.

Members: Any, AtomicNumber, AtomType, AtomicNumberIn, AtomicNumberNotIn, FormalCharge, NegativeFormalCharge, NumRadicalElectrons, HasChiralTag, MissingChiralTag, Isotope, HydrogenCount, HasImplicitHydrogen, ImplicitHydrogenCount, ImplicitHydrogenCountLessEqual, ImplicitValence, ExplicitValence, ExplicitDegree, ExplicitDegreeLessEqual, NonHydrogenDegree, NonHydrogenDegreeLessEqual, NonHydrogenDegreeGreaterEqual, HeavyAtomDegree, NumHeteroatomNeighbors, HasHeteroatomNeighbors, NumAliphaticHeteroatomNeighbors, HasAliphaticHeteroatomNeighbors, RingBondCount, RingBondCountLessEqual, HasRingBond, IsBridgehead, IsAromatic, IsUnsaturated, RecursiveSmarts, HasProperty, PropertyValue, RGroupLabel, MolFileAlias, HybridizationMatch, TotalDegree, TotalDegreeLessEqual, TotalDegreeGreaterEqual, TotalValence, TotalValenceLessEqual, TotalValenceGreaterEqual, InRing, NumAtomRings, InRingOfSize, InRingOfSizeLessEqual, InRingOfSizeGreaterEqual, SmallestRingSize, SmallestRingSizeLessEqual, SmallestRingSizeGreaterEqual, Mass, ChiralTagMatch, ChiralPermutationMatch, DegreeLessEqual, DegreeGreaterEqual, Range, UnsupportedFeature, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (63)
Any = AtomQueryPredicateKind.Any
AtomType = AtomQueryPredicateKind.AtomType
AtomicNumber = AtomQueryPredicateKind.AtomicNumber
AtomicNumberIn = AtomQueryPredicateKind.AtomicNumberIn
AtomicNumberNotIn = AtomQueryPredicateKind.AtomicNumberNotIn
ChiralPermutationMatch = AtomQueryPredicateKind.ChiralPermutationMatch
ChiralTagMatch = AtomQueryPredicateKind.ChiralTagMatch
DegreeGreaterEqual = AtomQueryPredicateKind.DegreeGreaterEqual
DegreeLessEqual = AtomQueryPredicateKind.DegreeLessEqual
ExplicitDegree = AtomQueryPredicateKind.ExplicitDegree
ExplicitDegreeLessEqual = AtomQueryPredicateKind.ExplicitDegreeLessEqual
ExplicitValence = AtomQueryPredicateKind.ExplicitValence
FormalCharge = AtomQueryPredicateKind.FormalCharge
HasAliphaticHeteroatomNeighbors = AtomQueryPredicateKind.HasAliphaticHeteroatomNeighbors
HasChiralTag = AtomQueryPredicateKind.HasChiralTag
HasHeteroatomNeighbors = AtomQueryPredicateKind.HasHeteroatomNeighbors
HasImplicitHydrogen = AtomQueryPredicateKind.HasImplicitHydrogen
HasProperty = AtomQueryPredicateKind.HasProperty
HasRingBond = AtomQueryPredicateKind.HasRingBond
HeavyAtomDegree = AtomQueryPredicateKind.HeavyAtomDegree
HybridizationMatch = AtomQueryPredicateKind.HybridizationMatch
HydrogenCount = AtomQueryPredicateKind.HydrogenCount
ImplicitHydrogenCount = AtomQueryPredicateKind.ImplicitHydrogenCount
ImplicitHydrogenCountLessEqual = AtomQueryPredicateKind.ImplicitHydrogenCountLessEqual
ImplicitValence = AtomQueryPredicateKind.ImplicitValence
InRing = AtomQueryPredicateKind.InRing
InRingOfSize = AtomQueryPredicateKind.InRingOfSize
InRingOfSizeGreaterEqual = AtomQueryPredicateKind.InRingOfSizeGreaterEqual
InRingOfSizeLessEqual = AtomQueryPredicateKind.InRingOfSizeLessEqual
IsAromatic = AtomQueryPredicateKind.IsAromatic
IsBridgehead = AtomQueryPredicateKind.IsBridgehead
IsUnsaturated = AtomQueryPredicateKind.IsUnsaturated
Isotope = AtomQueryPredicateKind.Isotope
Mass = AtomQueryPredicateKind.Mass
MissingChiralTag = AtomQueryPredicateKind.MissingChiralTag
MolFileAlias = AtomQueryPredicateKind.MolFileAlias
NegativeFormalCharge = AtomQueryPredicateKind.NegativeFormalCharge
NonHydrogenDegree = AtomQueryPredicateKind.NonHydrogenDegree
NonHydrogenDegreeGreaterEqual = AtomQueryPredicateKind.NonHydrogenDegreeGreaterEqual
NonHydrogenDegreeLessEqual = AtomQueryPredicateKind.NonHydrogenDegreeLessEqual
NumAliphaticHeteroatomNeighbors = AtomQueryPredicateKind.NumAliphaticHeteroatomNeighbors
NumAtomRings = AtomQueryPredicateKind.NumAtomRings
NumHeteroatomNeighbors = AtomQueryPredicateKind.NumHeteroatomNeighbors
NumRadicalElectrons = AtomQueryPredicateKind.NumRadicalElectrons
PropertyValue = AtomQueryPredicateKind.PropertyValue
RGroupLabel = AtomQueryPredicateKind.RGroupLabel
Range = AtomQueryPredicateKind.Range
RecursiveSmarts = AtomQueryPredicateKind.RecursiveSmarts
RingBondCount = AtomQueryPredicateKind.RingBondCount
RingBondCountLessEqual = AtomQueryPredicateKind.RingBondCountLessEqual
SmallestRingSize = AtomQueryPredicateKind.SmallestRingSize
SmallestRingSizeGreaterEqual = AtomQueryPredicateKind.SmallestRingSizeGreaterEqual
SmallestRingSizeLessEqual = AtomQueryPredicateKind.SmallestRingSizeLessEqual
TotalDegree = AtomQueryPredicateKind.TotalDegree
TotalDegreeGreaterEqual = AtomQueryPredicateKind.TotalDegreeGreaterEqual
TotalDegreeLessEqual = AtomQueryPredicateKind.TotalDegreeLessEqual
TotalValence = AtomQueryPredicateKind.TotalValence
TotalValenceGreaterEqual = AtomQueryPredicateKind.TotalValenceGreaterEqual
TotalValenceLessEqual = AtomQueryPredicateKind.TotalValenceLessEqual
UnsupportedFeature = AtomQueryPredicateKind.UnsupportedFeature
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Any': AtomQueryPredicateKind.Any, 'AtomicNumber': AtomQueryPredicateKind.AtomicNumber, 'AtomType': AtomQueryPredicateKind.AtomType, 'AtomicNumberIn': AtomQueryPredicateKind.AtomicNumberIn, 'AtomicNumberNotIn': AtomQueryPredicateKind.AtomicNumberNotIn, 'FormalCharge': AtomQueryPredicateKind.FormalCharge, 'NegativeFormalCharge': AtomQueryPredicateKind.NegativeFormalCharge, 'NumRadicalElectrons': AtomQueryPredicateKind.NumRadicalElectrons, 'HasChiralTag': AtomQueryPredicateKind.HasChiralTag, 'MissingChiralTag': AtomQueryPredicateKind.MissingChiralTag, 'Isotope': AtomQueryPredicateKind.Isotope, 'HydrogenCount': AtomQueryPredicateKind.HydrogenCount, 'HasImplicitHydrogen': AtomQueryPredicateKind.HasImplicitHydrogen, 'ImplicitHydrogenCount': AtomQueryPredicateKind.ImplicitHydrogenCount, 'ImplicitHydrogenCountLessEqual': AtomQueryPredicateKind.ImplicitHydrogenCountLessEqual, 'ImplicitValence': AtomQueryPredicateKind.ImplicitValence, 'ExplicitValence': AtomQueryPredicateKind.ExplicitValence, 'ExplicitDegree': AtomQueryPredicateKind.ExplicitDegree, 'ExplicitDegreeLessEqual': AtomQueryPredicateKind.ExplicitDegreeLessEqual, 'NonHydrogenDegree': AtomQueryPredicateKind.NonHydrogenDegree, 'NonHydrogenDegreeLessEqual': AtomQueryPredicateKind.NonHydrogenDegreeLessEqual, 'NonHydrogenDegreeGreaterEqual': AtomQueryPredicateKind.NonHydrogenDegreeGreaterEqual, 'HeavyAtomDegree': AtomQueryPredicateKind.HeavyAtomDegree, 'NumHeteroatomNeighbors': AtomQueryPredicateKind.NumHeteroatomNeighbors, 'HasHeteroatomNeighbors': AtomQueryPredicateKind.HasHeteroatomNeighbors, 'NumAliphaticHeteroatomNeighbors': AtomQueryPredicateKind.NumAliphaticHeteroatomNeighbors, 'HasAliphaticHeteroatomNeighbors': AtomQueryPredicateKind.HasAliphaticHeteroatomNeighbors, 'RingBondCount': AtomQueryPredicateKind.RingBondCount, 'RingBondCountLessEqual': AtomQueryPredicateKind.RingBondCountLessEqual, 'HasRingBond': AtomQueryPredicateKind.HasRingBond, 'IsBridgehead': AtomQueryPredicateKind.IsBridgehead, 'IsAromatic': AtomQueryPredicateKind.IsAromatic, 'IsUnsaturated': AtomQueryPredicateKind.IsUnsaturated, 'RecursiveSmarts': AtomQueryPredicateKind.RecursiveSmarts, 'HasProperty': AtomQueryPredicateKind.HasProperty, 'PropertyValue': AtomQueryPredicateKind.PropertyValue, 'RGroupLabel': AtomQueryPredicateKind.RGroupLabel, 'MolFileAlias': AtomQueryPredicateKind.MolFileAlias, 'HybridizationMatch': AtomQueryPredicateKind.HybridizationMatch, 'TotalDegree': AtomQueryPredicateKind.TotalDegree, 'TotalDegreeLessEqual': AtomQueryPredicateKind.TotalDegreeLessEqual, 'TotalDegreeGreaterEqual': AtomQueryPredicateKind.TotalDegreeGreaterEqual, 'TotalValence': AtomQueryPredicateKind.TotalValence, 'TotalValenceLessEqual': AtomQueryPredicateKind.TotalValenceLessEqual, 'TotalValenceGreaterEqual': AtomQueryPredicateKind.TotalValenceGreaterEqual, 'InRing': AtomQueryPredicateKind.InRing, 'NumAtomRings': AtomQueryPredicateKind.NumAtomRings, 'InRingOfSize': AtomQueryPredicateKind.InRingOfSize, 'InRingOfSizeLessEqual': AtomQueryPredicateKind.InRingOfSizeLessEqual, 'InRingOfSizeGreaterEqual': AtomQueryPredicateKind.InRingOfSizeGreaterEqual, 'SmallestRingSize': AtomQueryPredicateKind.SmallestRingSize, 'SmallestRingSizeLessEqual': AtomQueryPredicateKind.SmallestRingSizeLessEqual, 'SmallestRingSizeGreaterEqual': AtomQueryPredicateKind.SmallestRingSizeGreaterEqual, 'Mass': AtomQueryPredicateKind.Mass, 'ChiralTagMatch': AtomQueryPredicateKind.ChiralTagMatch, 'ChiralPermutationMatch': AtomQueryPredicateKind.ChiralPermutationMatch, 'DegreeLessEqual': AtomQueryPredicateKind.DegreeLessEqual, 'DegreeGreaterEqual': AtomQueryPredicateKind.DegreeGreaterEqual, 'Range': AtomQueryPredicateKind.Range, 'UnsupportedFeature': AtomQueryPredicateKind.UnsupportedFeature})
values = mappingproxy({0: AtomQueryPredicateKind.Any, 1: AtomQueryPredicateKind.AtomicNumber, 2: AtomQueryPredicateKind.AtomType, 3: AtomQueryPredicateKind.AtomicNumberIn, 4: AtomQueryPredicateKind.AtomicNumberNotIn, 5: AtomQueryPredicateKind.FormalCharge, 6: AtomQueryPredicateKind.NegativeFormalCharge, 7: AtomQueryPredicateKind.NumRadicalElectrons, 8: AtomQueryPredicateKind.HasChiralTag, 9: AtomQueryPredicateKind.MissingChiralTag, 10: AtomQueryPredicateKind.Isotope, 11: AtomQueryPredicateKind.HydrogenCount, 12: AtomQueryPredicateKind.HasImplicitHydrogen, 13: AtomQueryPredicateKind.ImplicitHydrogenCount, 14: AtomQueryPredicateKind.ImplicitHydrogenCountLessEqual, 15: AtomQueryPredicateKind.ImplicitValence, 16: AtomQueryPredicateKind.ExplicitValence, 17: AtomQueryPredicateKind.ExplicitDegree, 18: AtomQueryPredicateKind.ExplicitDegreeLessEqual, 19: AtomQueryPredicateKind.NonHydrogenDegree, 20: AtomQueryPredicateKind.NonHydrogenDegreeLessEqual, 21: AtomQueryPredicateKind.NonHydrogenDegreeGreaterEqual, 22: AtomQueryPredicateKind.HeavyAtomDegree, 23: AtomQueryPredicateKind.NumHeteroatomNeighbors, 24: AtomQueryPredicateKind.HasHeteroatomNeighbors, 25: AtomQueryPredicateKind.NumAliphaticHeteroatomNeighbors, 26: AtomQueryPredicateKind.HasAliphaticHeteroatomNeighbors, 27: AtomQueryPredicateKind.RingBondCount, 28: AtomQueryPredicateKind.RingBondCountLessEqual, 29: AtomQueryPredicateKind.HasRingBond, 30: AtomQueryPredicateKind.IsBridgehead, 31: AtomQueryPredicateKind.IsAromatic, 32: AtomQueryPredicateKind.IsUnsaturated, 33: AtomQueryPredicateKind.RecursiveSmarts, 34: AtomQueryPredicateKind.HasProperty, 35: AtomQueryPredicateKind.PropertyValue, 36: AtomQueryPredicateKind.RGroupLabel, 37: AtomQueryPredicateKind.MolFileAlias, 38: AtomQueryPredicateKind.HybridizationMatch, 39: AtomQueryPredicateKind.TotalDegree, 40: AtomQueryPredicateKind.TotalDegreeLessEqual, 41: AtomQueryPredicateKind.TotalDegreeGreaterEqual, 42: AtomQueryPredicateKind.TotalValence, 43: AtomQueryPredicateKind.TotalValenceLessEqual, 44: AtomQueryPredicateKind.TotalValenceGreaterEqual, 45: AtomQueryPredicateKind.InRing, 46: AtomQueryPredicateKind.NumAtomRings, 47: AtomQueryPredicateKind.InRingOfSize, 48: AtomQueryPredicateKind.InRingOfSizeLessEqual, 49: AtomQueryPredicateKind.InRingOfSizeGreaterEqual, 50: AtomQueryPredicateKind.SmallestRingSize, 51: AtomQueryPredicateKind.SmallestRingSizeLessEqual, 52: AtomQueryPredicateKind.SmallestRingSizeGreaterEqual, 53: AtomQueryPredicateKind.Mass, 54: AtomQueryPredicateKind.ChiralTagMatch, 55: AtomQueryPredicateKind.ChiralPermutationMatch, 56: AtomQueryPredicateKind.DegreeLessEqual, 57: AtomQueryPredicateKind.DegreeGreaterEqual, 58: AtomQueryPredicateKind.Range, 59: AtomQueryPredicateKind.UnsupportedFeature})
class cosmolkit.AtomRangeBounds

One-sided or two-sided numeric bounds with endpoint inclusion flags.

Members (6)
lower: int | None

Lower range endpoint, or None when this variant has no lower endpoint.

lower_open: bool | None

Whether the lower endpoint is excluded, or None when not applicable.

upper: int | None

Upper range endpoint, or None when this variant has no upper endpoint.

upper_open: bool | None

Whether the upper endpoint is excluded, or None when not applicable.

value: int | None

Typed payload of the selected predicate or one-sided bound; None for payload-free or differently structured variants.

variant: AtomRangeBoundsKind

Exact native predicate or bound variant; payload availability follows this variant.

class cosmolkit.AtomRangeBoundsKind(value)

Discriminants of AtomRangeBoundsKind.

Members: LessEqual, GreaterEqual, Inclusive, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
GreaterEqual = AtomRangeBoundsKind.GreaterEqual
Inclusive = AtomRangeBoundsKind.Inclusive
LessEqual = AtomRangeBoundsKind.LessEqual
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'LessEqual': AtomRangeBoundsKind.LessEqual, 'GreaterEqual': AtomRangeBoundsKind.GreaterEqual, 'Inclusive': AtomRangeBoundsKind.Inclusive})
values = mappingproxy({0: AtomRangeBoundsKind.LessEqual, 1: AtomRangeBoundsKind.GreaterEqual, 2: AtomRangeBoundsKind.Inclusive})
class cosmolkit.AtomRangeDataFunction

Native atom-data selector used by a range predicate, optionally constrained to ring sizes.

Members (5)
lower: int | None

Lower range endpoint, or None when this variant has no lower endpoint.

lower_open: bool | None

Whether the lower endpoint is excluded, or None when not applicable.

upper: int | None

Upper range endpoint, or None when this variant has no upper endpoint.

upper_open: bool | None

Whether the upper endpoint is excluded, or None when not applicable.

variant: AtomRangeDataFunctionKind

Exact native predicate or bound variant; payload availability follows this variant.

class cosmolkit.AtomRangeDataFunctionKind(value)

Discriminants of AtomRangeDataFunctionKind.

Members: ExplicitDegree, NonHydrogenDegree, TotalDegree, TotalValence, NumAtomRings, NumHeteroatomNeighbors, NumAliphaticHeteroatomNeighbors, MinRingSize, RingBondCount, ImplicitHydrogenCount, FormalCharge, NegativeFormalCharge, AtomRingSize, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (16)
AtomRingSize = AtomRangeDataFunctionKind.AtomRingSize
ExplicitDegree = AtomRangeDataFunctionKind.ExplicitDegree
FormalCharge = AtomRangeDataFunctionKind.FormalCharge
ImplicitHydrogenCount = AtomRangeDataFunctionKind.ImplicitHydrogenCount
MinRingSize = AtomRangeDataFunctionKind.MinRingSize
NegativeFormalCharge = AtomRangeDataFunctionKind.NegativeFormalCharge
NonHydrogenDegree = AtomRangeDataFunctionKind.NonHydrogenDegree
NumAliphaticHeteroatomNeighbors = AtomRangeDataFunctionKind.NumAliphaticHeteroatomNeighbors
NumAtomRings = AtomRangeDataFunctionKind.NumAtomRings
NumHeteroatomNeighbors = AtomRangeDataFunctionKind.NumHeteroatomNeighbors
RingBondCount = AtomRangeDataFunctionKind.RingBondCount
TotalDegree = AtomRangeDataFunctionKind.TotalDegree
TotalValence = AtomRangeDataFunctionKind.TotalValence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ExplicitDegree': AtomRangeDataFunctionKind.ExplicitDegree, 'NonHydrogenDegree': AtomRangeDataFunctionKind.NonHydrogenDegree, 'TotalDegree': AtomRangeDataFunctionKind.TotalDegree, 'TotalValence': AtomRangeDataFunctionKind.TotalValence, 'NumAtomRings': AtomRangeDataFunctionKind.NumAtomRings, 'NumHeteroatomNeighbors': AtomRangeDataFunctionKind.NumHeteroatomNeighbors, 'NumAliphaticHeteroatomNeighbors': AtomRangeDataFunctionKind.NumAliphaticHeteroatomNeighbors, 'MinRingSize': AtomRangeDataFunctionKind.MinRingSize, 'RingBondCount': AtomRangeDataFunctionKind.RingBondCount, 'ImplicitHydrogenCount': AtomRangeDataFunctionKind.ImplicitHydrogenCount, 'FormalCharge': AtomRangeDataFunctionKind.FormalCharge, 'NegativeFormalCharge': AtomRangeDataFunctionKind.NegativeFormalCharge, 'AtomRingSize': AtomRangeDataFunctionKind.AtomRingSize})
values = mappingproxy({0: AtomRangeDataFunctionKind.ExplicitDegree, 1: AtomRangeDataFunctionKind.NonHydrogenDegree, 2: AtomRangeDataFunctionKind.TotalDegree, 3: AtomRangeDataFunctionKind.TotalValence, 4: AtomRangeDataFunctionKind.NumAtomRings, 5: AtomRangeDataFunctionKind.NumHeteroatomNeighbors, 6: AtomRangeDataFunctionKind.NumAliphaticHeteroatomNeighbors, 7: AtomRangeDataFunctionKind.MinRingSize, 8: AtomRangeDataFunctionKind.RingBondCount, 9: AtomRangeDataFunctionKind.ImplicitHydrogenCount, 10: AtomRangeDataFunctionKind.FormalCharge, 11: AtomRangeDataFunctionKind.NegativeFormalCharge, 12: AtomRangeDataFunctionKind.AtomRingSize})
class cosmolkit.AtomRangeQuery

Native atom-data function and numeric range predicate.

Members (2)
bounds: AtomRangeBounds

Numeric bounds applied by this range query.

data_function: AtomRangeDataFunction

Native atom-data function evaluated before applying the bounds.

class cosmolkit.AtomSiteIdentityField(value)

Typed AtomSiteIdentityField values corresponding to the Rust enum.

Members: AsymId, CompId, AtomId, SeqId, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
AsymId = AtomSiteIdentityField.AsymId
AtomId = AtomSiteIdentityField.AtomId
CompId = AtomSiteIdentityField.CompId
SeqId = AtomSiteIdentityField.SeqId
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'AsymId': AtomSiteIdentityField.AsymId, 'CompId': AtomSiteIdentityField.CompId, 'AtomId': AtomSiteIdentityField.AtomId, 'SeqId': AtomSiteIdentityField.SeqId})
values = mappingproxy({0: AtomSiteIdentityField.AsymId, 1: AtomSiteIdentityField.CompId, 2: AtomSiteIdentityField.AtomId, 3: AtomSiteIdentityField.SeqId})
class cosmolkit.AtomSourceIds(serial=None)

Original atom serial identifier, distinct from a local atom row index.

Members (1)
serial: int | None

Source atom serial number, or None if absent.

class cosmolkit.AtomSpec(element)

Detached inputs for constructing an atom; with_* methods return independent specifications.

Members (6)
static new(element) → AtomSpec

Create an atom specification for an element with native default atom attributes.

with_atom_map(value) → AtomSpec

Return an independent atom specification with the atom-map number replaced.

with_explicit_hydrogens(value) → AtomSpec

Return an independent atom specification with the explicit hydrogen count replaced.

with_formal_charge(value) → AtomSpec

Return an independent atom specification with the requested formal charge.

with_isotope(value) → AtomSpec

Return an independent atom specification with the isotope mass number replaced.

with_no_implicit(value) → AtomSpec

Return an independent atom specification with implicit-hydrogen inference enabled or disabled.

exception cosmolkit.AtropisomerError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AtropisomerError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property actual: int | None

Observed value reported by the native check. Applies to AtropisomerError.RingAtomRowCount, AtropisomerError.RingBondRowCount, AtropisomerError.HybridizationAssignmentLength. None when this payload is absent.

property atom: int | None

Atom identifier implicated in the failure. Applies to AtropisomerError.CarrierCount, AtropisomerError.RingAtomOutOfRange, AtropisomerError.StereoGroupAtomOutOfRange. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to AtropisomerError.RingAtomOutOfRange, AtropisomerError.StereoGroupAtomOutOfRange. None when this payload is absent.

property bond: int | None

Bond index involved in the failure. Present for AtropisomerError.CandidateTraversalOutOfRange, AtropisomerError.CandidateTraversalDuplicate, AtropisomerError.CandidateTraversalUnexpected, AtropisomerError.CandidateTraversalMissing, AtropisomerError.RingBondOutOfRange, AtropisomerError.BondUpdate, AtropisomerError.StereoGroupBondOutOfRange, AtropisomerError.AssignmentBondOutOfRange, AtropisomerError.AxialBondOutOfRange, AtropisomerError.InvalidAtropisomerStereo; None when unavailable.

property bond_count: int | None

Bond count used when validating the reported bond reference. Applies to AtropisomerError.CandidateTraversalOutOfRange, AtropisomerError.RingBondOutOfRange, AtropisomerError.StereoGroupBondOutOfRange, AtropisomerError.AssignmentBondOutOfRange, AtropisomerError.AxialBondOutOfRange. None when this payload is absent.

property conformer: int | None

Readonly conformer payload of the ConformerNotThreeDimensional error variant; None for other variants.

property count: int | None

Readonly count payload of the CarrierCount error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Required value reported by the native check. Applies to AtropisomerError.RingAtomRowCount, AtropisomerError.RingBondRowCount, AtropisomerError.HybridizationAssignmentLength. None when this payload is absent.

property message: str | None

Readonly message payload of the SourcePrecondition error variant; None for other variants.

property normalization: StereoError | None

“error_payload”} Structured StereoError payload of AtropisomerError.Normalization; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stereo: BondStereo | None

Readonly stereo payload of the InvalidAtropisomerStereo error variant; None for other variants.

property variant: AtropisomerErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AtropisomerErrorKind(value)

Discriminants of AtropisomerErrorKind.

Members: StereoGroup, SourcePrecondition, CandidateTraversalOutOfRange, CandidateTraversalDuplicate, CandidateTraversalUnexpected, CandidateTraversalMissing, Valence, Conjugation, Hybridization, Normalization, CarrierCount, RingFinding, InvalidTopology, InvalidCoordinates, ConformerNotThreeDimensional, RingInfoNotSssr, RingAtomOutOfRange, RingBondOutOfRange, RingAtomRowCount, RingBondRowCount, HybridizationAssignmentLength, BondUpdate, StereoGroupAtomOutOfRange, StereoGroupBondOutOfRange, AssignmentBondOutOfRange, AxialBondOutOfRange, InvalidAtropisomerStereo, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (30)
AssignmentBondOutOfRange = AtropisomerErrorKind.AssignmentBondOutOfRange
AxialBondOutOfRange = AtropisomerErrorKind.AxialBondOutOfRange
BondUpdate = AtropisomerErrorKind.BondUpdate
CandidateTraversalDuplicate = AtropisomerErrorKind.CandidateTraversalDuplicate
CandidateTraversalMissing = AtropisomerErrorKind.CandidateTraversalMissing
CandidateTraversalOutOfRange = AtropisomerErrorKind.CandidateTraversalOutOfRange
CandidateTraversalUnexpected = AtropisomerErrorKind.CandidateTraversalUnexpected
CarrierCount = AtropisomerErrorKind.CarrierCount
ConformerNotThreeDimensional = AtropisomerErrorKind.ConformerNotThreeDimensional
Conjugation = AtropisomerErrorKind.Conjugation
Hybridization = AtropisomerErrorKind.Hybridization
HybridizationAssignmentLength = AtropisomerErrorKind.HybridizationAssignmentLength
InvalidAtropisomerStereo = AtropisomerErrorKind.InvalidAtropisomerStereo
InvalidCoordinates = AtropisomerErrorKind.InvalidCoordinates
InvalidTopology = AtropisomerErrorKind.InvalidTopology
Normalization = AtropisomerErrorKind.Normalization
RingAtomOutOfRange = AtropisomerErrorKind.RingAtomOutOfRange
RingAtomRowCount = AtropisomerErrorKind.RingAtomRowCount
RingBondOutOfRange = AtropisomerErrorKind.RingBondOutOfRange
RingBondRowCount = AtropisomerErrorKind.RingBondRowCount
RingFinding = AtropisomerErrorKind.RingFinding
RingInfoNotSssr = AtropisomerErrorKind.RingInfoNotSssr
SourcePrecondition = AtropisomerErrorKind.SourcePrecondition
StereoGroup = AtropisomerErrorKind.StereoGroup
StereoGroupAtomOutOfRange = AtropisomerErrorKind.StereoGroupAtomOutOfRange
StereoGroupBondOutOfRange = AtropisomerErrorKind.StereoGroupBondOutOfRange
Valence = AtropisomerErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': AtropisomerErrorKind.StereoGroup, 'SourcePrecondition': AtropisomerErrorKind.SourcePrecondition, 'CandidateTraversalOutOfRange': AtropisomerErrorKind.CandidateTraversalOutOfRange, 'CandidateTraversalDuplicate': AtropisomerErrorKind.CandidateTraversalDuplicate, 'CandidateTraversalUnexpected': AtropisomerErrorKind.CandidateTraversalUnexpected, 'CandidateTraversalMissing': AtropisomerErrorKind.CandidateTraversalMissing, 'Valence': AtropisomerErrorKind.Valence, 'Conjugation': AtropisomerErrorKind.Conjugation, 'Hybridization': AtropisomerErrorKind.Hybridization, 'Normalization': AtropisomerErrorKind.Normalization, 'CarrierCount': AtropisomerErrorKind.CarrierCount, 'RingFinding': AtropisomerErrorKind.RingFinding, 'InvalidTopology': AtropisomerErrorKind.InvalidTopology, 'InvalidCoordinates': AtropisomerErrorKind.InvalidCoordinates, 'ConformerNotThreeDimensional': AtropisomerErrorKind.ConformerNotThreeDimensional, 'RingInfoNotSssr': AtropisomerErrorKind.RingInfoNotSssr, 'RingAtomOutOfRange': AtropisomerErrorKind.RingAtomOutOfRange, 'RingBondOutOfRange': AtropisomerErrorKind.RingBondOutOfRange, 'RingAtomRowCount': AtropisomerErrorKind.RingAtomRowCount, 'RingBondRowCount': AtropisomerErrorKind.RingBondRowCount, 'HybridizationAssignmentLength': AtropisomerErrorKind.HybridizationAssignmentLength, 'BondUpdate': AtropisomerErrorKind.BondUpdate, 'StereoGroupAtomOutOfRange': AtropisomerErrorKind.StereoGroupAtomOutOfRange, 'StereoGroupBondOutOfRange': AtropisomerErrorKind.StereoGroupBondOutOfRange, 'AssignmentBondOutOfRange': AtropisomerErrorKind.AssignmentBondOutOfRange, 'AxialBondOutOfRange': AtropisomerErrorKind.AxialBondOutOfRange, 'InvalidAtropisomerStereo': AtropisomerErrorKind.InvalidAtropisomerStereo})
values = mappingproxy({0: AtropisomerErrorKind.StereoGroup, 1: AtropisomerErrorKind.SourcePrecondition, 2: AtropisomerErrorKind.CandidateTraversalOutOfRange, 3: AtropisomerErrorKind.CandidateTraversalDuplicate, 4: AtropisomerErrorKind.CandidateTraversalUnexpected, 5: AtropisomerErrorKind.CandidateTraversalMissing, 6: AtropisomerErrorKind.Valence, 7: AtropisomerErrorKind.Conjugation, 8: AtropisomerErrorKind.Hybridization, 9: AtropisomerErrorKind.Normalization, 10: AtropisomerErrorKind.CarrierCount, 11: AtropisomerErrorKind.RingFinding, 12: AtropisomerErrorKind.InvalidTopology, 13: AtropisomerErrorKind.InvalidCoordinates, 14: AtropisomerErrorKind.ConformerNotThreeDimensional, 15: AtropisomerErrorKind.RingInfoNotSssr, 16: AtropisomerErrorKind.RingAtomOutOfRange, 17: AtropisomerErrorKind.RingBondOutOfRange, 18: AtropisomerErrorKind.RingAtomRowCount, 19: AtropisomerErrorKind.RingBondRowCount, 20: AtropisomerErrorKind.HybridizationAssignmentLength, 21: AtropisomerErrorKind.BondUpdate, 22: AtropisomerErrorKind.StereoGroupAtomOutOfRange, 23: AtropisomerErrorKind.StereoGroupBondOutOfRange, 24: AtropisomerErrorKind.AssignmentBondOutOfRange, 25: AtropisomerErrorKind.AxialBondOutOfRange, 26: AtropisomerErrorKind.InvalidAtropisomerStereo})
exception cosmolkit.AttachmentExpansionError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AttachmentExpansionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property actual: int | None

Readonly actual payload of the ValueCount error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the ValueCount error variant; None for other variants.

property source: TopologyValidationError | CoordinateValidationError | QueryStateError | AtomPropertyError | TopologyEditError | ValenceError | HydrogenError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AttachmentExpansionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AttachmentExpansionErrorKind(value)

Discriminants of AttachmentExpansionErrorKind.

Members: Topology, Coordinates, ValueCount, Query, Property, Edit, Valence, Placement, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
Coordinates = AttachmentExpansionErrorKind.Coordinates
Edit = AttachmentExpansionErrorKind.Edit
Placement = AttachmentExpansionErrorKind.Placement
Property = AttachmentExpansionErrorKind.Property
Query = AttachmentExpansionErrorKind.Query
Topology = AttachmentExpansionErrorKind.Topology
Valence = AttachmentExpansionErrorKind.Valence
ValueCount = AttachmentExpansionErrorKind.ValueCount
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Topology': AttachmentExpansionErrorKind.Topology, 'Coordinates': AttachmentExpansionErrorKind.Coordinates, 'ValueCount': AttachmentExpansionErrorKind.ValueCount, 'Query': AttachmentExpansionErrorKind.Query, 'Property': AttachmentExpansionErrorKind.Property, 'Edit': AttachmentExpansionErrorKind.Edit, 'Valence': AttachmentExpansionErrorKind.Valence, 'Placement': AttachmentExpansionErrorKind.Placement})
values = mappingproxy({0: AttachmentExpansionErrorKind.Topology, 1: AttachmentExpansionErrorKind.Coordinates, 2: AttachmentExpansionErrorKind.ValueCount, 3: AttachmentExpansionErrorKind.Query, 4: AttachmentExpansionErrorKind.Property, 5: AttachmentExpansionErrorKind.Edit, 6: AttachmentExpansionErrorKind.Valence, 7: AttachmentExpansionErrorKind.Placement})
exception cosmolkit.AutomaticForceFieldConstructionError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AutomaticForceFieldConstructionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: UffParamError | UffTypingError | ForceFieldConstructionError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AutomaticForceFieldConstructionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AutomaticForceFieldConstructionErrorKind(value)

Discriminants of AutomaticForceFieldConstructionErrorKind.

Members: ParameterTable, Typing, Construction, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Construction = AutomaticForceFieldConstructionErrorKind.Construction
ParameterTable = AutomaticForceFieldConstructionErrorKind.ParameterTable
Typing = AutomaticForceFieldConstructionErrorKind.Typing
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ParameterTable': AutomaticForceFieldConstructionErrorKind.ParameterTable, 'Typing': AutomaticForceFieldConstructionErrorKind.Typing, 'Construction': AutomaticForceFieldConstructionErrorKind.Construction})
values = mappingproxy({0: AutomaticForceFieldConstructionErrorKind.ParameterTable, 1: AutomaticForceFieldConstructionErrorKind.Typing, 2: AutomaticForceFieldConstructionErrorKind.Construction})
exception cosmolkit.AvalonEngineError(*args, **kwargs)

AvalonEngineError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property reason: str

Original explanation of invalid arguments or Avalon conversion failure.

property variant: AvalonEngineErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.AvalonEngineErrorKind(value)

Discriminants of AvalonEngineErrorKind.

Members: InvalidArguments, AvalonConversion, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
AvalonConversion = AvalonEngineErrorKind.AvalonConversion
InvalidArguments = AvalonEngineErrorKind.InvalidArguments
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidArguments': AvalonEngineErrorKind.InvalidArguments, 'AvalonConversion': AvalonEngineErrorKind.AvalonConversion})
values = mappingproxy({0: AvalonEngineErrorKind.InvalidArguments, 1: AvalonEngineErrorKind.AvalonConversion})
exception cosmolkit.AvalonFingerprintError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

AvalonFingerprintError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: MolecularIoError | AvalonEngineError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: AvalonFingerprintErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.AvalonFingerprintErrorKind(value)

Discriminants of AvalonFingerprintErrorKind.

Members: Input, Engine, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Engine = AvalonFingerprintErrorKind.Engine
Input = AvalonFingerprintErrorKind.Input
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Input': AvalonFingerprintErrorKind.Input, 'Engine': AvalonFingerprintErrorKind.Engine})
values = mappingproxy({0: AvalonFingerprintErrorKind.Input, 1: AvalonFingerprintErrorKind.Engine})
class cosmolkit.AvalonFingerprintFlags

Avalon fingerprint feature-selection bit mask. Combine named flags with the bitwise OR operator.

Members (26)
ALL_FEATURES = <cosmolkit.AvalonFingerprintFlags object>
ATOM_CLASS_PATH = <cosmolkit.AvalonFingerprintFlags object>
ATOM_COUNT = <cosmolkit.AvalonFingerprintFlags object>
ATOM_SYMBOL_PATH = <cosmolkit.AvalonFingerprintFlags object>
AUGMENTED_ATOM = <cosmolkit.AvalonFingerprintFlags object>
AUGMENTED_BOND = <cosmolkit.AvalonFingerprintFlags object>
BOND_PATH = <cosmolkit.AvalonFingerprintFlags object>
CLASS_SPIDERS = <cosmolkit.AvalonFingerprintFlags object>
DEGREE_PATH = <cosmolkit.AvalonFingerprintFlags object>
FEATURE_PAIRS = <cosmolkit.AvalonFingerprintFlags object>
HCOUNT_CLASS_PATH = <cosmolkit.AvalonFingerprintFlags object>
HCOUNT_PAIR = <cosmolkit.AvalonFingerprintFlags object>
HCOUNT_PATH = <cosmolkit.AvalonFingerprintFlags object>
NON_SSS_BITS = <cosmolkit.AvalonFingerprintFlags object>
RING_PATH = <cosmolkit.AvalonFingerprintFlags object>
RING_PATTERN = <cosmolkit.AvalonFingerprintFlags object>
RING_SIZE_COUNTS = <cosmolkit.AvalonFingerprintFlags object>
SCAFFOLD_COLORS = <cosmolkit.AvalonFingerprintFlags object>
SCAFFOLD_IDS = <cosmolkit.AvalonFingerprintFlags object>
SHORTCUT_LABELS = <cosmolkit.AvalonFingerprintFlags object>
SIMILARITY = <cosmolkit.AvalonFingerprintFlags object>
bits: int

Underlying integer bit mask.

contains(other) → bool

Whether this mask includes every bit set in the supplied mask.

static from_bits(bits) → AvalonFingerprintFlags | None

Construct flags from an integer, returning None when unknown bits are present.

static from_bits_retain(bits) → AvalonFingerprintFlags

Construct flags while retaining all supplied bits, including unknown bits.

class cosmolkit.AvalonFingerprintParams(*, n_bits=Ellipsis, is_query=Ellipsis, bit_flags=Ellipsis)

Parameters for the source-backed Avalon bit-vector API.

Members (3)
bit_flags: int

Avalon feature families included in the fingerprint.

is_query: bool

Generate query rather than target fingerprint features.

n_bits: int

Number of bits in the Avalon fingerprint.

exception cosmolkit.BatchError(*args, **kwargs)

BatchError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property index: int

Zero-based input record index at which the batch operation failed.

property message: str

Native message describing this record’s failure.

property operation: str

Canonical name of the failed batch operation.

property source: SmilesError | OperationError | MolecularIoError | SdfError | MolWriteError | DrawingError | DrawingWriteError | BatchImageError | SmilesWriteError | ConformerRunError | AtomPairReadError | MorganReadError | TopologicalTorsionReadError | AtomPairError | MolPostError | SdfReadError | SdfWriteError | PatternFingerprintError | LayeredFingerprintError | BatchValidationError | IoError | Utf8Error | FromUtf8Error | ExternalError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.BatchErrorMode(value)

Typed BatchErrorMode values corresponding to the Rust enum.

Members: Strict, KeepErrors, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
KEEP = BatchErrorMode.KeepErrors
KeepErrors = BatchErrorMode.KeepErrors
RAISE = BatchErrorMode.Strict
Strict = BatchErrorMode.Strict
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Strict': BatchErrorMode.Strict, 'RAISE': BatchErrorMode.Strict, 'KeepErrors': BatchErrorMode.KeepErrors, 'KEEP': BatchErrorMode.KeepErrors})
values = mappingproxy({0: BatchErrorMode.Strict, 1: BatchErrorMode.KeepErrors})
class cosmolkit.BatchExportParams(*, format=Ellipsis, errors=Ellipsis, n_jobs=Ellipsis, progress_bar=Ellipsis)

SDF export format and optional batch execution overrides.

Members (4)
errors: BatchErrorMode | None

The live batch resolves inheritance; detached exports default to Strict.

format: SdfFormat

SDF mol-block format for exported records.

n_jobs: int | None

Optional worker count; None inherits the batch setting.

progress_bar: bool | None

Optional progress reporting setting; None inherits the batch setting.

class cosmolkit.BatchExportReport

Ordered batch export totals and retained per-record failures.

Members (5)
errors: list[BatchError]

Independent list of per-record export errors, preserving structured causes.

failed: int

Number of records that failed to export.

success: int

Number of records successfully written.

total: int

Total number of records processed by the export.

write_report(path) → None

Write the native export report to the supplied filesystem path.

class cosmolkit.BatchFingerprintAdditionalOutput

Immutable view keeps the actual result alive; constructing it never copies provenance. Individual reads only allocate their requested Python value.

Members (5)
atom_counts: list[int] | None

Per-atom feature contribution counts, or None when not collected.

atom_to_bits: list[list[int]] | None

Contributing fingerprint bit identifiers for each atom, or None when not collected.

atoms_per_bit: dict[int, list[list[int]]] | None

Bit identifiers mapped to participating atom sets, or None when not collected.

bit_info_map: dict[int, list[tuple[int, int]]] | None

Bit identifiers mapped to native feature descriptors (center/radius or atom-pair endpoints, depending on the generator), or None when not collected.

bit_paths: dict[int, list[list[int]]] | None

Bit identifiers mapped to contributing native paths, or None when not collected.

class cosmolkit.BatchFingerprintOutput

One batch record’s fingerprint and optional native provenance output.

Members (2)
additional_output: BatchFingerprintAdditionalOutput

Owner-retaining view of collected provenance; raises BatchFingerprintOutputError when provenance was not requested.

fingerprint: Fingerprint

Bit fingerprint for this batch record.

exception cosmolkit.BatchFingerprintOutputError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BatchFingerprintOutputError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property fingerprint_kind: str | None

Readonly fingerprint_kind payload of the MissingAdditionalOutput error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BatchFingerprintOutputErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BatchFingerprintOutputErrorKind(value)

Discriminants of BatchFingerprintOutputErrorKind.

Members: MissingAdditionalOutput, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
MissingAdditionalOutput = BatchFingerprintOutputErrorKind.MissingAdditionalOutput
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingAdditionalOutput': BatchFingerprintOutputErrorKind.MissingAdditionalOutput})
values = mappingproxy({0: BatchFingerprintOutputErrorKind.MissingAdditionalOutput})
exception cosmolkit.BatchImageError(*args, **kwargs)

Failure in the batch domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BatchImageError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property format: str | None

Format involved in the failed conversion. Applies to BatchImageError.InvalidFormat. None when this payload is absent.

property source: DrawingWriteError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BatchImageErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BatchImageErrorKind(value)

Discriminants of BatchImageErrorKind.

Members: InvalidFormat, Write, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
InvalidFormat = BatchImageErrorKind.InvalidFormat
Write = BatchImageErrorKind.Write
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidFormat': BatchImageErrorKind.InvalidFormat, 'Write': BatchImageErrorKind.Write})
values = mappingproxy({0: BatchImageErrorKind.InvalidFormat, 1: BatchImageErrorKind.Write})
class cosmolkit.BatchImageParams(*, format=Ellipsis, width=Ellipsis, height=Ellipsis, execution=Ellipsis, filenames=Ellipsis, report_path=Ellipsis)

Per-image output format, dimensions, names and batch execution settings.

Members (6)
execution: BatchParams

Batch scheduling and error-handling options.

filenames: tuple[str | None, ...] | None

Optional per-record output names; absent entries use generated names.

format: str

Image format to write, such as png or svg.

height: int

Height of each image in pixels.

report_path: pathlib.Path | None

Optional path for the image export report.

width: int

Width of each image in pixels.

class cosmolkit.BatchParams(*, errors=Ellipsis, n_jobs=Ellipsis, progress_bar=Ellipsis)

Per-call scheduling and error policy; overrides never mutate stored batch configuration.

Members (3)
errors: BatchErrorMode | None

None inherits the batch policy; constructors without a batch use Strict.

n_jobs: int | None

Inherit a stored batch setting when absent, otherwise default to one worker.

progress_bar: bool | None

Override progress-bar display, or inherit the batch setting when absent.

class cosmolkit.BatchQueryParams(*, n_jobs=Ellipsis, progress_bar=Ellipsis, progress_callback=None)

Native batch query execution overrides and optional per-record progress notification.

Members (3)
n_jobs: int | None

Inherit a stored batch setting when absent, otherwise default to one worker.

progress_bar: bool | None

Optional progress reporting; None inherits the stored batch setting.

progress_callback: collections.abc.Callable[[], None] | None

Optional zero-argument notification after each completed query row. Retained input errors reject the query before any notification; callback exceptions propagate.

exception cosmolkit.BatchValidationError(*args, **kwargs)

BatchValidationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property errors: int

Number of invalid batch records.

property record_errors: list[BatchError]

“error_payload”} Return a copy of the per-record BatchError list, retaining record indices and the native causes. Editing the list does not modify this exception.

Type:

{“role”

class cosmolkit.BestAlignmentParameters(*, probe_conformer_id=Ellipsis, reference_conformer_id=Ellipsis, atom_maps=Ellipsis, weights=Ellipsis, reflect=Ellipsis, max_iterations=Ellipsis, max_matches=Ellipsis, symmetrize_conjugated_terminal_groups=Ellipsis, ignore_hydrogens=Ellipsis, num_threads=Ellipsis)

Symmetry-aware best alignment options over candidate atom correspondences.

Members (11)
atom_maps: tuple[tuple[AlignmentAtomMap, ...], ...]

Candidate probe-to-reference atom mappings; an empty collection requests native match enumeration.

ignore_hydrogens: bool

Ignore hydrogen atoms during native match enumeration.

max_iterations: int

Maximum iterations for native alignment optimization.

max_matches: int

Maximum number of candidate atom mappings considered.

static new(probe_conformer_id=Ellipsis, reference_conformer_id=Ellipsis, atom_maps=Ellipsis, weights=Ellipsis, reflect=Ellipsis, max_iterations=Ellipsis, max_matches=Ellipsis, symmetrize_conjugated_terminal_groups=Ellipsis, ignore_hydrogens=Ellipsis, num_threads=Ellipsis) → BestAlignmentParameters

Create an independent configuration through the native constructor using the supplied field values.

num_threads: int

Number of native alignment worker threads.

probe_conformer_id: int

Probe conformer identifier; -1 selects the native default conformer.

reference_conformer_id: int

Reference conformer identifier; -1 selects the native default conformer.

reflect: bool

Allow reflection while determining the alignment transform.

symmetrize_conjugated_terminal_groups: bool

Treat conjugated terminal groups symmetrically when selecting matches.

weights: tuple[float, ...] | None

Optional alignment weights in atom-map order.

class cosmolkit.BioAssembly(name, author_determined, software_determined, special_kind, oligomeric_count, oligomeric_details, software_name, buried_surface_area, surface_area, solvent_free_energy_change, generators)

Biological assembly definition with source provenance, reported metrics and generation rules.

Members (11)
author_determined: bool

Whether the source marks this assembly as author-determined.

buried_surface_area: float

Buried surface-area value reported for this assembly.

generators: list[BioAssemblyGenerator]

Independent list of generators defining which chains and transforms build the assembly.

name: str

Source identifier or name of this assembly or operator.

oligomeric_count: int

Reported number of components in the oligomeric assembly.

oligomeric_details: str

Source description of the oligomeric assembly.

software_determined: bool

Whether the source marks this assembly as software-determined.

software_name: str

Name of the software used to determine this assembly.

solvent_free_energy_change: float

Solvent free-energy change reported for this assembly.

special_kind: BioAssemblySpecialKind

Stored special assembly classification.

surface_area: float

Surface-area value reported for this assembly.

class cosmolkit.BioAssemblyGenerator(*, chains=Ellipsis, subchains=Ellipsis, operators=None)

Chain and subchain selections together with the operators that generate an assembly.

Members (3)
chains: list[str]

Independent list of chain identifiers to which the generator applies.

operators: list[BioAssemblyOperator]

Independent list of assembly operators applied by this generator.

subchains: list[str]

Independent list of subchain identifiers to which the generator applies.

class cosmolkit.BioAssemblyOperator(name, operator_type, transform)

Named affine operator used to generate a biological assembly.

Members (3)
name: str | None

Source identifier or name of this assembly or operator.

operator_type: str | None

Source classification of the assembly operator, or None if absent.

transform: BioTransform

Affine transform associated with this symmetry or assembly operator.

class cosmolkit.BioAssemblySpecialKind(value)

Typed BioAssemblySpecialKind values corresponding to the Rust enum.

Members: NotApplicable, CompleteIcosahedral, RepresentativeHelical, CompletePoint, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
CompleteIcosahedral = BioAssemblySpecialKind.CompleteIcosahedral
CompletePoint = BioAssemblySpecialKind.CompletePoint
NotApplicable = BioAssemblySpecialKind.NotApplicable
RepresentativeHelical = BioAssemblySpecialKind.RepresentativeHelical
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NotApplicable': BioAssemblySpecialKind.NotApplicable, 'CompleteIcosahedral': BioAssemblySpecialKind.CompleteIcosahedral, 'RepresentativeHelical': BioAssemblySpecialKind.RepresentativeHelical, 'CompletePoint': BioAssemblySpecialKind.CompletePoint})
values = mappingproxy({0: BioAssemblySpecialKind.NotApplicable, 1: BioAssemblySpecialKind.CompleteIcosahedral, 2: BioAssemblySpecialKind.RepresentativeHelical, 3: BioAssemblySpecialKind.CompletePoint})
class cosmolkit.BioAsu(value)

Typed BioAsu values corresponding to the Rust enum.

Members: Same, Different, Any, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
Any = BioAsu.Any
Different = BioAsu.Different
Same = BioAsu.Same
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Same': BioAsu.Same, 'Different': BioAsu.Different, 'Any': BioAsu.Any})
values = mappingproxy({0: BioAsu.Same, 1: BioAsu.Different, 2: BioAsu.Any})
class cosmolkit.BioAtom

Owned BioAtom view retaining its structure version.

Hierarchy and coordinate reads use that retained structure. Editing another COW structure value does not invalidate this object or alter its values. value() returns the detached row without its owner context.

Members (17)
altloc: AltLocLabel | None

Alternate-location label, or None for an unlabeled location.

anisou: list[float]

U11, U22, U33, U12, U13, U23.

Type:

Anisotropic displacement components in native order

atomic_number: int

Atomic number of this atom’s element.

b_iso: float

Stored isotropic B factor.

calculation_flag: BioCalcFlag

Source calculation status of this atom.

element: Element

Element of this atom.

formal_charge: int

Stored signed formal charge of the atom.

fraction: float

Stored atom fraction value from the source structure.

id: int

Stable local row identifier in the retained structure, not a source-file serial number.

isotope_mass_number: int | None

Explicit isotope mass number, or None if unspecified.

name: AtomName

Source atom or residue name retained by this hierarchy object.

occupancy: float

Stored site occupancy.

position: list[float]

Cartesian position (x, y, z) from the retained structure’s coordinate block.

residue_id: int

Local identifier of the residue containing this atom.

source: AtomSourceIds

Source-file identifiers retained separately from local row indices.

tls_group_id: int

Stored translation/libration/screw group identifier.

value() → BioAtomRow

Return a detached row copy without structure ownership or contextual traversal.

class cosmolkit.BioAtomRow(residue_id, name, element, isotope_mass_number, altloc, formal_charge, calc_flag, occupancy, b_iso, anisou, tls_group_id, fraction, source)

Detached atom metadata row. Cartesian positions belong to the structure’s separate coordinate block.

Members (13)
altloc: AltLocLabel | None

Alternate-location identifier, or None if unlabelled.

anisou: list[float]

Six independent components of the anisotropic displacement tensor.

b_iso: float

Isotropic atomic displacement parameter.

calc_flag: BioCalcFlag

Source classification of whether the atom position was calculated or determined.

element: Element

Chemical element assigned to this atom.

formal_charge: int

Formal charge stored on the atom.

fraction: float

Isotopic fraction retained by the native atom row.

isotope_mass_number: int | None

Explicit isotope mass number, or None for natural isotopic composition.

name: AtomName

Source residue or atom name, preserving its native representation.

occupancy: float

Occupancy reported for this atom.

residue_id: int

Local identifier of the parent residue.

source: AtomSourceIds

Source-format identifiers, distinct from local structure row indices.

tls_group_id: int

TLS refinement group identifier stored for this atom.

class cosmolkit.BioBasicRefinementInfo(*, resolution_high=None, resolution_low=None, completeness=None, reflection_count=None, work_set_count=None, rfree_set_count=None, r_all=None, r_work=None, r_free=None, cc_fo_fc_work=None, cc_fo_fc_free=None, fsc_work=None, fsc_free=None, cc_intensity_work=None, cc_intensity_free=None)

Readonly refinement statistics for reflection work and free sets; unavailable values retain native sentinels.

Members (15)
cc_fo_fc_free: float

Observed/calculated structure-factor correlation for the free set.

cc_fo_fc_work: float

Observed/calculated structure-factor correlation for the working set.

cc_intensity_free: float

Intensity correlation for the free set.

cc_intensity_work: float

Intensity correlation for the working set.

completeness: float

Reported completeness of the refinement data.

fsc_free: float

Fourier-shell correlation reported for the free set.

fsc_work: float

Fourier-shell correlation reported for the working set.

r_all: float

R factor over all reflections.

r_free: float

R factor over the free reflections.

r_work: float

R factor over the working reflections.

reflection_count: int

Total reflection count.

resolution_high: float

High-resolution refinement limit in angstroms.

resolution_low: float

Low-resolution refinement limit in angstroms.

rfree_set_count: int

Number of reflections in the R-free set.

work_set_count: int

Number of reflections in the working set.

class cosmolkit.BioCalcFlag(value)

Typed BioCalcFlag values corresponding to the Rust enum.

Members: NotSet, NoHydrogen, Determined, Calculated, Dummy, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (8)
Calculated = BioCalcFlag.Calculated
Determined = BioCalcFlag.Determined
Dummy = BioCalcFlag.Dummy
NoHydrogen = BioCalcFlag.NoHydrogen
NotSet = BioCalcFlag.NotSet
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NotSet': BioCalcFlag.NotSet, 'NoHydrogen': BioCalcFlag.NoHydrogen, 'Determined': BioCalcFlag.Determined, 'Calculated': BioCalcFlag.Calculated, 'Dummy': BioCalcFlag.Dummy})
values = mappingproxy({0: BioCalcFlag.NotSet, 1: BioCalcFlag.NoHydrogen, 2: BioCalcFlag.Determined, 3: BioCalcFlag.Calculated, 4: BioCalcFlag.Dummy})
class cosmolkit.BioChain

Owned BioChain view retaining its structure version.

Hierarchy and coordinate reads use that retained structure. Editing another COW structure value does not invalidate this object or alter its values. value() returns the detached row without its owner context.

Members (9)
entity_id: int | None

Associated entity’s local identifier, or None when no entity is assigned. Associated entity’s local row identifier, or None if unassigned.

id: int

Stable local row identifier in the retained structure, not a source-file serial number.

kind: ChainKind

Stored chain classification; this read does not infer a new classification.

model_id: int

Local identifier of the model containing this chain.

num_residues: int

Number of residue rows in this chain.

residue_span: BioRowSpan

Half-open span of this chain’s residue rows in the retained structure.

residues: list[BioResidue]

Residues in stored order, each retaining the same structure version.

source: ChainSourceIds

Source-format chain identifiers, distinct from local row identifiers.

value() → BioChainRow

Return a detached row copy without structure ownership or contextual traversal.

class cosmolkit.BioChainRow(model_id, entity_id, residue_span, kind, source)

Detached chain row containing parent identifiers and a residue span, without an owning structure.

Members (5)
entity_id: int | None

Local entity row identifier, or None if unassigned.

kind: ChainKind

Stored chain classification.

model_id: int

Local index of the parent model row.

residue_span: BioRowSpan

Half-open range of residue rows belonging to this chain.

source: ChainSourceIds

Source-format identifiers, distinct from local row indices.

class cosmolkit.BioCisPep(*, partner_c=None, partner_n=None, model_num=None, only_altloc=None, reported_angle=None)

Cis-peptide record with partner addresses, model and reported angle.

Members (5)
model_num: int

Source model number associated with the cis-peptide record.

only_altloc: int

Alternate-location restriction retained in the cis-peptide record.

partner_c: AtomAddress

Address of the carbon-side cis-peptide partner.

partner_n: AtomAddress

Address of the nitrogen-side cis-peptide partner.

reported_angle: float

Peptide angle reported by the source, in degrees.

class cosmolkit.BioConnection(*, name=None, link_id=None, kind=None, asu=None, partner1=None, partner2=None, reported_distance=None, reported_sym=None)

Reported inter-atom connection with partner addresses and symmetry metadata.

Members (8)
asu: BioAsu

Relationship of the connection partners to the asymmetric unit.

kind: BioConnectionKind

Native connection classification.

Chemical link identifier reported by the source.

name: str

Name or identifier retained in this source record.

partner1: AtomAddress

Address of the first connection partner.

partner2: AtomAddress

Address of the second connection partner.

reported_distance: float

Inter-partner distance reported in the source.

reported_sym: list[int]

Four-component symmetry identifier retained for the reported connection.

class cosmolkit.BioConnectionKind(value)

Typed BioConnectionKind values corresponding to the Rust enum.

Members: Covale, Disulf, Hydrog, MetalC, Unknown, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (8)
Covale = BioConnectionKind.Covale
Disulf = BioConnectionKind.Disulf
Hydrog = BioConnectionKind.Hydrog
MetalC = BioConnectionKind.MetalC
Unknown = BioConnectionKind.Unknown
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Covale': BioConnectionKind.Covale, 'Disulf': BioConnectionKind.Disulf, 'Hydrog': BioConnectionKind.Hydrog, 'MetalC': BioConnectionKind.MetalC, 'Unknown': BioConnectionKind.Unknown})
values = mappingproxy({0: BioConnectionKind.Covale, 1: BioConnectionKind.Disulf, 2: BioConnectionKind.Hydrog, 3: BioConnectionKind.MetalC, 4: BioConnectionKind.Unknown})
class cosmolkit.BioCoordinateBlock(positions)

Cartesian atom coordinates stored as three-component rows; positions returns an independent NumPy array.

Members (3)
is_empty: bool

Whether there are no coordinate rows.

len: int

Number of stored Cartesian coordinate rows.

positions: numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]

[“numpy”],”type”:”numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]”} Independent float64 NumPy array with shape (num_atoms, 3), in stored atom order.

Type:

{“role”

Type:

“return_type”,”imports”

class cosmolkit.BioCoordinateFormat(value)

Typed BioCoordinateFormat values corresponding to the Rust enum.

Members: Unknown, Detect, Pdb, Mmcif, Mmjson, ChemComp, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (9)
ChemComp = BioCoordinateFormat.ChemComp
Detect = BioCoordinateFormat.Detect
Mmcif = BioCoordinateFormat.Mmcif
Mmjson = BioCoordinateFormat.Mmjson
Pdb = BioCoordinateFormat.Pdb
Unknown = BioCoordinateFormat.Unknown
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unknown': BioCoordinateFormat.Unknown, 'Detect': BioCoordinateFormat.Detect, 'Pdb': BioCoordinateFormat.Pdb, 'Mmcif': BioCoordinateFormat.Mmcif, 'Mmjson': BioCoordinateFormat.Mmjson, 'ChemComp': BioCoordinateFormat.ChemComp})
values = mappingproxy({0: BioCoordinateFormat.Unknown, 1: BioCoordinateFormat.Detect, 2: BioCoordinateFormat.Pdb, 3: BioCoordinateFormat.Mmcif, 4: BioCoordinateFormat.Mmjson, 5: BioCoordinateFormat.ChemComp})
class cosmolkit.BioCrystalCell(*, a=Ellipsis, b=Ellipsis, c=Ellipsis, alpha=Ellipsis, beta=Ellipsis, gamma=Ellipsis)

Crystallographic unit cell: lengths in angstroms and angles in degrees.

Members (6)
a: float

Length of the a axis in angstroms.

alpha: float

Angle between b and c in degrees.

b: float

Length of the b axis in angstroms.

beta: float

Angle between a and c in degrees.

c: float

Length of the c axis in angstroms.

gamma: float

Angle between a and b in degrees.

class cosmolkit.BioCrystalInfo(cell, space_group_hm, z_pdb, orthogonal, fractional, explicit_matrices, cs_count, symmetry_images)

Unit-cell geometry, coordinate transforms and retained crystallographic symmetry metadata.

Members (13)
cell: BioCrystalCell

Independent copy of the stored unit-cell parameters.

cs_count: int

Stored number of crystallographic symmetry images.

explicit_matrices: bool

Whether the coordinate conversion matrices were explicitly supplied.

fractional: BioTransform

Transform from Cartesian to fractional coordinates.

is_crystal: bool

Whether the native cell information represents a crystallographic unit cell.

orthogonal: BioTransform

Transform from fractional to Cartesian coordinates.

reciprocal_cosines: list[float]

Cosines of the three reciprocal-cell angles.

reciprocal_lengths: list[float]

Three reciprocal-cell axis lengths, in a*, b*, c* order.

space_group_hm: str | None

Hermann-Mauguin space-group designation, or None if absent.

space_group_number: int | None

International space-group number inferred from the stored designation, or None if unresolved.

symmetry_images: list[BioTransform]

Independent list of retained symmetry-image transforms.

volume: float

Unit-cell volume computed from the stored cell geometry.

z_pdb: str | None

Source PDB Z value as text, or None if absent.

class cosmolkit.BioDiffractionInfo(*, id=None, temperature=None, source=None, source_type=None, synchrotron=None, beamline=None, wavelengths=None, scattering_type=None, mono_or_laue=None, monochromator=None, collection_date=None, optics=None, detector=None, detector_make=None)

Readonly diffraction-experiment metadata preserved from the structural file.

Members (14)
beamline: str

Beamline identifier.

collection_date: str

Data collection date as recorded in the source.

detector: str

Detector technology description.

detector_make: str

Detector manufacturer or model description.

id: str

Source diffraction-experiment identifier.

mono_or_laue: int

Native single-byte monochromatic/Laue classification marker.

monochromator: str

Monochromator description.

optics: str

Beam optics description.

scattering_type: str

Scattering experiment type.

source: str

Radiation source description.

source_type: str

Radiation source type.

synchrotron: str

Synchrotron facility name.

temperature: float

Reported experiment temperature in kelvin.

wavelengths: str

Source wavelength description, preserved as text.

class cosmolkit.BioEntityDbRef(*, db_name=Ellipsis, accession_code=Ellipsis, id_code=Ellipsis, isoform=Ellipsis, seq_begin=None, seq_end=None, db_begin=None, db_end=None, label_seq_begin=None, label_seq_end=None)

Source sequence range and corresponding external database accession and range.

Members (10)
accession_code: str

Accession code in the external database.

db_begin: PdbSeqId

First database residue identifier in the mapping.

db_end: PdbSeqId

Last database residue identifier in the mapping.

db_name: str

Name of the external sequence database.

id_code: str

External database entry identifier.

isoform: str

External database isoform identifier.

label_seq_begin: int | None

First mmCIF label sequence number in the mapping, or None.

label_seq_end: int | None

Last mmCIF label sequence number in the mapping, or None.

seq_begin: PdbSeqId

First source residue identifier in the database mapping.

seq_end: PdbSeqId

Last source residue identifier in the database mapping.

class cosmolkit.BioEntityRow(kind, polymer_kind, reflects_microhetero, full_sequence, dbrefs, sifts_unp_accessions, subchains, source)

Detached biological entity metadata, sequence and database references; no owning structure.

Members (9)
dbrefs: list[BioEntityDbRef]

Independent list of external sequence database references.

static first_mon(mon_list) → str

Return the first monomer name from a comma-separated microheterogeneity list.

full_sequence: list[str]

Independent list of source monomer names for the complete sequence.

kind: EntityKind

Stored native classification of this entity or residue.

polymer_kind: PolymerKind

Polymer classification stored for the entity.

reflects_microhetero: bool

Whether the sequence records microheterogeneity.

sifts_unp_accessions: list[str]

UniProt accessions referenced by residue SIFTS mappings.

source: EntitySourceIds

Source-format identifiers, distinct from local structure row indices.

subchains: list[str]

Source subchain identifiers associated with this entity.

class cosmolkit.BioExperimentalCrystalInfo(*, id=None, description=None, ph=None, ph_range=None, diffractions=None)

Crystal identifier, preparation description, pH and diffraction records.

Members (5)
description: str

Source description of crystal preparation or properties.

diffractions: list[BioDiffractionInfo]

Diffraction measurements associated with this crystal.

id: str

Crystal identifier in the source.

ph: float

Reported crystal preparation pH.

ph_range: str

Source text describing the pH range.

class cosmolkit.BioExperimentInfo(*, method=None, number_of_crystals=None, unique_reflections=None, b_wilson=None, diffraction_ids=None, reflections=None, shells=None)

Experimental method and diffraction/reflection statistics reported for a structure.

Members (7)
b_wilson: float

Wilson B factor reported for the experiment.

diffraction_ids: list[str]

Identifiers linking this experiment to diffraction records.

method: str

Experimental method recorded by the source.

number_of_crystals: int

Reported number of crystals used.

reflections: BioReflectionsInfo

Overall reflection statistics.

shells: list[BioReflectionsInfo]

Reflection statistics by resolution shell.

unique_reflections: int

Reported number of unique reflections.

class cosmolkit.BioHelix(*, start=None, end=None, pdb_helix_class=None, length=None)

Reported helical secondary-structure segment and PDB helix classification.

Members (5)
end: AtomAddress

Address marking the end of this secondary-structure segment.

length: int

Reported helix length in residues.

pdb_helix_class: BioHelixClass

PDB helix classification.

set_helix_class_as_int(n) → None

Assign the helix class using the native PDB integer-code conversion.

start: AtomAddress

Address marking the beginning of this secondary-structure segment.

class cosmolkit.BioHelixClass(value)

Typed BioHelixClass values corresponding to the Rust enum.

Members: UnknownHelix, RAlpha, ROmega, RPi, RGamma, R310, LAlpha, LOmega, LGamma, Helix27, HelixPolyProlineNone, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (14)
Helix27 = BioHelixClass.Helix27
HelixPolyProlineNone = BioHelixClass.HelixPolyProlineNone
LAlpha = BioHelixClass.LAlpha
LGamma = BioHelixClass.LGamma
LOmega = BioHelixClass.LOmega
R310 = BioHelixClass.R310
RAlpha = BioHelixClass.RAlpha
RGamma = BioHelixClass.RGamma
ROmega = BioHelixClass.ROmega
RPi = BioHelixClass.RPi
UnknownHelix = BioHelixClass.UnknownHelix
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnknownHelix': BioHelixClass.UnknownHelix, 'RAlpha': BioHelixClass.RAlpha, 'ROmega': BioHelixClass.ROmega, 'RPi': BioHelixClass.RPi, 'RGamma': BioHelixClass.RGamma, 'R310': BioHelixClass.R310, 'LAlpha': BioHelixClass.LAlpha, 'LOmega': BioHelixClass.LOmega, 'LGamma': BioHelixClass.LGamma, 'Helix27': BioHelixClass.Helix27, 'HelixPolyProlineNone': BioHelixClass.HelixPolyProlineNone})
values = mappingproxy({0: BioHelixClass.UnknownHelix, 1: BioHelixClass.RAlpha, 2: BioHelixClass.ROmega, 3: BioHelixClass.RPi, 4: BioHelixClass.RGamma, 5: BioHelixClass.R310, 6: BioHelixClass.LAlpha, 7: BioHelixClass.LOmega, 8: BioHelixClass.LGamma, 9: BioHelixClass.Helix27, 10: BioHelixClass.HelixPolyProlineNone})
class cosmolkit.BioMetadata(*, authors=None, solved_by=None, starting_model=None, remark_300_detail=None, experiments=None, crystals=None, refinement=None, software=None)

Detached experimental, authorship and refinement metadata for a biological structure.

Members (8)
authors: list[str]

Source author names in retained order.

crystals: list[BioExperimentalCrystalInfo]

Crystal preparation and diffraction records.

experiments: list[BioExperimentInfo]

Experimental records.

refinement: list[BioRefinementInfo]

Refinement records.

remark_300_detail: str

Retained PDB REMARK 300 details.

software: list[BioSoftwareItem]

Software records reported by the source.

solved_by: str

Reported structure solution method.

starting_model: str

Description of the starting structural model.

exception cosmolkit.BioMmcifReadError(*args, **kwargs)

BioMmcifReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: CifReadError | BioStructureError | CoordinateBlockSelectionError | MmcifCrystalInfoError | MmcifTlsInfoError | MmcifAtomSiteGroupingError | MmcifEntityInfoError | MmcifHelixError | MmcifSheetError | MmcifConnectionError | MmcifCisPepError | MmcifModResError | MmcifAssemblyError | MmcifSiftsUnpError | MmcifCcdRestoreError | MmcifAtomSiteRowOutOfBounds | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property stage: BioMmcifReadStage

mmCIF reading stage that failed.

class cosmolkit.BioMmcifReadStage(value)

Typed BioMmcifReadStage values corresponding to the Rust enum.

Members: CifDocument, CoordinateBlock, CrystalCell, Refinement, Tls, Experimental, Reflections, Software, Ncs, FractionalTransform, Origx, AnisotropicU, AtomSites, EntitySequence, Helices, Sheets, Connections, CisPeptides, ModifiedResidues, Assemblies, SiftsUnp, CcdRestoration, Materialization, StructureValidation, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (27)
AnisotropicU = BioMmcifReadStage.AnisotropicU
Assemblies = BioMmcifReadStage.Assemblies
AtomSites = BioMmcifReadStage.AtomSites
CcdRestoration = BioMmcifReadStage.CcdRestoration
CifDocument = BioMmcifReadStage.CifDocument
CisPeptides = BioMmcifReadStage.CisPeptides
Connections = BioMmcifReadStage.Connections
CoordinateBlock = BioMmcifReadStage.CoordinateBlock
CrystalCell = BioMmcifReadStage.CrystalCell
EntitySequence = BioMmcifReadStage.EntitySequence
Experimental = BioMmcifReadStage.Experimental
FractionalTransform = BioMmcifReadStage.FractionalTransform
Helices = BioMmcifReadStage.Helices
Materialization = BioMmcifReadStage.Materialization
ModifiedResidues = BioMmcifReadStage.ModifiedResidues
Ncs = BioMmcifReadStage.Ncs
Origx = BioMmcifReadStage.Origx
Refinement = BioMmcifReadStage.Refinement
Reflections = BioMmcifReadStage.Reflections
Sheets = BioMmcifReadStage.Sheets
SiftsUnp = BioMmcifReadStage.SiftsUnp
Software = BioMmcifReadStage.Software
StructureValidation = BioMmcifReadStage.StructureValidation
Tls = BioMmcifReadStage.Tls
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'CifDocument': BioMmcifReadStage.CifDocument, 'CoordinateBlock': BioMmcifReadStage.CoordinateBlock, 'CrystalCell': BioMmcifReadStage.CrystalCell, 'Refinement': BioMmcifReadStage.Refinement, 'Tls': BioMmcifReadStage.Tls, 'Experimental': BioMmcifReadStage.Experimental, 'Reflections': BioMmcifReadStage.Reflections, 'Software': BioMmcifReadStage.Software, 'Ncs': BioMmcifReadStage.Ncs, 'FractionalTransform': BioMmcifReadStage.FractionalTransform, 'Origx': BioMmcifReadStage.Origx, 'AnisotropicU': BioMmcifReadStage.AnisotropicU, 'AtomSites': BioMmcifReadStage.AtomSites, 'EntitySequence': BioMmcifReadStage.EntitySequence, 'Helices': BioMmcifReadStage.Helices, 'Sheets': BioMmcifReadStage.Sheets, 'Connections': BioMmcifReadStage.Connections, 'CisPeptides': BioMmcifReadStage.CisPeptides, 'ModifiedResidues': BioMmcifReadStage.ModifiedResidues, 'Assemblies': BioMmcifReadStage.Assemblies, 'SiftsUnp': BioMmcifReadStage.SiftsUnp, 'CcdRestoration': BioMmcifReadStage.CcdRestoration, 'Materialization': BioMmcifReadStage.Materialization, 'StructureValidation': BioMmcifReadStage.StructureValidation})
values = mappingproxy({0: BioMmcifReadStage.CifDocument, 1: BioMmcifReadStage.CoordinateBlock, 2: BioMmcifReadStage.CrystalCell, 3: BioMmcifReadStage.Refinement, 4: BioMmcifReadStage.Tls, 5: BioMmcifReadStage.Experimental, 6: BioMmcifReadStage.Reflections, 7: BioMmcifReadStage.Software, 8: BioMmcifReadStage.Ncs, 9: BioMmcifReadStage.FractionalTransform, 10: BioMmcifReadStage.Origx, 11: BioMmcifReadStage.AnisotropicU, 12: BioMmcifReadStage.AtomSites, 13: BioMmcifReadStage.EntitySequence, 14: BioMmcifReadStage.Helices, 15: BioMmcifReadStage.Sheets, 16: BioMmcifReadStage.Connections, 17: BioMmcifReadStage.CisPeptides, 18: BioMmcifReadStage.ModifiedResidues, 19: BioMmcifReadStage.Assemblies, 20: BioMmcifReadStage.SiftsUnp, 21: BioMmcifReadStage.CcdRestoration, 22: BioMmcifReadStage.Materialization, 23: BioMmcifReadStage.StructureValidation})
exception cosmolkit.BioMmcifWriteError(*args, **kwargs)

BioMmcifWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property field: str | None

Field whose content or type caused the failure. Applies to BioMmcifWriteError.InvalidText. None when this payload is absent.

property path: pathlib.Path | None

Filesystem path involved in the operation. Applies to BioMmcifWriteError.FileWrite. None when this payload is absent.

property source: BioStructureError | CifReadError | IoError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause. Source name associated with the CIF input, not an exception cause.

Type:

{“role”

property variant: BioMmcifWriteErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.BioMmcifWriteErrorKind(value)

Discriminants of BioMmcifWriteErrorKind.

Members: Structure, Cif, InvalidText, Io, FileWrite, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
Cif = BioMmcifWriteErrorKind.Cif
FileWrite = BioMmcifWriteErrorKind.FileWrite
InvalidText = BioMmcifWriteErrorKind.InvalidText
Io = BioMmcifWriteErrorKind.Io
Structure = BioMmcifWriteErrorKind.Structure
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Structure': BioMmcifWriteErrorKind.Structure, 'Cif': BioMmcifWriteErrorKind.Cif, 'InvalidText': BioMmcifWriteErrorKind.InvalidText, 'Io': BioMmcifWriteErrorKind.Io, 'FileWrite': BioMmcifWriteErrorKind.FileWrite})
values = mappingproxy({0: BioMmcifWriteErrorKind.Structure, 1: BioMmcifWriteErrorKind.Cif, 2: BioMmcifWriteErrorKind.InvalidText, 3: BioMmcifWriteErrorKind.Io, 4: BioMmcifWriteErrorKind.FileWrite})
class cosmolkit.BioMmcifWriteParams(*, atoms=Ellipsis, block_name=Ellipsis, entry=Ellipsis, database_status=Ellipsis, author=Ellipsis, cell=Ellipsis, symmetry=Ellipsis, entity=Ellipsis, entity_poly=Ellipsis, struct_ref=Ellipsis, chem_comp=Ellipsis, exptl=Ellipsis, diffrn=Ellipsis, reflns=Ellipsis, refine=Ellipsis, title_keywords=Ellipsis, ncs=Ellipsis, struct_asym=Ellipsis, origx=Ellipsis, struct_conf=Ellipsis, struct_sheet=Ellipsis, struct_biol=Ellipsis, assembly=Ellipsis, conn=Ellipsis, cis=Ellipsis, modres=Ellipsis, scale=Ellipsis, atom_type=Ellipsis, entity_poly_seq=Ellipsis, tls=Ellipsis, software=Ellipsis, group_pdb=Ellipsis, auth_all=Ellipsis, prefer_pairs=Ellipsis, compact=Ellipsis, misuse_hash=Ellipsis, align_pairs=Ellipsis, align_loops=Ellipsis)

Full source-defined mmCIF category switches and canonical CIF layout controls.

The default enables every category and group_pdb; auth_all is false. Switches are flattened into this single IO-owned parameter value.

Members (38)
align_loops: int

Max loop column width used for value alignment (0 = no alignment).

align_pairs: int

Column at which pair values start (0 = single space).

assembly: bool

Emit assembly definitions and operators.

atom_type: bool

Emit atom-type metadata.

atoms: bool

Emit atom coordinates and associated atom-site data.

auth_all: bool

Emit _atom_site.auth_atom_id/auth_comp_id in addition to label ids.

author: bool

Emit author information.

block_name: bool

Set the CIF data-block name from the structure.

cell: bool

Emit crystallographic unit-cell parameters.

chem_comp: bool

Emit chemical-component definitions.

cis: bool

Emit cis-peptide annotations.

compact: bool

Omit blank lines between categories (blocks still separated).

conn: bool

Emit explicit structural connections.

database_status: bool

Emit deposition and database-status metadata.

diffrn: bool

Emit diffraction-experiment metadata.

entity: bool

Emit molecular entity definitions.

entity_poly: bool

Emit polymer entity classifications.

entity_poly_seq: bool

Emit polymer entity sequences.

entry: bool

Emit entry-identification metadata.

exptl: bool

Emit experimental-method metadata.

group_pdb: bool

Emit the _atom_site.group_PDB column (ATOM/HETATM records).

misuse_hash: bool

Put # empty comments before/after categories.

modres: bool

Emit modified-residue annotations.

ncs: bool

Emit non-crystallographic symmetry operators.

origx: bool

Emit the original-coordinate transform.

prefer_pairs: bool

Write single-row loops as tag/value pairs.

refine: bool

Emit refinement statistics and restraints.

reflns: bool

Emit reflection statistics.

scale: bool

Emit fractional-coordinate transformation information.

software: bool

Emit software provenance recorded in the structure.

struct_asym: bool

Emit asymmetric-unit chain/entity associations.

struct_biol: bool

Emit biological-structure metadata.

struct_conf: bool

Emit helical and other conformational annotations.

struct_ref: bool

Emit reference-database links.

struct_sheet: bool

Emit beta-sheet annotations.

symmetry: bool

Emit space-group symmetry metadata.

title_keywords: bool

Emit the structure title and keywords.

tls: bool

Emit translation/libration/screw refinement metadata.

class cosmolkit.BioModel

Owned BioModel view retaining its structure version.

Hierarchy and coordinate reads use that retained structure. Editing another COW structure value does not invalidate this object or alter its values. value() returns the detached row without its owner context.

Members (6)
chain_span: BioRowSpan

Half-open span of this model’s chain rows in the retained structure.

chains: list[BioChain]

Chains in stored order, each retaining the same structure version.

id: int

Stable local row identifier in the retained structure, not a source-file serial number.

num_chains: int

Number of chains in this model.

source_model_number: int | None

Model number recorded by the input format, or None if it was not supplied.

value() → BioModelRow

Return a detached row copy without structure ownership or contextual traversal.

class cosmolkit.BioModelRow(chain_span, source_model_number)

Detached model row containing its chain span and optional source model number.

Members (2)
chain_span: BioRowSpan

Half-open range of chain rows belonging to this model.

source_model_number: int | None

Model number from the input file, or None if absent.

class cosmolkit.BioModRes(*, chain_name=None, res_id=None, parent_comp_id=None, mod_id=None, details=None)

Modified-residue record linking a source residue to its parent chemical component.

Members (5)
chain_name: str

Source chain identifier.

details: str

Source explanation of the residue modification.

mod_id: str

Modification identifier.

parent_comp_id: str

Parent chemical-component identifier for the modified residue.

res_id: ResidueAddress

Address of the modified residue.

exception cosmolkit.BioMoleculeConversionError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BioMoleculeConversionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: AtomPropertyError | TopologyValidationError | CoordinateValidationError | ValenceError | TopologyEditError | PropertyUIntReadError | MoleculePropertyError | BondValueError | QueryStateError | CleanupError | PropertyCacheError | RingFindingError | KekulizeError | RadicalError | AromaticityError | ConjugationError | HybridizationError | AtropisomerError | StereoError | AdjustHsError | StereoOrderError | StereoGroupError | PropertyIntReadError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: BioStructureError | TopologyValidationError | PdbPostprocessError | SanitizeError | HydrogenError | ValenceError | StereoError

“error_payload”} Concrete native payload describing why conversion of the biological structure failed.

Type:

{“role”

property variant: BioMoleculeConversionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BioMoleculeConversionErrorKind(value)

Discriminants of BioMoleculeConversionErrorKind.

Members: Structure, Topology, Chemistry, Sanitize, Hydrogens, Valence, Stereo, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (10)
Chemistry = BioMoleculeConversionErrorKind.Chemistry
Hydrogens = BioMoleculeConversionErrorKind.Hydrogens
Sanitize = BioMoleculeConversionErrorKind.Sanitize
Stereo = BioMoleculeConversionErrorKind.Stereo
Structure = BioMoleculeConversionErrorKind.Structure
Topology = BioMoleculeConversionErrorKind.Topology
Valence = BioMoleculeConversionErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Structure': BioMoleculeConversionErrorKind.Structure, 'Topology': BioMoleculeConversionErrorKind.Topology, 'Chemistry': BioMoleculeConversionErrorKind.Chemistry, 'Sanitize': BioMoleculeConversionErrorKind.Sanitize, 'Hydrogens': BioMoleculeConversionErrorKind.Hydrogens, 'Valence': BioMoleculeConversionErrorKind.Valence, 'Stereo': BioMoleculeConversionErrorKind.Stereo})
values = mappingproxy({0: BioMoleculeConversionErrorKind.Structure, 1: BioMoleculeConversionErrorKind.Topology, 2: BioMoleculeConversionErrorKind.Chemistry, 3: BioMoleculeConversionErrorKind.Sanitize, 4: BioMoleculeConversionErrorKind.Hydrogens, 5: BioMoleculeConversionErrorKind.Valence, 6: BioMoleculeConversionErrorKind.Stereo})
exception cosmolkit.BioMoleculeError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BioMoleculeError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: BioMoleculeConversionError | OperationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BioMoleculeErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BioMoleculeErrorKind(value)

Discriminants of BioMoleculeErrorKind.

Members: Conversion, Construction, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Construction = BioMoleculeErrorKind.Construction
Conversion = BioMoleculeErrorKind.Conversion
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Conversion': BioMoleculeErrorKind.Conversion, 'Construction': BioMoleculeErrorKind.Construction})
values = mappingproxy({0: BioMoleculeErrorKind.Conversion, 1: BioMoleculeErrorKind.Construction})
class cosmolkit.BioMoleculeParams(*, sanitize=Ellipsis, remove_hs=Ellipsis, flavor=Ellipsis, proximity_bonding=Ellipsis)

Canonical detached structural conversion controls.

Members (4)
flavor: PdbReadFlags

PDB atom and connectivity interpretation flags.

proximity_bonding: bool

Infer bonds from spatial proximity where applicable.

remove_hs: bool

Remove removable explicit hydrogens during molecular conversion.

sanitize: bool

Sanitize the molecular topology after converting the structure.

class cosmolkit.BioNcsOperator(id, given, transform)

Non-crystallographic symmetry operator with its source identifier and transform.

Members (3)
given: bool

Whether this NCS operator is marked as already represented by the input coordinates.

id: str

Identifier of this non-crystallographic symmetry operator in the source structure.

transform: BioTransform

Affine transform associated with this symmetry or assembly operator.

exception cosmolkit.BioOperationError(*args, **kwargs)

BioOperationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: BioStructureError | ProteinProjectionError | BioSelectionCopyError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property variant: BioOperationErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.BioOperationErrorKind(value)

Discriminants of BioOperationErrorKind.

Members: Structure, Protein, Selection, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Protein = BioOperationErrorKind.Protein
Selection = BioOperationErrorKind.Selection
Structure = BioOperationErrorKind.Structure
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Structure': BioOperationErrorKind.Structure, 'Protein': BioOperationErrorKind.Protein, 'Selection': BioOperationErrorKind.Selection})
values = mappingproxy({0: BioOperationErrorKind.Structure, 1: BioOperationErrorKind.Protein, 2: BioOperationErrorKind.Selection})
exception cosmolkit.BioPdbReadError(*args, **kwargs)

BioPdbReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property line_number: int | None

PDB source line number, or None when unavailable.

property record_tag: bytes | None

Original four-byte PDB record tag, or None when unavailable.

property source: PdbReaderCause

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property stage: BioPdbReadStage

PDB reading stage that failed.

class cosmolkit.BioPdbReadParams(*, max_line_length=Ellipsis, check_non_ascii=Ellipsis, ignore_ter=Ellipsis, split_chain_on_ter=Ellipsis, skip_remarks=Ellipsis)

Source options for reading PDB text into the detached BIO hierarchy.

Members (5)
check_non_ascii: bool

Record the first line containing a non-ASCII byte without rejecting it.

ignore_ter: bool

Ignore TER records completely.

max_line_length: int

Values <= 0 or > 120 are normalized to Gemmi’s 120-byte maximum.

skip_remarks: bool

Retain raw remarks but skip their later metadata interpretation.

split_chain_on_ter: bool

Split chain parts at TER without inferring residue entity kinds.

class cosmolkit.BioPdbReadStage(value)

Typed BioPdbReadStage values corresponding to the Rust enum.

Members: Stream, Record, Finalization, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
Finalization = BioPdbReadStage.Finalization
Record = BioPdbReadStage.Record
Stream = BioPdbReadStage.Stream
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Stream': BioPdbReadStage.Stream, 'Record': BioPdbReadStage.Record, 'Finalization': BioPdbReadStage.Finalization})
values = mappingproxy({0: BioPdbReadStage.Stream, 1: BioPdbReadStage.Record, 2: BioPdbReadStage.Finalization})
exception cosmolkit.BioPdbWriteError(*args, **kwargs)

BioPdbWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (11)
property chain: str | None

Structural chain involved in the failure. Applies to BioPdbWriteError.ChainNameTooLong. None when this payload is absent.

property detail: str | None

Additional native diagnostic detail. Applies to BioPdbWriteError.UnrepresentableField. None when this payload is absent.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property field: str | None

Field whose content or type caused the failure. Applies to BioPdbWriteError.UnrepresentableField. None when this payload is absent.

property from_: int | None

Starting endpoint reported by the native failure. Applies to BioPdbWriteError.SerialIncrementOverflow. None when this payload is absent.

property length: int | None

Length reported by the failed native check. Applies to BioPdbWriteError.ChainNameTooLong. None when this payload is absent.

property path: pathlib.Path | None

Filesystem path involved in the operation. Applies to BioPdbWriteError.Io. None when this payload is absent.

property serial: int | None

Source serial number implicated in the failure. Applies to BioPdbWriteError.NegativeSerial, BioPdbWriteError.SerialOffsetOverflow. None when this payload is absent.

property source: BioStructureError | IoError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property value: int | None

Value rejected or reported by the native operation. Applies to BioPdbWriteError.NegativeBase36Value. None when this payload is absent.

property variant: BioPdbWriteErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.BioPdbWriteErrorKind(value)

Discriminants of BioPdbWriteErrorKind.

Members: InvalidStructure, ChainNameTooLong, NegativeSerial, SerialIncrementOverflow, SerialOffsetOverflow, NegativeBase36Value, UnrepresentableField, Io, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
ChainNameTooLong = BioPdbWriteErrorKind.ChainNameTooLong
InvalidStructure = BioPdbWriteErrorKind.InvalidStructure
Io = BioPdbWriteErrorKind.Io
NegativeBase36Value = BioPdbWriteErrorKind.NegativeBase36Value
NegativeSerial = BioPdbWriteErrorKind.NegativeSerial
SerialIncrementOverflow = BioPdbWriteErrorKind.SerialIncrementOverflow
SerialOffsetOverflow = BioPdbWriteErrorKind.SerialOffsetOverflow
UnrepresentableField = BioPdbWriteErrorKind.UnrepresentableField
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidStructure': BioPdbWriteErrorKind.InvalidStructure, 'ChainNameTooLong': BioPdbWriteErrorKind.ChainNameTooLong, 'NegativeSerial': BioPdbWriteErrorKind.NegativeSerial, 'SerialIncrementOverflow': BioPdbWriteErrorKind.SerialIncrementOverflow, 'SerialOffsetOverflow': BioPdbWriteErrorKind.SerialOffsetOverflow, 'NegativeBase36Value': BioPdbWriteErrorKind.NegativeBase36Value, 'UnrepresentableField': BioPdbWriteErrorKind.UnrepresentableField, 'Io': BioPdbWriteErrorKind.Io})
values = mappingproxy({0: BioPdbWriteErrorKind.InvalidStructure, 1: BioPdbWriteErrorKind.ChainNameTooLong, 2: BioPdbWriteErrorKind.NegativeSerial, 3: BioPdbWriteErrorKind.SerialIncrementOverflow, 4: BioPdbWriteErrorKind.SerialOffsetOverflow, 5: BioPdbWriteErrorKind.NegativeBase36Value, 6: BioPdbWriteErrorKind.UnrepresentableField, 7: BioPdbWriteErrorKind.Io})
class cosmolkit.BioPdbWriteParams(*, ter_records=Ellipsis, numbered_ter=Ellipsis, ter_ignores_type=Ellipsis, preserve_serial=Ellipsis, end_record=Ellipsis)

Exactly five source-default bool fields (pinned PdbWriteOptions, NOT minimal()).

Members (5)
end_record: bool

Write the terminating END record.

numbered_ter: bool

Assign serial numbers to TER records.

preserve_serial: bool

Preserve atom serial numbers instead of renumbering output.

ter_ignores_type: bool

Write TER records without restricting them to polymer entities.

ter_records: bool

Write TER records at polymer chain endings.

exception cosmolkit.BioReadError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BioReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property format: BioCoordinateFormat | None

“error_payload”} Format involved in the failed conversion. Applies to BioReadError.WrongFormat. None when this payload is absent.

Type:

{“role”

property path: pathlib.Path | None

Filesystem path involved in the operation. Applies to BioReadError.Io, BioReadError.Utf8, BioReadError.UnknownFileFormat. None when this payload is absent.

property source: IoError | FromUtf8Error | BioPdbReadError | CifReadError | BioMmcifReadError | MmjsonReadError | ChemCompModelError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property source_name: str | None

Readonly source_name payload of the WrongFormat error variant; None for other variants.

property variant: BioReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BioReadErrorKind(value)

Discriminants of BioReadErrorKind.

Members: Io, Utf8, Pdb, Cif, Mmcif, Mmjson, ChemComp, WrongFormat, UnknownFileFormat, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
ChemComp = BioReadErrorKind.ChemComp
Cif = BioReadErrorKind.Cif
Io = BioReadErrorKind.Io
Mmcif = BioReadErrorKind.Mmcif
Mmjson = BioReadErrorKind.Mmjson
Pdb = BioReadErrorKind.Pdb
UnknownFileFormat = BioReadErrorKind.UnknownFileFormat
Utf8 = BioReadErrorKind.Utf8
WrongFormat = BioReadErrorKind.WrongFormat
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Io': BioReadErrorKind.Io, 'Utf8': BioReadErrorKind.Utf8, 'Pdb': BioReadErrorKind.Pdb, 'Cif': BioReadErrorKind.Cif, 'Mmcif': BioReadErrorKind.Mmcif, 'Mmjson': BioReadErrorKind.Mmjson, 'ChemComp': BioReadErrorKind.ChemComp, 'WrongFormat': BioReadErrorKind.WrongFormat, 'UnknownFileFormat': BioReadErrorKind.UnknownFileFormat})
values = mappingproxy({0: BioReadErrorKind.Io, 1: BioReadErrorKind.Utf8, 2: BioReadErrorKind.Pdb, 3: BioReadErrorKind.Cif, 4: BioReadErrorKind.Mmcif, 5: BioReadErrorKind.Mmjson, 6: BioReadErrorKind.ChemComp, 7: BioReadErrorKind.WrongFormat, 8: BioReadErrorKind.UnknownFileFormat})
class cosmolkit.BioReadParams(*, format=Ellipsis, source_name=Ellipsis)

Structural-coordinate input format and source label used in parsing diagnostics.

Members (2)
format: BioCoordinateFormat

Input coordinate format; detection follows the native reader’s format policy.

source_name: str

Source label attached to parsing diagnostics, not a file to open.

class cosmolkit.BioRefinementInfo(*, id=None, cross_validation_method=None, rfree_selection_method=None, bin_count=None, mean_b=None, aniso_b=None, luzzati_error=None, dpi_blow_r=None, dpi_blow_rfree=None, dpi_cruickshank_r=None, dpi_cruickshank_rfree=None, remarks=None, basic=None, bins=None, restr_stats=None, tls_groups=None)

Refinement methods, quality statistics and retained restraint/TLS records.

Members (16)
aniso_b: list[float]

Six components of the reported anisotropic B tensor.

basic: BioBasicRefinementInfo

Overall refinement statistics.

bin_count: int

Reported number of resolution bins.

bins: list[BioBasicRefinementInfo]

Refinement statistics for each resolution bin.

cross_validation_method: str

Reported cross-validation method.

dpi_blow_r: float

Blow diffraction precision index calculated from R.

dpi_blow_rfree: float

Blow diffraction precision index calculated from free R.

dpi_cruickshank_r: float

Cruickshank diffraction precision index calculated from R.

dpi_cruickshank_rfree: float

Cruickshank diffraction precision index calculated from free R.

id: str

Refinement identifier from the source.

luzzati_error: float

Coordinate error estimated by the Luzzati method.

mean_b: float

Mean atomic B factor.

remarks: str

Additional source refinement remarks.

restr_stats: list[BioRefinementRestraint]

Reported restraint statistics.

rfree_selection_method: str

Method used to select the free-R reflection set.

tls_groups: list[BioTlsGroup]

Translation/libration/screw refinement groups.

class cosmolkit.BioRefinementRestraint(*, name=None, count=None, weight=None, function=None, dev_ideal=None)

Readonly statistics for one refinement restraint category.

Members (5)
count: int

Number of restraints in this category.

dev_ideal: float

Reported deviation from the ideal restraint target.

function: str

Restraint function description from the source.

name: str

Restraint category name.

weight: float

Reported restraint weight.

class cosmolkit.BioReflectionsInfo(*, resolution_high=None, resolution_low=None, completeness=None, redundancy=None, r_merge=None, r_sym=None, mean_i_over_sigma=None)

Readonly diffraction-reflection statistics. Omitted values retain native missing-value sentinels.

Members (7)
completeness: float

Reported reflection completeness.

mean_i_over_sigma: float

Mean intensity divided by its standard uncertainty.

r_merge: float

Merging R factor.

r_sym: float

Symmetry-related R factor.

redundancy: float

Reported measurement redundancy.

resolution_high: float

High-resolution limit in angstroms.

resolution_low: float

Low-resolution limit in angstroms.

class cosmolkit.BioResidue

Owned BioResidue view retaining its structure version.

Hierarchy and coordinate reads use that retained structure. Editing another COW structure value does not invalidate this object or alter its values. value() returns the detached row without its owner context.

Members (14)
atom_span: BioRowSpan

Half-open span of this residue’s atom rows in the retained structure.

atoms: list[BioAtom]

Atom views in stored residue order, each retaining the same structure version.

chain_id: int

Local identifier of the chain containing this residue.

entity_id: int | None

Local entity identifier associated with this residue, or None when unassigned.

entity_kind: EntityKind

Stored entity category associated with this residue.

het_flag: int | None

Source ATOM/HETATM classification marker, or None when unavailable.

id: int

Stable local row identifier in the retained structure, not a source-file serial number.

kind: ResidueKind

Stored residue classification.

name: str

Source atom or residue name retained by this hierarchy object.

num_atoms: int

Number of atom rows in this residue, including retained alternate locations.

residue_info_kind: ResidueInfoKind

Chemical residue classification from the canonical residue information table.

sifts_unp: BioSiftsUnpResidue

Stored SIFTS UniProt mapping for this residue.

source: ResidueSourceIds

Source-file identifiers retained separately from local row indices.

value() → BioResidueRow

Return a detached row copy without structure ownership or contextual traversal.

class cosmolkit.BioResidueRow(chain_id, atom_span, name, residue_info_kind, entity_kind, entity_id, het_flag, source, sifts_unp)

Detached residue row with a parent chain identifier and atom span; no owning structure.

Members (10)
atom_span: BioRowSpan

Half-open span of atom rows belonging to this residue.

chain_id: int

Local identifier of the parent chain.

entity_id: int | None

Parent entity identifier, or None if unassigned.

entity_kind: EntityKind

Entity classification associated with this residue.

het_flag: int | None

Source heteroatom-record flag, or None if absent.

kind: ResidueKind

Stored native classification of this entity or residue.

name: str

Source residue or atom name, preserving its native representation.

residue_info_kind: ResidueInfoKind

Residue-information classification stored in the row.

sifts_unp: BioSiftsUnpResidue

Retained UniProt residue mapping.

source: ResidueSourceIds

Source-format identifiers, distinct from local structure row indices.

exception cosmolkit.BioRowChainError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BioRowChainError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BioRowChainErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BioRowChainErrorKind(value)

Discriminants of BioRowChainErrorKind.

Members: MissingCanonicalChainName, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
MissingCanonicalChainName = BioRowChainErrorKind.MissingCanonicalChainName
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingCanonicalChainName': BioRowChainErrorKind.MissingCanonicalChainName})
values = mappingproxy({0: BioRowChainErrorKind.MissingCanonicalChainName})
exception cosmolkit.BioRowModelError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BioRowModelError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BioRowModelErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BioRowModelErrorKind(value)

Discriminants of BioRowModelErrorKind.

Members: MissingModelNumber, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
MissingModelNumber = BioRowModelErrorKind.MissingModelNumber
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingModelNumber': BioRowModelErrorKind.MissingModelNumber})
values = mappingproxy({0: BioRowModelErrorKind.MissingModelNumber})
class cosmolkit.BioRowSpan(start, len)

Checked half-open range of rows represented by an inclusive start and row count.

Members (5)
end: int

Exclusive ending row index.

static from_usize(start, len) → BioRowSpan

Create a checked row span from platform-sized start and length values.

is_empty: bool

Whether the span contains zero rows.

len: int

Number of rows in the span.

start: int

Inclusive starting row index.

exception cosmolkit.BioRowTraverseError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BioRowTraverseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: BioRowModelError | BioRowChainError

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BioRowTraverseErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BioRowTraverseErrorKind(value)

Discriminants of BioRowTraverseErrorKind.

Members: Model, Chain, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Chain = BioRowTraverseErrorKind.Chain
Model = BioRowTraverseErrorKind.Model
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Model': BioRowTraverseErrorKind.Model, 'Chain': BioRowTraverseErrorKind.Chain})
values = mappingproxy({0: BioRowTraverseErrorKind.Model, 1: BioRowTraverseErrorKind.Chain})
class cosmolkit.BioSelection

Parsed CID selector for models, chains, residues and atoms in a biological structure.

Members (2)
static from_cid(cid) → BioSelection

Parse a CID expression into a reusable structure selector.

to_cid() → str

Serialize this selection as a CID expression.

exception cosmolkit.BioSelectionCopyCause(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BioSelectionCopyCause is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: BioStructureError | BioRowTraverseError

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BioSelectionCopyCauseKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BioSelectionCopyCauseKind(value)

Discriminants of BioSelectionCopyCauseKind.

Members: Structure, Traverse, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Structure = BioSelectionCopyCauseKind.Structure
Traverse = BioSelectionCopyCauseKind.Traverse
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Structure': BioSelectionCopyCauseKind.Structure, 'Traverse': BioSelectionCopyCauseKind.Traverse})
values = mappingproxy({0: BioSelectionCopyCauseKind.Structure, 1: BioSelectionCopyCauseKind.Traverse})
exception cosmolkit.BioSelectionCopyError(*args, **kwargs)

BioSelectionCopyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: BioStructureError | BioRowTraverseError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.BioSelectionMatchError(*args, **kwargs)

BioSelectionMatchError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: BioRowTraverseError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.BioSelectionParseError(*args, **kwargs)

BioSelectionParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property cid: str | None

CID expression that failed syntax parsing; None for sequence-ID range failures.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property info: str | None

Optional syntax-parser explanation; None for sequence-ID range failures.

property pos: int | None

Syntax failure position in the CID expression; None for sequence-ID range failures.

property variant: BioSelectionParseErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.BioSelectionParseErrorKind(value)

Discriminants of BioSelectionParseErrorKind.

Members: Syntax, SeqidRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
SeqidRange = BioSelectionParseErrorKind.SeqidRange
Syntax = BioSelectionParseErrorKind.Syntax
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Syntax': BioSelectionParseErrorKind.Syntax, 'SeqidRange': BioSelectionParseErrorKind.SeqidRange})
values = mappingproxy({0: BioSelectionParseErrorKind.Syntax, 1: BioSelectionParseErrorKind.SeqidRange})
class cosmolkit.BioSheet(sheet_id, strands=None)

Named beta sheet containing ordered strand records.

Members (2)
name: str

Name or identifier retained in this source record.

strands: list[BioStrand]

Independent strand records belonging to this sheet.

class cosmolkit.BioSiftsUnpResidue(*, residue=Ellipsis, accession_index=Ellipsis, number=Ellipsis)

SIFTS mapping of a structure residue to a UniProt accession index and residue number.

Members (3)
accession_index: int

Index into the entity’s SIFTS UniProt accession list.

number: int

Mapped UniProt residue number.

residue: int | None

Optional residue character encoded by the SIFTS mapping.

class cosmolkit.BioSoftwareClassification(value)

Typed BioSoftwareClassification values corresponding to the Rust enum.

Members: DataCollection, DataExtraction, DataProcessing, DataReduction, DataScaling, ModelBuilding, Phasing, Refinement, Unspecified, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (12)
DataCollection = BioSoftwareClassification.DataCollection
DataExtraction = BioSoftwareClassification.DataExtraction
DataProcessing = BioSoftwareClassification.DataProcessing
DataReduction = BioSoftwareClassification.DataReduction
DataScaling = BioSoftwareClassification.DataScaling
ModelBuilding = BioSoftwareClassification.ModelBuilding
Phasing = BioSoftwareClassification.Phasing
Refinement = BioSoftwareClassification.Refinement
Unspecified = BioSoftwareClassification.Unspecified
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'DataCollection': BioSoftwareClassification.DataCollection, 'DataExtraction': BioSoftwareClassification.DataExtraction, 'DataProcessing': BioSoftwareClassification.DataProcessing, 'DataReduction': BioSoftwareClassification.DataReduction, 'DataScaling': BioSoftwareClassification.DataScaling, 'ModelBuilding': BioSoftwareClassification.ModelBuilding, 'Phasing': BioSoftwareClassification.Phasing, 'Refinement': BioSoftwareClassification.Refinement, 'Unspecified': BioSoftwareClassification.Unspecified})
values = mappingproxy({0: BioSoftwareClassification.DataCollection, 1: BioSoftwareClassification.DataExtraction, 2: BioSoftwareClassification.DataProcessing, 3: BioSoftwareClassification.DataReduction, 4: BioSoftwareClassification.DataScaling, 5: BioSoftwareClassification.ModelBuilding, 6: BioSoftwareClassification.Phasing, 7: BioSoftwareClassification.Refinement, 8: BioSoftwareClassification.Unspecified})
class cosmolkit.BioSoftwareItem(*, name=Ellipsis, version=Ellipsis, date=Ellipsis, description=Ellipsis, contact_author=Ellipsis, contact_author_email=Ellipsis, classification=None)

Software provenance reported during structure determination or refinement.

Members (7)
classification: BioSoftwareClassification

Role of the software in structure determination.

contact_author: str

Contact author recorded for the software.

contact_author_email: str

Contact author’s email address.

date: str

Reported software date.

description: str

Source description of the software.

name: str

Name of the software reported in the source.

version: str

Reported software version.

class cosmolkit.BioStrand(start, end, hbond_atom2, hbond_atom1, sense, name)

Reported beta strand with its boundaries, orientation and hydrogen-bond anchors.

Members (6)
end: AtomAddress

Address marking the end of this secondary-structure segment.

hbond_atom1: AtomAddress

First atom address in the reported sheet hydrogen bond.

hbond_atom2: AtomAddress

Second atom address in the reported sheet hydrogen bond.

name: str

Name or identifier retained in this source record.

sense: int

native parallel/antiparallel sense code.

Type:

Strand orientation relative to its predecessor

start: AtomAddress

Address marking the beginning of this secondary-structure segment.

exception cosmolkit.BioStructureError(*args, **kwargs)

BioStructureError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (17)
property actual_start: int | None

Actual start of the next span. Present for BioStructureError.NonContiguousSpan; None when unavailable.

property atom_count: int | None

Number of atoms available to the operation. Present for BioStructureError.CoordinateCountMismatch; None when unavailable.

property coordinate_count: int | None

Number of supplied coordinate rows. Present for BioStructureError.CoordinateCountMismatch; None when unavailable.

property covered: int | None

Number of rows covered by the supplied spans. Present for BioStructureError.IncompleteCoverage; None when unavailable.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property entity_id: int | None

Entity identifier associated with the failure. Present for BioStructureError.EntitySubchainMismatch; None when unavailable.

property expected_start: int | None

Required start of the next contiguous span. Present for BioStructureError.NonContiguousSpan; None when unavailable.

property index: int | None

Index associated with the failure. Present for BioStructureError.ParentMismatch, BioStructureError.RowReferenceOutOfBounds; None when unavailable.

property len: int | None

Length of the invalid span or collection. Present for BioStructureError.RowSpanOverflow, BioStructureError.RowSpanOutOfBounds, BioStructureError.TableTooLarge; None when unavailable.

property operation: str | None

Operation name or registered operation descriptor reporting the failure. Present for BioStructureError.EmptyResidueSpan; None when unavailable.

property source_message: str | None

Message of the immediate native cause, or None when no cause exists.

property start: int | None

Start of the invalid row span. Present for BioStructureError.RowSpanOverflow, BioStructureError.RowSpanOutOfBounds; None when unavailable.

property subchain: str | None

Subchain identifier associated with the failure. Present for BioStructureError.EntitySubchainMismatch; None when unavailable.

property table: str | None

Name of the affected structure table. Present for BioStructureError.TableTooLarge, BioStructureError.NonContiguousSpan, BioStructureError.IncompleteCoverage, BioStructureError.ParentMismatch, BioStructureError.RowReferenceOutOfBounds; None when unavailable.

property table_len: int | None

Length of the referenced structure table. Present for BioStructureError.RowSpanOutOfBounds, BioStructureError.IncompleteCoverage, BioStructureError.RowReferenceOutOfBounds; None when unavailable.

property value: int | None

Original value rejected by the operation. Present for BioStructureError.RowIndexTooLarge; None when unavailable.

property variant: BioStructureErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.BioStructureErrorKind(value)

Discriminants of BioStructureErrorKind.

Members: RowIndexTooLarge, RowSpanOverflow, RowSpanOutOfBounds, TableTooLarge, NonContiguousSpan, IncompleteCoverage, ParentMismatch, RowReferenceOutOfBounds, CoordinateCountMismatch, EntitySubchainMismatch, EmptyResidueSpan, ImpossibleCrystalAngle, AtomNotFound, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (16)
AtomNotFound = BioStructureErrorKind.AtomNotFound
CoordinateCountMismatch = BioStructureErrorKind.CoordinateCountMismatch
EmptyResidueSpan = BioStructureErrorKind.EmptyResidueSpan
EntitySubchainMismatch = BioStructureErrorKind.EntitySubchainMismatch
ImpossibleCrystalAngle = BioStructureErrorKind.ImpossibleCrystalAngle
IncompleteCoverage = BioStructureErrorKind.IncompleteCoverage
NonContiguousSpan = BioStructureErrorKind.NonContiguousSpan
ParentMismatch = BioStructureErrorKind.ParentMismatch
RowIndexTooLarge = BioStructureErrorKind.RowIndexTooLarge
RowReferenceOutOfBounds = BioStructureErrorKind.RowReferenceOutOfBounds
RowSpanOutOfBounds = BioStructureErrorKind.RowSpanOutOfBounds
RowSpanOverflow = BioStructureErrorKind.RowSpanOverflow
TableTooLarge = BioStructureErrorKind.TableTooLarge
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'RowIndexTooLarge': BioStructureErrorKind.RowIndexTooLarge, 'RowSpanOverflow': BioStructureErrorKind.RowSpanOverflow, 'RowSpanOutOfBounds': BioStructureErrorKind.RowSpanOutOfBounds, 'TableTooLarge': BioStructureErrorKind.TableTooLarge, 'NonContiguousSpan': BioStructureErrorKind.NonContiguousSpan, 'IncompleteCoverage': BioStructureErrorKind.IncompleteCoverage, 'ParentMismatch': BioStructureErrorKind.ParentMismatch, 'RowReferenceOutOfBounds': BioStructureErrorKind.RowReferenceOutOfBounds, 'CoordinateCountMismatch': BioStructureErrorKind.CoordinateCountMismatch, 'EntitySubchainMismatch': BioStructureErrorKind.EntitySubchainMismatch, 'EmptyResidueSpan': BioStructureErrorKind.EmptyResidueSpan, 'ImpossibleCrystalAngle': BioStructureErrorKind.ImpossibleCrystalAngle, 'AtomNotFound': BioStructureErrorKind.AtomNotFound})
values = mappingproxy({0: BioStructureErrorKind.RowIndexTooLarge, 1: BioStructureErrorKind.RowSpanOverflow, 2: BioStructureErrorKind.RowSpanOutOfBounds, 3: BioStructureErrorKind.TableTooLarge, 4: BioStructureErrorKind.NonContiguousSpan, 5: BioStructureErrorKind.IncompleteCoverage, 6: BioStructureErrorKind.ParentMismatch, 7: BioStructureErrorKind.RowReferenceOutOfBounds, 8: BioStructureErrorKind.CoordinateCountMismatch, 9: BioStructureErrorKind.EntitySubchainMismatch, 10: BioStructureErrorKind.EmptyResidueSpan, 11: BioStructureErrorKind.ImpossibleCrystalAngle, 12: BioStructureErrorKind.AtomNotFound})
class cosmolkit.BioStructureParts(*, input_format, models, chains, residues, atoms, entities, connections, cispeps, mod_residues, helices, sheets, ncs_operators, assemblies, metadata, source_state, coordinates, crystal)

Detached structural rows, coordinates and metadata for validated BioStructure construction.

Members (17)
assemblies: list[BioAssembly]

Independent list of detached BioAssembly values in stored order; these rows do not retain an owning structure.

atoms: list[BioAtomRow]

Independent list of detached BioAtomRow values in stored order; these rows do not retain an owning structure.

chains: list[BioChainRow]

Independent list of detached BioChainRow values in stored order; these rows do not retain an owning structure.

cispeps: list[BioCisPep]

Independent list of detached BioCisPep values in stored order; these rows do not retain an owning structure.

connections: list[BioConnection]

Independent list of detached BioConnection values in stored order; these rows do not retain an owning structure.

coordinates: BioCoordinateBlock

Detached coordinate block in atom-row order.

crystal: BioCrystalInfo | None

Crystallographic cell and symmetry information, or None when absent.

entities: list[BioEntityRow]

Independent list of detached BioEntityRow values in stored order; these rows do not retain an owning structure.

helices: list[BioHelix]

Independent list of detached BioHelix values in stored order; these rows do not retain an owning structure.

input_format: BioCoordinateFormat

Coordinate-file format recorded by the source reader.

metadata: BioMetadata

Detached copy of experimental, refinement and provenance metadata.

mod_residues: list[BioModRes]

Independent list of detached BioModRes values in stored order; these rows do not retain an owning structure.

models: list[BioModelRow]

Independent list of detached BioModelRow values in stored order; these rows do not retain an owning structure.

ncs_operators: list[BioNcsOperator]

Independent list of detached BioNcsOperator values in stored order; these rows do not retain an owning structure.

residues: list[BioResidueRow]

Independent list of detached BioResidueRow values in stored order; these rows do not retain an owning structure.

sheets: list[BioSheet]

Independent list of detached BioSheet values in stored order; these rows do not retain an owning structure.

source_state: BioStructureSourceState

Detached source-format state, including retained record annotations.

class cosmolkit.BioStructureSourceState(*, name=Ellipsis, resolution=Ellipsis, conect_map=None, has_d_fraction=Ellipsis, non_ascii_line=Ellipsis, ter_status=Ellipsis, has_origx=Ellipsis, origx=None, info=None, raw_remarks=Ellipsis)

Source-format metadata and parsing state retained with a biological structure.

Members (10)
conect_map: dict[int, list[int]]

PDB CONECT relationships keyed by atom serial number.

has_d_fraction: bool

Whether the input supplied deuterium-fraction information.

has_origx: bool

Whether the source supplied an ORIGX transformation.

info: dict[str, str]

Source metadata key/value pairs.

name: str

Structure name retained in the source metadata.

non_ascii_line: int

Native source line indicator for non-ASCII input.

origx: BioTransform

Original-coordinate transformation retained from the source.

raw_remarks: list[str]

Retained raw PDB REMARK records in source order.

resolution: float

Resolution reported by the source structure.

ter_status: int

Stored native status of PDB TER record handling.

class cosmolkit.BioTlsGroup(*, num_id=None, id=None, origin=None, t=None, l=None, s=None, selections=None)

Translation/libration/screw refinement group, its origin and atom selections.

Members (7)
id: str

Textual source identifier for this TLS group.

l: list[float]

Six independent components of the symmetric libration tensor.

num_id: int

Numeric source identifier for this TLS group.

origin: list[float]

Cartesian origin of the TLS model.

s: list[list[float]]

Three-by-three screw tensor.

selections: list[BioTlsSelection]

Chain/residue selections belonging to this TLS group.

t: list[float]

Six independent components of the symmetric translation tensor.

class cosmolkit.BioTlsSelection(*, chain=None, res_begin=None, res_end=None, details=Ellipsis)

Chain and residue range to which a TLS refinement group applies.

Members (4)
chain: str

Chain identifier selected by this TLS range.

details: str

Additional source description of this TLS selection.

res_begin: PdbSeqId

First residue sequence identifier of the TLS selection.

res_end: PdbSeqId

Last residue sequence identifier of the TLS selection.

class cosmolkit.BioTransform(matrix=Ellipsis, translation=Ellipsis)

Three-dimensional affine transform with a 3-by-3 matrix and three-component translation.

Members (3)
approx(other, epsilon) → bool

Whether matrix and translation components match within the supplied native tolerance.

matrix: numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]

[“numpy”], “type”: “numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]”} Independent float64 NumPy array of shape (3, 3) containing the linear transform.

Type:

{“role”

Type:

“return_type”, “imports”

translation: numpy.ndarray[tuple[int], numpy.dtype[numpy.float64]]

[“numpy”], “type”: “numpy.ndarray[tuple[int], numpy.dtype[numpy.float64]]”} Independent float64 NumPy array of shape (3,) containing the translation vector.

Type:

{“role”

Type:

“return_type”, “imports”

class cosmolkit.Bond

Detached readonly bond data, including endpoints, order and stored stereochemical annotations.

Members (16)
begin: int

Zero-based index of the bond’s begin atom.

cip_descriptor: CipDescriptor | None

Stored CIP descriptor, or None if absent; invalid stored values raise CipDescriptorError.

cip_neighbor_order: list[int] | None

Stored CIP neighbor ordering as atom indices, or None if absent; invalid encodings raise CipDescriptorError.

direction: BondDirection

Stored drawing or directional bond annotation.

direction_code: int

Integer code of the stored bond direction.

direction_name: str

Canonical name of the stored bond direction.

end: int

Zero-based index of the bond’s end atom.

id: int

Zero-based identifier within the originating topology.

is_aromatic: bool

Stored aromaticity flag; reading does not perform aromaticity perception.

order: BondOrder

Stored chemical bond order.

order_code: int

Integer code of the stored bond order.

order_name: str

Canonical name of the stored bond order.

stereo: BondStereo

Stored bond stereochemical assignment.

stereo_atoms: list[int] | None

Pair of reference atom indices defining bond stereo, or None when unassigned.

stereo_code: int

Integer code of the stored bond stereo assignment.

stereo_name: str

Canonical name of the stored bond stereo assignment.

class cosmolkit.BondDirection(value)

Typed BondDirection values corresponding to the Rust enum.

Members: None, BeginWedge, BeginDash, EndDownRight, EndUpRight, EitherDouble, Unknown, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (17)
BEGINDASH = BondDirection.BeginDash
BEGINWEDGE = BondDirection.BeginWedge
BeginDash = BondDirection.BeginDash
BeginWedge = BondDirection.BeginWedge
EITHERDOUBLE = BondDirection.EitherDouble
ENDDOWNRIGHT = BondDirection.EndDownRight
ENDUPRIGHT = BondDirection.EndUpRight
EitherDouble = BondDirection.EitherDouble
EndDownRight = BondDirection.EndDownRight
EndUpRight = BondDirection.EndUpRight
NONE = BondDirection.None_
None_ = BondDirection.None_
UNKNOWN = BondDirection.Unknown
Unknown = BondDirection.Unknown
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'None_': BondDirection.None_, 'NONE': BondDirection.None_, 'BeginWedge': BondDirection.BeginWedge, 'BEGINWEDGE': BondDirection.BeginWedge, 'BeginDash': BondDirection.BeginDash, 'BEGINDASH': BondDirection.BeginDash, 'EndDownRight': BondDirection.EndDownRight, 'ENDDOWNRIGHT': BondDirection.EndDownRight, 'EndUpRight': BondDirection.EndUpRight, 'ENDUPRIGHT': BondDirection.EndUpRight, 'EitherDouble': BondDirection.EitherDouble, 'EITHERDOUBLE': BondDirection.EitherDouble, 'Unknown': BondDirection.Unknown, 'UNKNOWN': BondDirection.Unknown})
values = mappingproxy({0: BondDirection.None_, 1: BondDirection.BeginWedge, 2: BondDirection.BeginDash, 3: BondDirection.EndDownRight, 4: BondDirection.EndUpRight, 5: BondDirection.EitherDouble, 6: BondDirection.Unknown})
exception cosmolkit.BondDirectionStereoError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BondDirectionStereoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property atropisomer: AtropisomerError | None

“error_payload”} Structured AtropisomerError payload of BondDirectionStereoError.Atropisomer; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property message: str | None

Detailed native diagnostic message. Applies to BondDirectionStereoError.InvalidState. None when this payload is absent.

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of BondDirectionStereoError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: BondDirectionStereoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BondDirectionStereoErrorKind(value)

Discriminants of BondDirectionStereoErrorKind.

Members: InvalidState, Valence, Atropisomer, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Atropisomer = BondDirectionStereoErrorKind.Atropisomer
InvalidState = BondDirectionStereoErrorKind.InvalidState
Valence = BondDirectionStereoErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidState': BondDirectionStereoErrorKind.InvalidState, 'Valence': BondDirectionStereoErrorKind.Valence, 'Atropisomer': BondDirectionStereoErrorKind.Atropisomer})
values = mappingproxy({0: BondDirectionStereoErrorKind.InvalidState, 1: BondDirectionStereoErrorKind.Valence, 2: BondDirectionStereoErrorKind.Atropisomer})
class cosmolkit.BondEndPointsParseErrorKind(value)

Typed BondEndPointsParseErrorKind values corresponding to the Rust enum.

Members: InvalidArgument, OutOfRange, UnrepresentableEndpoint, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
InvalidArgument = BondEndPointsParseErrorKind.InvalidArgument
OutOfRange = BondEndPointsParseErrorKind.OutOfRange
UnrepresentableEndpoint = BondEndPointsParseErrorKind.UnrepresentableEndpoint
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidArgument': BondEndPointsParseErrorKind.InvalidArgument, 'OutOfRange': BondEndPointsParseErrorKind.OutOfRange, 'UnrepresentableEndpoint': BondEndPointsParseErrorKind.UnrepresentableEndpoint})
values = mappingproxy({0: BondEndPointsParseErrorKind.InvalidArgument, 1: BondEndPointsParseErrorKind.OutOfRange, 2: BondEndPointsParseErrorKind.UnrepresentableEndpoint})
class cosmolkit.BondOrder(value)

Typed BondOrder values corresponding to the Rust enum.

Members: Unspecified, Single, Double, Triple, Quadruple, Quintuple, Hextuple, OneAndHalf, TwoAndHalf, ThreeAndHalf, FourAndHalf, FiveAndHalf, Aromatic, Ionic, Hydrogen, ThreeCenter, DativeOne, Dative, DativeLeft, DativeRight, Other, Zero, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (47)
AROMATIC = BondOrder.Aromatic
Aromatic = BondOrder.Aromatic
DATIVE = BondOrder.Dative
DATIVEL = BondOrder.DativeLeft
DATIVEONE = BondOrder.DativeOne
DATIVER = BondOrder.DativeRight
DOUBLE = BondOrder.Double
Dative = BondOrder.Dative
DativeLeft = BondOrder.DativeLeft
DativeOne = BondOrder.DativeOne
DativeRight = BondOrder.DativeRight
Double = BondOrder.Double
FIVEANDAHALF = BondOrder.FiveAndHalf
FOURANDAHALF = BondOrder.FourAndHalf
FiveAndHalf = BondOrder.FiveAndHalf
FourAndHalf = BondOrder.FourAndHalf
HEXTUPLE = BondOrder.Hextuple
HYDROGEN = BondOrder.Hydrogen
Hextuple = BondOrder.Hextuple
Hydrogen = BondOrder.Hydrogen
IONIC = BondOrder.Ionic
Ionic = BondOrder.Ionic
ONEANDAHALF = BondOrder.OneAndHalf
OTHER = BondOrder.Other
OneAndHalf = BondOrder.OneAndHalf
Other = BondOrder.Other
QUADRUPLE = BondOrder.Quadruple
QUINTUPLE = BondOrder.Quintuple
Quadruple = BondOrder.Quadruple
Quintuple = BondOrder.Quintuple
SINGLE = BondOrder.Single
Single = BondOrder.Single
THREEANDAHALF = BondOrder.ThreeAndHalf
THREECENTER = BondOrder.ThreeCenter
TRIPLE = BondOrder.Triple
TWOANDAHALF = BondOrder.TwoAndHalf
ThreeAndHalf = BondOrder.ThreeAndHalf
ThreeCenter = BondOrder.ThreeCenter
Triple = BondOrder.Triple
TwoAndHalf = BondOrder.TwoAndHalf
UNSPECIFIED = BondOrder.Unspecified
Unspecified = BondOrder.Unspecified
ZERO = BondOrder.Zero
Zero = BondOrder.Zero
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unspecified': BondOrder.Unspecified, 'UNSPECIFIED': BondOrder.Unspecified, 'Single': BondOrder.Single, 'SINGLE': BondOrder.Single, 'Double': BondOrder.Double, 'DOUBLE': BondOrder.Double, 'Triple': BondOrder.Triple, 'TRIPLE': BondOrder.Triple, 'Quadruple': BondOrder.Quadruple, 'QUADRUPLE': BondOrder.Quadruple, 'Quintuple': BondOrder.Quintuple, 'QUINTUPLE': BondOrder.Quintuple, 'Hextuple': BondOrder.Hextuple, 'HEXTUPLE': BondOrder.Hextuple, 'OneAndHalf': BondOrder.OneAndHalf, 'ONEANDAHALF': BondOrder.OneAndHalf, 'TwoAndHalf': BondOrder.TwoAndHalf, 'TWOANDAHALF': BondOrder.TwoAndHalf, 'ThreeAndHalf': BondOrder.ThreeAndHalf, 'THREEANDAHALF': BondOrder.ThreeAndHalf, 'FourAndHalf': BondOrder.FourAndHalf, 'FOURANDAHALF': BondOrder.FourAndHalf, 'FiveAndHalf': BondOrder.FiveAndHalf, 'FIVEANDAHALF': BondOrder.FiveAndHalf, 'Aromatic': BondOrder.Aromatic, 'AROMATIC': BondOrder.Aromatic, 'Ionic': BondOrder.Ionic, 'IONIC': BondOrder.Ionic, 'Hydrogen': BondOrder.Hydrogen, 'HYDROGEN': BondOrder.Hydrogen, 'ThreeCenter': BondOrder.ThreeCenter, 'THREECENTER': BondOrder.ThreeCenter, 'DativeOne': BondOrder.DativeOne, 'DATIVEONE': BondOrder.DativeOne, 'Dative': BondOrder.Dative, 'DATIVE': BondOrder.Dative, 'DativeLeft': BondOrder.DativeLeft, 'DATIVEL': BondOrder.DativeLeft, 'DativeRight': BondOrder.DativeRight, 'DATIVER': BondOrder.DativeRight, 'Other': BondOrder.Other, 'OTHER': BondOrder.Other, 'Zero': BondOrder.Zero, 'ZERO': BondOrder.Zero})
values = mappingproxy({0: BondOrder.Unspecified, 1: BondOrder.Single, 2: BondOrder.Double, 3: BondOrder.Triple, 4: BondOrder.Quadruple, 5: BondOrder.Quintuple, 6: BondOrder.Hextuple, 7: BondOrder.OneAndHalf, 8: BondOrder.TwoAndHalf, 9: BondOrder.ThreeAndHalf, 10: BondOrder.FourAndHalf, 11: BondOrder.FiveAndHalf, 12: BondOrder.Aromatic, 13: BondOrder.Ionic, 14: BondOrder.Hydrogen, 15: BondOrder.ThreeCenter, 16: BondOrder.DativeOne, 17: BondOrder.Dative, 18: BondOrder.DativeLeft, 19: BondOrder.DativeRight, 20: BondOrder.Other, 21: BondOrder.Zero})
class cosmolkit.BondQueryPredicate

Read-only native bond predicate retained by a SMARTS writer diagnostic; variant determines its payload.

Members (3)
name: str | None

Property name in a PropertyValue predicate, or None for other variants.

value: BondOrder | list[BondOrder] | bool | BondDirection | BondStereo | int | str | None

Typed payload of the selected predicate or one-sided bound; None for payload-free or differently structured variants.

variant: BondQueryPredicateKind

Exact native predicate or bound variant; payload availability follows this variant.

class cosmolkit.BondQueryPredicateKind(value)

Discriminants of BondQueryPredicateKind.

Members: Any, Order, OrderIn, IsAromatic, IsInRing, Direction, Stereo, HasStereo, IsConjugated, NumRingBonds, InRingOfSize, MinRingSize, NumRingBondsGreaterEqual, NumRingBondsLessEqual, MolFileQueryCode, HasProperty, PropertyValue, UnsupportedFeature, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (21)
Any = BondQueryPredicateKind.Any
Direction = BondQueryPredicateKind.Direction
HasProperty = BondQueryPredicateKind.HasProperty
HasStereo = BondQueryPredicateKind.HasStereo
InRingOfSize = BondQueryPredicateKind.InRingOfSize
IsAromatic = BondQueryPredicateKind.IsAromatic
IsConjugated = BondQueryPredicateKind.IsConjugated
IsInRing = BondQueryPredicateKind.IsInRing
MinRingSize = BondQueryPredicateKind.MinRingSize
MolFileQueryCode = BondQueryPredicateKind.MolFileQueryCode
NumRingBonds = BondQueryPredicateKind.NumRingBonds
NumRingBondsGreaterEqual = BondQueryPredicateKind.NumRingBondsGreaterEqual
NumRingBondsLessEqual = BondQueryPredicateKind.NumRingBondsLessEqual
Order = BondQueryPredicateKind.Order
OrderIn = BondQueryPredicateKind.OrderIn
PropertyValue = BondQueryPredicateKind.PropertyValue
Stereo = BondQueryPredicateKind.Stereo
UnsupportedFeature = BondQueryPredicateKind.UnsupportedFeature
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Any': BondQueryPredicateKind.Any, 'Order': BondQueryPredicateKind.Order, 'OrderIn': BondQueryPredicateKind.OrderIn, 'IsAromatic': BondQueryPredicateKind.IsAromatic, 'IsInRing': BondQueryPredicateKind.IsInRing, 'Direction': BondQueryPredicateKind.Direction, 'Stereo': BondQueryPredicateKind.Stereo, 'HasStereo': BondQueryPredicateKind.HasStereo, 'IsConjugated': BondQueryPredicateKind.IsConjugated, 'NumRingBonds': BondQueryPredicateKind.NumRingBonds, 'InRingOfSize': BondQueryPredicateKind.InRingOfSize, 'MinRingSize': BondQueryPredicateKind.MinRingSize, 'NumRingBondsGreaterEqual': BondQueryPredicateKind.NumRingBondsGreaterEqual, 'NumRingBondsLessEqual': BondQueryPredicateKind.NumRingBondsLessEqual, 'MolFileQueryCode': BondQueryPredicateKind.MolFileQueryCode, 'HasProperty': BondQueryPredicateKind.HasProperty, 'PropertyValue': BondQueryPredicateKind.PropertyValue, 'UnsupportedFeature': BondQueryPredicateKind.UnsupportedFeature})
values = mappingproxy({0: BondQueryPredicateKind.Any, 1: BondQueryPredicateKind.Order, 2: BondQueryPredicateKind.OrderIn, 3: BondQueryPredicateKind.IsAromatic, 4: BondQueryPredicateKind.IsInRing, 5: BondQueryPredicateKind.Direction, 6: BondQueryPredicateKind.Stereo, 7: BondQueryPredicateKind.HasStereo, 8: BondQueryPredicateKind.IsConjugated, 9: BondQueryPredicateKind.NumRingBonds, 10: BondQueryPredicateKind.InRingOfSize, 11: BondQueryPredicateKind.MinRingSize, 12: BondQueryPredicateKind.NumRingBondsGreaterEqual, 13: BondQueryPredicateKind.NumRingBondsLessEqual, 14: BondQueryPredicateKind.MolFileQueryCode, 15: BondQueryPredicateKind.HasProperty, 16: BondQueryPredicateKind.PropertyValue, 17: BondQueryPredicateKind.UnsupportedFeature})
class cosmolkit.BondSpec(begin, end, order)

Detached bond-construction inputs: zero-based endpoint atom identifiers and bond order.

Members (1)
static new(begin, end, order) → BondSpec

Create a bond specification with zero-based endpoint indices and the requested bond order.

class cosmolkit.BondStereo(value)

Typed BondStereo values corresponding to the Rust enum.

Members: None, Any, Z, E, Cis, Trans, AtropCw, AtropCcw, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (19)
Any = BondStereo.Any
AtropCcw = BondStereo.AtropCcw
AtropCw = BondStereo.AtropCw
Cis = BondStereo.Cis
E = BondStereo.E
None_ = BondStereo.None_
STEREOANY = BondStereo.Any
STEREOATROPCCW = BondStereo.AtropCcw
STEREOATROPCW = BondStereo.AtropCw
STEREOCIS = BondStereo.Cis
STEREOE = BondStereo.E
STEREONONE = BondStereo.None_
STEREOTRANS = BondStereo.Trans
STEREOZ = BondStereo.Z
Trans = BondStereo.Trans
Z = BondStereo.Z
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'None_': BondStereo.None_, 'STEREONONE': BondStereo.None_, 'Any': BondStereo.Any, 'STEREOANY': BondStereo.Any, 'Z': BondStereo.Z, 'STEREOZ': BondStereo.Z, 'E': BondStereo.E, 'STEREOE': BondStereo.E, 'Cis': BondStereo.Cis, 'STEREOCIS': BondStereo.Cis, 'Trans': BondStereo.Trans, 'STEREOTRANS': BondStereo.Trans, 'AtropCw': BondStereo.AtropCw, 'STEREOATROPCW': BondStereo.AtropCw, 'AtropCcw': BondStereo.AtropCcw, 'STEREOATROPCCW': BondStereo.AtropCcw})
values = mappingproxy({0: BondStereo.None_, 1: BondStereo.Any, 2: BondStereo.Z, 3: BondStereo.E, 4: BondStereo.Cis, 5: BondStereo.Trans, 6: BondStereo.AtropCw, 7: BondStereo.AtropCcw})
exception cosmolkit.BondValueError(*args, **kwargs)

Failure in the model domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BondValueError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property computed_list_kind: PropertyValueError | None

“error_payload”} Structured PropertyValueError payload of BondValueError.ComputedListKind; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BondValueErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BondValueErrorKind(value)

Discriminants of BondValueErrorKind.

Members: StereoAtomsRequired, EmptyPropertyKey, ComputedListKind, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
ComputedListKind = BondValueErrorKind.ComputedListKind
EmptyPropertyKey = BondValueErrorKind.EmptyPropertyKey
StereoAtomsRequired = BondValueErrorKind.StereoAtomsRequired
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoAtomsRequired': BondValueErrorKind.StereoAtomsRequired, 'EmptyPropertyKey': BondValueErrorKind.EmptyPropertyKey, 'ComputedListKind': BondValueErrorKind.ComputedListKind})
values = mappingproxy({0: BondValueErrorKind.StereoAtomsRequired, 1: BondValueErrorKind.EmptyPropertyKey, 2: BondValueErrorKind.ComputedListKind})
class cosmolkit.BoundKind(value)

Typed BoundKind values corresponding to the Rust enum.

Members: Upper, Lower, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Lower = BoundKind.Lower
Upper = BoundKind.Upper
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Upper': BoundKind.Upper, 'Lower': BoundKind.Lower})
values = mappingproxy({0: BoundKind.Upper, 1: BoundKind.Lower})
exception cosmolkit.BoundsMatrixError(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BoundsMatrixError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (12)
property actual: int | None

Readonly actual payload of the DataLengthTooShort error variant; None for other variants.

property axis: MatrixAxis | None

“error_payload”} Coordinate axis involved in the failure. Applies to BoundsMatrixError.IndexOutOfBounds. None when this payload is absent.

Type:

{“role”

property column: int | None

Readonly column payload of the InvalidBound error variant; None for other variants.

property dimension: int | None

Coordinate or matrix dimension involved in the failure. Applies to BoundsMatrixError.DimensionOverflow, BoundsMatrixError.IndexOutOfBounds. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property elements: int | None

Readonly elements payload of the AllocationFailed error variant; None for other variants.

property expected: int | None

Readonly expected payload of the DataLengthTooShort error variant; None for other variants.

property index: int | None

Readonly index payload of the IndexOutOfBounds error variant; None for other variants.

property kind: BoundKind | None

“error_payload”} Native failure-specific category or value kind. Applies to BoundsMatrixError.InvalidBound. None when this payload is absent.

Type:

{“role”

property row: int | None

Readonly row payload of the InvalidBound error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: BoundsMatrixErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BoundsMatrixErrorKind(value)

Discriminants of BoundsMatrixErrorKind.

Members: DimensionOverflow, AllocationFailed, DataLengthTooShort, IndexOutOfBounds, InvalidBound, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
AllocationFailed = BoundsMatrixErrorKind.AllocationFailed
DataLengthTooShort = BoundsMatrixErrorKind.DataLengthTooShort
DimensionOverflow = BoundsMatrixErrorKind.DimensionOverflow
IndexOutOfBounds = BoundsMatrixErrorKind.IndexOutOfBounds
InvalidBound = BoundsMatrixErrorKind.InvalidBound
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'DimensionOverflow': BoundsMatrixErrorKind.DimensionOverflow, 'AllocationFailed': BoundsMatrixErrorKind.AllocationFailed, 'DataLengthTooShort': BoundsMatrixErrorKind.DataLengthTooShort, 'IndexOutOfBounds': BoundsMatrixErrorKind.IndexOutOfBounds, 'InvalidBound': BoundsMatrixErrorKind.InvalidBound})
values = mappingproxy({0: BoundsMatrixErrorKind.DimensionOverflow, 1: BoundsMatrixErrorKind.AllocationFailed, 2: BoundsMatrixErrorKind.DataLengthTooShort, 3: BoundsMatrixErrorKind.IndexOutOfBounds, 4: BoundsMatrixErrorKind.InvalidBound})
exception cosmolkit.BoundsQueryError(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

BoundsQueryError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property bounds: GraphBoundsError | None

“error_payload”} Structured GraphBoundsError payload of BoundsQueryError.Bounds; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property conjugation: ConjugationError | None

“error_payload”} Structured native error payload. Present for BoundsQueryError.Conjugation; None when unavailable.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property hybridization: HybridizationError | None

“error_payload”} Structured native error payload. Present for BoundsQueryError.Hybridization; None when unavailable.

Type:

{“role”

property rings: RingFindingError | None

“error_payload”} Structured native error payload. Present for BoundsQueryError.Rings; None when unavailable.

Type:

{“role”

property source: TopologyValidationError | MappingValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | BoundsMatrixError | UffBoundsError | MatrixError | ValenceError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured native error payload. Present for BoundsQueryError.Topology; None when unavailable.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of BoundsQueryError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: BoundsQueryErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.BoundsQueryErrorKind(value)

Discriminants of BoundsQueryErrorKind.

Members: Topology, Valence, Rings, Conjugation, Hybridization, Bounds, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
Bounds = BoundsQueryErrorKind.Bounds
Conjugation = BoundsQueryErrorKind.Conjugation
Hybridization = BoundsQueryErrorKind.Hybridization
Rings = BoundsQueryErrorKind.Rings
Topology = BoundsQueryErrorKind.Topology
Valence = BoundsQueryErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Topology': BoundsQueryErrorKind.Topology, 'Valence': BoundsQueryErrorKind.Valence, 'Rings': BoundsQueryErrorKind.Rings, 'Conjugation': BoundsQueryErrorKind.Conjugation, 'Hybridization': BoundsQueryErrorKind.Hybridization, 'Bounds': BoundsQueryErrorKind.Bounds})
values = mappingproxy({0: BoundsQueryErrorKind.Topology, 1: BoundsQueryErrorKind.Valence, 2: BoundsQueryErrorKind.Rings, 3: BoundsQueryErrorKind.Conjugation, 4: BoundsQueryErrorKind.Hybridization, 5: BoundsQueryErrorKind.Bounds})
exception cosmolkit.CanonicalRankError(*args, **kwargs)

Failure in the canonical_rank domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CanonicalRankError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (22)
property actual: int | None

Observed value reported by the native check. Applies to CanonicalRankError.AtomMaskLength, CanonicalRankError.BondMaskLength, CanonicalRankError.AtomSymbolLength, CanonicalRankError.BondSymbolLength. None when this payload is absent.

property actual_atoms: int | None

Readonly actual_atoms payload of the PreparedRingLength error variant; None for other variants.

property actual_bonds: int | None

Readonly actual_bonds payload of the PreparedRingLength error variant; None for other variants.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to CanonicalRankError.ComponentAtomOutOfRange, CanonicalRankError.PreparedValenceLength. None when this payload is absent.

property atom_index: int | None

Atom index involved in the native failure. Applies to CanonicalRankError.UnsignedRankOverflow, CanonicalRankError.InvalidPropertyKind, CanonicalRankError.ComponentAtomOutOfRange, CanonicalRankError.DuplicateComponentAtom, CanonicalRankError.PreparedValenceInvalid. None when this payload is absent.

property branch: str | None

Readonly branch payload of the ProtocolDebt error variant; None for other variants.

property carrier: int | None

Readonly carrier payload of the TemplateAttachmentRemap error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Required value reported by the native check. Applies to CanonicalRankError.AtomMaskLength, CanonicalRankError.BondMaskLength, CanonicalRankError.AtomSymbolLength, CanonicalRankError.BondSymbolLength. None when this payload is absent.

property expected_atoms: int | None

Readonly expected_atoms payload of the PreparedRingLength error variant; None for other variants.

property expected_bonds: int | None

Readonly expected_bonds payload of the PreparedRingLength error variant; None for other variants.

property explicit_len: int | None

Readonly explicit_len payload of the PreparedValenceLength error variant; None for other variants.

property implicit_len: int | None

Readonly implicit_len payload of the PreparedValenceLength error variant; None for other variants.

property kind: PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to CanonicalRankError.InvalidPropertyKind. None when this payload is absent.

Type:

{“role”

property property: str | None

Property name involved in the failure. Applies to CanonicalRankError.UnsignedRankOverflow, CanonicalRankError.InvalidPropertyKind. None when this payload is absent.

property reason: str | None

Readonly reason payload of the ProtocolDebt error variant; None for other variants.

property rings: RingFindingError | None

“error_payload”} Structured RingFindingError payload of CanonicalRankError.RingFinding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | TemplateAttachmentOrderError | MoleculePropertyError | TopologyValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of CanonicalRankError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property value: int | None

Readonly value payload of the UnsignedRankOverflow error variant; None for other variants.

property variant: CanonicalRankErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.CanonicalRankErrorKind(value)

Discriminants of CanonicalRankErrorKind.

Members: HanoiScratchTooSmall, StereoGroup, UnsignedRankOverflow, InvalidPropertyKind, ComponentAtomOutOfRange, DuplicateComponentAtom, AtomMaskLength, BondMaskLength, AtomSymbolLength, BondSymbolLength, PreparedValenceLength, PreparedValenceInvalid, PreparedRingLength, ProtocolDebt, TemplateAttachmentRemap, RingFinding, Valence, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (20)
AtomMaskLength = CanonicalRankErrorKind.AtomMaskLength
AtomSymbolLength = CanonicalRankErrorKind.AtomSymbolLength
BondMaskLength = CanonicalRankErrorKind.BondMaskLength
BondSymbolLength = CanonicalRankErrorKind.BondSymbolLength
ComponentAtomOutOfRange = CanonicalRankErrorKind.ComponentAtomOutOfRange
DuplicateComponentAtom = CanonicalRankErrorKind.DuplicateComponentAtom
HanoiScratchTooSmall = CanonicalRankErrorKind.HanoiScratchTooSmall
InvalidPropertyKind = CanonicalRankErrorKind.InvalidPropertyKind
PreparedRingLength = CanonicalRankErrorKind.PreparedRingLength
PreparedValenceInvalid = CanonicalRankErrorKind.PreparedValenceInvalid
PreparedValenceLength = CanonicalRankErrorKind.PreparedValenceLength
ProtocolDebt = CanonicalRankErrorKind.ProtocolDebt
RingFinding = CanonicalRankErrorKind.RingFinding
StereoGroup = CanonicalRankErrorKind.StereoGroup
TemplateAttachmentRemap = CanonicalRankErrorKind.TemplateAttachmentRemap
UnsignedRankOverflow = CanonicalRankErrorKind.UnsignedRankOverflow
Valence = CanonicalRankErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'HanoiScratchTooSmall': CanonicalRankErrorKind.HanoiScratchTooSmall, 'StereoGroup': CanonicalRankErrorKind.StereoGroup, 'UnsignedRankOverflow': CanonicalRankErrorKind.UnsignedRankOverflow, 'InvalidPropertyKind': CanonicalRankErrorKind.InvalidPropertyKind, 'ComponentAtomOutOfRange': CanonicalRankErrorKind.ComponentAtomOutOfRange, 'DuplicateComponentAtom': CanonicalRankErrorKind.DuplicateComponentAtom, 'AtomMaskLength': CanonicalRankErrorKind.AtomMaskLength, 'BondMaskLength': CanonicalRankErrorKind.BondMaskLength, 'AtomSymbolLength': CanonicalRankErrorKind.AtomSymbolLength, 'BondSymbolLength': CanonicalRankErrorKind.BondSymbolLength, 'PreparedValenceLength': CanonicalRankErrorKind.PreparedValenceLength, 'PreparedValenceInvalid': CanonicalRankErrorKind.PreparedValenceInvalid, 'PreparedRingLength': CanonicalRankErrorKind.PreparedRingLength, 'ProtocolDebt': CanonicalRankErrorKind.ProtocolDebt, 'TemplateAttachmentRemap': CanonicalRankErrorKind.TemplateAttachmentRemap, 'RingFinding': CanonicalRankErrorKind.RingFinding, 'Valence': CanonicalRankErrorKind.Valence})
values = mappingproxy({0: CanonicalRankErrorKind.HanoiScratchTooSmall, 1: CanonicalRankErrorKind.StereoGroup, 2: CanonicalRankErrorKind.UnsignedRankOverflow, 3: CanonicalRankErrorKind.InvalidPropertyKind, 4: CanonicalRankErrorKind.ComponentAtomOutOfRange, 5: CanonicalRankErrorKind.DuplicateComponentAtom, 6: CanonicalRankErrorKind.AtomMaskLength, 7: CanonicalRankErrorKind.BondMaskLength, 8: CanonicalRankErrorKind.AtomSymbolLength, 9: CanonicalRankErrorKind.BondSymbolLength, 10: CanonicalRankErrorKind.PreparedValenceLength, 11: CanonicalRankErrorKind.PreparedValenceInvalid, 12: CanonicalRankErrorKind.PreparedRingLength, 13: CanonicalRankErrorKind.ProtocolDebt, 14: CanonicalRankErrorKind.TemplateAttachmentRemap, 15: CanonicalRankErrorKind.RingFinding, 16: CanonicalRankErrorKind.Valence})
class cosmolkit.ChainKind(value)

Typed ChainKind values corresponding to the Rust enum.

Members: Protein, Dna, Rna, ProteinDnaComplex, ProteinRnaComplex, LigandOnly, WaterOnly, Mixed, Unknown, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (12)
Dna = ChainKind.Dna
LigandOnly = ChainKind.LigandOnly
Mixed = ChainKind.Mixed
Protein = ChainKind.Protein
ProteinDnaComplex = ChainKind.ProteinDnaComplex
ProteinRnaComplex = ChainKind.ProteinRnaComplex
Rna = ChainKind.Rna
Unknown = ChainKind.Unknown
WaterOnly = ChainKind.WaterOnly
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Protein': ChainKind.Protein, 'Dna': ChainKind.Dna, 'Rna': ChainKind.Rna, 'ProteinDnaComplex': ChainKind.ProteinDnaComplex, 'ProteinRnaComplex': ChainKind.ProteinRnaComplex, 'LigandOnly': ChainKind.LigandOnly, 'WaterOnly': ChainKind.WaterOnly, 'Mixed': ChainKind.Mixed, 'Unknown': ChainKind.Unknown})
values = mappingproxy({0: ChainKind.Protein, 1: ChainKind.Dna, 2: ChainKind.Rna, 3: ChainKind.ProteinDnaComplex, 4: ChainKind.ProteinRnaComplex, 5: ChainKind.LigandOnly, 6: ChainKind.WaterOnly, 7: ChainKind.Mixed, 8: ChainKind.Unknown})
class cosmolkit.ChainSourceIds(auth_chain_id, label_asym_id)

Author and label chain identifiers retained from structural coordinate files.

Members (2)
auth_chain_id: str | None

Author-provided chain identifier, or None if absent.

label_asym_id: str | None

mmCIF label_asym_id identifying the asymmetric unit chain, or None.

exception cosmolkit.ChemCompAtomError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ChemCompAtomError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property column: int | None

Readonly column payload of the MissingValue error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property row: int | None

Row reported by the native failure. Applies to ChemCompAtomError.MissingValue, ChemCompAtomError.NameOutsideCanonicalBoundary, ChemCompAtomError.ChargeOutsideSourceDefinedRange. None when this payload is absent.

property source: CifReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to ChemCompAtomError.NameOutsideCanonicalBoundary, ChemCompAtomError.ChargeOutsideSourceDefinedRange. None when this payload is absent.

property variant: ChemCompAtomErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ChemCompAtomErrorKind(value)

Discriminants of ChemCompAtomErrorKind.

Members: MissingValue, NameOutsideCanonicalBoundary, ChargeOutsideSourceDefinedRange, Number, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
ChargeOutsideSourceDefinedRange = ChemCompAtomErrorKind.ChargeOutsideSourceDefinedRange
MissingValue = ChemCompAtomErrorKind.MissingValue
NameOutsideCanonicalBoundary = ChemCompAtomErrorKind.NameOutsideCanonicalBoundary
Number = ChemCompAtomErrorKind.Number
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingValue': ChemCompAtomErrorKind.MissingValue, 'NameOutsideCanonicalBoundary': ChemCompAtomErrorKind.NameOutsideCanonicalBoundary, 'ChargeOutsideSourceDefinedRange': ChemCompAtomErrorKind.ChargeOutsideSourceDefinedRange, 'Number': ChemCompAtomErrorKind.Number})
values = mappingproxy({0: ChemCompAtomErrorKind.MissingValue, 1: ChemCompAtomErrorKind.NameOutsideCanonicalBoundary, 2: ChemCompAtomErrorKind.ChargeOutsideSourceDefinedRange, 3: ChemCompAtomErrorKind.Number})
exception cosmolkit.ChemCompModelError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ChemCompModelError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: CifReadError | ChemCompAtomError | BioStructureError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to ChemCompModelError.ResidueName. None when this payload is absent.

property variant: ChemCompModelErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ChemCompModelErrorKind(value)

Discriminants of ChemCompModelErrorKind.

Members: NotChemComp, Table, Atom, Hierarchy, ResidueName, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
Atom = ChemCompModelErrorKind.Atom
Hierarchy = ChemCompModelErrorKind.Hierarchy
NotChemComp = ChemCompModelErrorKind.NotChemComp
ResidueName = ChemCompModelErrorKind.ResidueName
Table = ChemCompModelErrorKind.Table
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NotChemComp': ChemCompModelErrorKind.NotChemComp, 'Table': ChemCompModelErrorKind.Table, 'Atom': ChemCompModelErrorKind.Atom, 'Hierarchy': ChemCompModelErrorKind.Hierarchy, 'ResidueName': ChemCompModelErrorKind.ResidueName})
values = mappingproxy({0: ChemCompModelErrorKind.NotChemComp, 1: ChemCompModelErrorKind.Table, 2: ChemCompModelErrorKind.Atom, 3: ChemCompModelErrorKind.Hierarchy, 4: ChemCompModelErrorKind.ResidueName})
class cosmolkit.ChemistryProblem(operation, error)

One sanitization-stage diagnostic with its concrete native error.

Members (2)
error: ChemistryProblemError

Concrete structured error associated with this chemistry problem.

operation: SanitizeStage

Sanitization stage that reported this chemistry problem.

exception cosmolkit.ChemistryProblemError(*args, **kwargs)

Failure in the sanitize domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ChemistryProblemError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property kekulize: KekulizeError | None

“error_payload”} Structured KekulizeError payload of ChemistryProblemError.Kekulize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: TopologyValidationError | MappingValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of ChemistryProblemError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: ChemistryProblemErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ChemistryProblemErrorKind(value)

Discriminants of ChemistryProblemErrorKind.

Members: Valence, Kekulize, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Kekulize = ChemistryProblemErrorKind.Kekulize
Valence = ChemistryProblemErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Valence': ChemistryProblemErrorKind.Valence, 'Kekulize': ChemistryProblemErrorKind.Kekulize})
values = mappingproxy({0: ChemistryProblemErrorKind.Valence, 1: ChemistryProblemErrorKind.Kekulize})
class cosmolkit.ChemistryProblemReport(problems=None)

Ordered chemistry problems reported by the non-throwing native detector.

Members (1)
problems: list[ChemistryProblem]

Independent list of chemistry problems in native detection order.

class cosmolkit.ChiralTag(value)

Typed ChiralTag values corresponding to the Rust enum.

Members: Unspecified, TetrahedralCw, TetrahedralCcw, Other, Tetrahedral, Allene, SquarePlanar, TrigonalBipyramidal, Octahedral, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (21)
Allene = ChiralTag.Allene
CHI_ALLENE = ChiralTag.Allene
CHI_OCTAHEDRAL = ChiralTag.Octahedral
CHI_OTHER = ChiralTag.Other
CHI_SQUAREPLANAR = ChiralTag.SquarePlanar
CHI_TETRAHEDRAL = ChiralTag.Tetrahedral
CHI_TETRAHEDRAL_CCW = ChiralTag.TetrahedralCcw
CHI_TETRAHEDRAL_CW = ChiralTag.TetrahedralCw
CHI_TRIGONALBIPYRAMIDAL = ChiralTag.TrigonalBipyramidal
CHI_UNSPECIFIED = ChiralTag.Unspecified
Octahedral = ChiralTag.Octahedral
Other = ChiralTag.Other
SquarePlanar = ChiralTag.SquarePlanar
Tetrahedral = ChiralTag.Tetrahedral
TetrahedralCcw = ChiralTag.TetrahedralCcw
TetrahedralCw = ChiralTag.TetrahedralCw
TrigonalBipyramidal = ChiralTag.TrigonalBipyramidal
Unspecified = ChiralTag.Unspecified
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unspecified': ChiralTag.Unspecified, 'CHI_UNSPECIFIED': ChiralTag.Unspecified, 'TetrahedralCw': ChiralTag.TetrahedralCw, 'CHI_TETRAHEDRAL_CW': ChiralTag.TetrahedralCw, 'TetrahedralCcw': ChiralTag.TetrahedralCcw, 'CHI_TETRAHEDRAL_CCW': ChiralTag.TetrahedralCcw, 'Other': ChiralTag.Other, 'CHI_OTHER': ChiralTag.Other, 'Tetrahedral': ChiralTag.Tetrahedral, 'CHI_TETRAHEDRAL': ChiralTag.Tetrahedral, 'Allene': ChiralTag.Allene, 'CHI_ALLENE': ChiralTag.Allene, 'SquarePlanar': ChiralTag.SquarePlanar, 'CHI_SQUAREPLANAR': ChiralTag.SquarePlanar, 'TrigonalBipyramidal': ChiralTag.TrigonalBipyramidal, 'CHI_TRIGONALBIPYRAMIDAL': ChiralTag.TrigonalBipyramidal, 'Octahedral': ChiralTag.Octahedral, 'CHI_OCTAHEDRAL': ChiralTag.Octahedral})
values = mappingproxy({0: ChiralTag.Unspecified, 1: ChiralTag.TetrahedralCw, 2: ChiralTag.TetrahedralCcw, 3: ChiralTag.Other, 4: ChiralTag.Tetrahedral, 5: ChiralTag.Allene, 6: ChiralTag.SquarePlanar, 7: ChiralTag.TrigonalBipyramidal, 8: ChiralTag.Octahedral})
exception cosmolkit.CifReadError(*args, **kwargs)

CifReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property column: int

Column reported by the CIF parser.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property kind: CifReadErrorKind

“error_payload”} Native CIF parsing error category.

Type:

{“role”

property line: int

Line reported by the CIF parser.

property message: str

Original CIF parser explanation.

property source: str

Source name associated with the CIF input, not an exception cause.

class cosmolkit.CifReadErrorKind(value)

Typed CifReadErrorKind values corresponding to the Rust enum.

Members: Syntax, MissingValue, DuplicateName, InvalidLoop, InvalidValue, OutOfRange, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (9)
DuplicateName = CifReadErrorKind.DuplicateName
InvalidLoop = CifReadErrorKind.InvalidLoop
InvalidValue = CifReadErrorKind.InvalidValue
MissingValue = CifReadErrorKind.MissingValue
OutOfRange = CifReadErrorKind.OutOfRange
Syntax = CifReadErrorKind.Syntax
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Syntax': CifReadErrorKind.Syntax, 'MissingValue': CifReadErrorKind.MissingValue, 'DuplicateName': CifReadErrorKind.DuplicateName, 'InvalidLoop': CifReadErrorKind.InvalidLoop, 'InvalidValue': CifReadErrorKind.InvalidValue, 'OutOfRange': CifReadErrorKind.OutOfRange})
values = mappingproxy({0: CifReadErrorKind.Syntax, 1: CifReadErrorKind.MissingValue, 2: CifReadErrorKind.DuplicateName, 3: CifReadErrorKind.InvalidLoop, 4: CifReadErrorKind.InvalidValue, 5: CifReadErrorKind.OutOfRange})
class cosmolkit.CipDescriptor(value)

Typed CipDescriptor values corresponding to the Rust enum.

Members: R, S, LowerR, LowerS, E, Z, LowerE, LowerZ, M, P, LowerM, LowerP, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (22)
E = CipDescriptor.E
LowerE = CipDescriptor.LowerE
LowerM = CipDescriptor.LowerM
LowerP = CipDescriptor.LowerP
LowerR = CipDescriptor.LowerR
LowerS = CipDescriptor.LowerS
LowerZ = CipDescriptor.LowerZ
M = CipDescriptor.M
P = CipDescriptor.P
R = CipDescriptor.R
S = CipDescriptor.S
Z = CipDescriptor.Z
as_str() → str

Canonical textual CIP descriptor, retaining case distinctions such as R versus r.

e = CipDescriptor.LowerE
m = CipDescriptor.LowerM
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'R': CipDescriptor.R, 'S': CipDescriptor.S, 'LowerR': CipDescriptor.LowerR, 'r': CipDescriptor.LowerR, 'LowerS': CipDescriptor.LowerS, 's': CipDescriptor.LowerS, 'E': CipDescriptor.E, 'Z': CipDescriptor.Z, 'LowerE': CipDescriptor.LowerE, 'e': CipDescriptor.LowerE, 'LowerZ': CipDescriptor.LowerZ, 'z': CipDescriptor.LowerZ, 'M': CipDescriptor.M, 'P': CipDescriptor.P, 'LowerM': CipDescriptor.LowerM, 'm': CipDescriptor.LowerM, 'LowerP': CipDescriptor.LowerP, 'p': CipDescriptor.LowerP})
p = CipDescriptor.LowerP
r = CipDescriptor.LowerR
s = CipDescriptor.LowerS
values = mappingproxy({0: CipDescriptor.R, 1: CipDescriptor.S, 2: CipDescriptor.LowerR, 3: CipDescriptor.LowerS, 4: CipDescriptor.E, 5: CipDescriptor.Z, 6: CipDescriptor.LowerE, 7: CipDescriptor.LowerZ, 8: CipDescriptor.M, 9: CipDescriptor.P, 10: CipDescriptor.LowerM, 11: CipDescriptor.LowerP})
z = CipDescriptor.LowerZ
exception cosmolkit.CipDescriptorError(*args, **kwargs)

CipDescriptorError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property detail: str | None

Explanation of an invalid neighbor-order encoding, or None for other variants.

property domain: str

Error domain for CIP descriptor and neighbor-order access.

property property_error: PropertyValueError | None

“error_payload”} Underlying property-type failure payload, or None. This payload does not invent an additional exception cause.

Type:

{“role”

property value: str | None

Stored text that failed descriptor or neighbor-order parsing, or None for a property-type error.

property variant: CipDescriptorErrorKind

Native CIP error category determining which payload fields are present.

class cosmolkit.CipDescriptorErrorKind(value)

Discriminants of CipDescriptorErrorKind.

Members: InvalidNeighborOrder, Property, InvalidStoredDescriptor, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
InvalidNeighborOrder = CipDescriptorErrorKind.InvalidNeighborOrder
InvalidStoredDescriptor = CipDescriptorErrorKind.InvalidStoredDescriptor
Property = CipDescriptorErrorKind.Property
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidNeighborOrder': CipDescriptorErrorKind.InvalidNeighborOrder, 'Property': CipDescriptorErrorKind.Property, 'InvalidStoredDescriptor': CipDescriptorErrorKind.InvalidStoredDescriptor})
values = mappingproxy({0: CipDescriptorErrorKind.InvalidNeighborOrder, 1: CipDescriptorErrorKind.Property, 2: CipDescriptorErrorKind.InvalidStoredDescriptor})
exception cosmolkit.CipLabelerError(*args, **kwargs)

Failure in the cip domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CipLabelerError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (25)
property atom: int | None

Atom identifier implicated in the failure. Applies to CipLabelerError.UnsignedPropertyRead, CipLabelerError.InvalidPropertyKind, CipLabelerError.BondNotIncident, CipLabelerError.UnsupportedConfiguration, CipLabelerError.AtomProperty. None when this payload is absent.

property atom_count: int | None

Readonly atom_count payload of the AtomIndexOutOfRange error variant; None for other variants.

property atropisomer: AtropisomerError | None

“error_payload”} Structured AtropisomerError payload of CipLabelerError.Atropisomer; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property bond: int | None

Bond identifier implicated in the failure. Applies to CipLabelerError.BondNotIncident, CipLabelerError.BondValue. None when this payload is absent.

property bond_count: int | None

Readonly bond_count payload of the BondIndexOutOfRange error variant; None for other variants.

property detail: str | None

Readonly detail payload of the InvalidInternalState error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property double_stereo: DoubleBondStereoError | None

“error_payload”} Structured DoubleBondStereoError payload of CipLabelerError.DoubleStereo; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property edge: int | None

Readonly edge payload of the EdgeEndpointMismatch error variant; None for other variants.

property index: int | None

Index reported by the failing native check. Applies to CipLabelerError.AtomIndexOutOfRange, CipLabelerError.BondIndexOutOfRange, CipLabelerError.SourceIndexWidthExceeded. None when this payload is absent.

property kekulize: KekulizeError | None

“error_payload”} Structured KekulizeError payload of CipLabelerError.Kekulize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property kind: PropertyValueKind | str | None

“error_payload”} Native failure-specific category or value kind. Applies to CipLabelerError.InvalidPropertyKind, CipLabelerError.SourceIndexWidthExceeded. None when this payload is absent.

Type:

{“role”

property limit: int | None

Readonly limit payload of the TooManyNodes error variant; None for other variants.

property molecule_property: MoleculePropertyError | None

“error_payload”} Structured MoleculePropertyError payload of CipLabelerError.MoleculeProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property node: int | None

Readonly node payload of the EdgeEndpointMismatch error variant; None for other variants.

property order: BondOrder | None

Readonly order payload of the NonIntegerBondOrder error variant; None for other variants.

property periodic_table: PeriodicTableError | None

“error_payload”} Structured PeriodicTableError payload of CipLabelerError.PeriodicTable; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property property: str | None

Property name involved in the failure. Applies to CipLabelerError.UnsignedPropertyRead, CipLabelerError.InvalidPropertyKind. None when this payload is absent.

property ring_finding: RingFindingError | None

“error_payload”} Structured RingFindingError payload of CipLabelerError.RingFinding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | StereoOrderError | AtomPropertyError | PropertyIntReadError | TemplateAttachmentOrderError | MappingValidationError | PropertyUIntReadError | CanonicalRankError | DoubleBondStereoError | MoleculePropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property tag: ChiralTag | None

Readonly tag payload of the UnsupportedConfiguration error variant; None for other variants.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of CipLabelerError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of CipLabelerError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: CipLabelerErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.CipLabelerErrorKind(value)

Discriminants of CipLabelerErrorKind.

Members: UnsignedPropertyRead, InvalidPropertyKind, AtomIndexOutOfRange, BondIndexOutOfRange, SourceIndexWidthExceeded, BondNotIncident, NonIntegerBondOrder, EdgeEndpointMismatch, TooManyNodes, MaxIterationsExceeded, ControlCCaught, UnexpectedUpEdgeOrdering, NoSequenceRuleProvided, EmptyPairListReference, DescriptorListLengthMismatch, InvalidStereoDescriptor, SubstituentsShouldBeTopologicallyEquivalent, SomethingUnexpected, Rule4bInstanceNotInRuleSet, Rule5NewInstanceNotInRuleSet, ParityVectorsMustHaveSize4, EmptyConfigurationFoci, BadTetrahedralConfig, TetrahedralConfigurationMustHave4Carriers, DescriptorNotSupportedForAtoms, InvalidAtomDescriptor, CarrierMismatch, BadSp2BondFoci, BadSp2BondConfig, IncorrectNumberOfStereoAtoms, DescriptorNotSupportedForDoubleBonds, InvalidBondDescriptor, BadAtropisomerBondFoci, BadAtropisomerBondConfig, DescriptorNotSupportedForAtropisomerBonds, InvalidInternalState, UnsupportedConfiguration, InvalidTopology, AtomProperty, BondValue, MoleculeProperty, Atropisomer, DoubleStereo, RingFinding, Valence, Kekulize, PeriodicTable, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (50)
AtomIndexOutOfRange = CipLabelerErrorKind.AtomIndexOutOfRange
AtomProperty = CipLabelerErrorKind.AtomProperty
Atropisomer = CipLabelerErrorKind.Atropisomer
BadAtropisomerBondConfig = CipLabelerErrorKind.BadAtropisomerBondConfig
BadAtropisomerBondFoci = CipLabelerErrorKind.BadAtropisomerBondFoci
BadSp2BondConfig = CipLabelerErrorKind.BadSp2BondConfig
BadSp2BondFoci = CipLabelerErrorKind.BadSp2BondFoci
BadTetrahedralConfig = CipLabelerErrorKind.BadTetrahedralConfig
BondIndexOutOfRange = CipLabelerErrorKind.BondIndexOutOfRange
BondNotIncident = CipLabelerErrorKind.BondNotIncident
BondValue = CipLabelerErrorKind.BondValue
CarrierMismatch = CipLabelerErrorKind.CarrierMismatch
ControlCCaught = CipLabelerErrorKind.ControlCCaught
DescriptorListLengthMismatch = CipLabelerErrorKind.DescriptorListLengthMismatch
DescriptorNotSupportedForAtoms = CipLabelerErrorKind.DescriptorNotSupportedForAtoms
DescriptorNotSupportedForAtropisomerBonds = CipLabelerErrorKind.DescriptorNotSupportedForAtropisomerBonds
DescriptorNotSupportedForDoubleBonds = CipLabelerErrorKind.DescriptorNotSupportedForDoubleBonds
DoubleStereo = CipLabelerErrorKind.DoubleStereo
EdgeEndpointMismatch = CipLabelerErrorKind.EdgeEndpointMismatch
EmptyConfigurationFoci = CipLabelerErrorKind.EmptyConfigurationFoci
EmptyPairListReference = CipLabelerErrorKind.EmptyPairListReference
IncorrectNumberOfStereoAtoms = CipLabelerErrorKind.IncorrectNumberOfStereoAtoms
InvalidAtomDescriptor = CipLabelerErrorKind.InvalidAtomDescriptor
InvalidBondDescriptor = CipLabelerErrorKind.InvalidBondDescriptor
InvalidInternalState = CipLabelerErrorKind.InvalidInternalState
InvalidPropertyKind = CipLabelerErrorKind.InvalidPropertyKind
InvalidStereoDescriptor = CipLabelerErrorKind.InvalidStereoDescriptor
InvalidTopology = CipLabelerErrorKind.InvalidTopology
Kekulize = CipLabelerErrorKind.Kekulize
MaxIterationsExceeded = CipLabelerErrorKind.MaxIterationsExceeded
MoleculeProperty = CipLabelerErrorKind.MoleculeProperty
NoSequenceRuleProvided = CipLabelerErrorKind.NoSequenceRuleProvided
NonIntegerBondOrder = CipLabelerErrorKind.NonIntegerBondOrder
ParityVectorsMustHaveSize4 = CipLabelerErrorKind.ParityVectorsMustHaveSize4
PeriodicTable = CipLabelerErrorKind.PeriodicTable
RingFinding = CipLabelerErrorKind.RingFinding
Rule4bInstanceNotInRuleSet = CipLabelerErrorKind.Rule4bInstanceNotInRuleSet
Rule5NewInstanceNotInRuleSet = CipLabelerErrorKind.Rule5NewInstanceNotInRuleSet
SomethingUnexpected = CipLabelerErrorKind.SomethingUnexpected
SourceIndexWidthExceeded = CipLabelerErrorKind.SourceIndexWidthExceeded
SubstituentsShouldBeTopologicallyEquivalent = CipLabelerErrorKind.SubstituentsShouldBeTopologicallyEquivalent
TetrahedralConfigurationMustHave4Carriers = CipLabelerErrorKind.TetrahedralConfigurationMustHave4Carriers
TooManyNodes = CipLabelerErrorKind.TooManyNodes
UnexpectedUpEdgeOrdering = CipLabelerErrorKind.UnexpectedUpEdgeOrdering
UnsignedPropertyRead = CipLabelerErrorKind.UnsignedPropertyRead
UnsupportedConfiguration = CipLabelerErrorKind.UnsupportedConfiguration
Valence = CipLabelerErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnsignedPropertyRead': CipLabelerErrorKind.UnsignedPropertyRead, 'InvalidPropertyKind': CipLabelerErrorKind.InvalidPropertyKind, 'AtomIndexOutOfRange': CipLabelerErrorKind.AtomIndexOutOfRange, 'BondIndexOutOfRange': CipLabelerErrorKind.BondIndexOutOfRange, 'SourceIndexWidthExceeded': CipLabelerErrorKind.SourceIndexWidthExceeded, 'BondNotIncident': CipLabelerErrorKind.BondNotIncident, 'NonIntegerBondOrder': CipLabelerErrorKind.NonIntegerBondOrder, 'EdgeEndpointMismatch': CipLabelerErrorKind.EdgeEndpointMismatch, 'TooManyNodes': CipLabelerErrorKind.TooManyNodes, 'MaxIterationsExceeded': CipLabelerErrorKind.MaxIterationsExceeded, 'ControlCCaught': CipLabelerErrorKind.ControlCCaught, 'UnexpectedUpEdgeOrdering': CipLabelerErrorKind.UnexpectedUpEdgeOrdering, 'NoSequenceRuleProvided': CipLabelerErrorKind.NoSequenceRuleProvided, 'EmptyPairListReference': CipLabelerErrorKind.EmptyPairListReference, 'DescriptorListLengthMismatch': CipLabelerErrorKind.DescriptorListLengthMismatch, 'InvalidStereoDescriptor': CipLabelerErrorKind.InvalidStereoDescriptor, 'SubstituentsShouldBeTopologicallyEquivalent': CipLabelerErrorKind.SubstituentsShouldBeTopologicallyEquivalent, 'SomethingUnexpected': CipLabelerErrorKind.SomethingUnexpected, 'Rule4bInstanceNotInRuleSet': CipLabelerErrorKind.Rule4bInstanceNotInRuleSet, 'Rule5NewInstanceNotInRuleSet': CipLabelerErrorKind.Rule5NewInstanceNotInRuleSet, 'ParityVectorsMustHaveSize4': CipLabelerErrorKind.ParityVectorsMustHaveSize4, 'EmptyConfigurationFoci': CipLabelerErrorKind.EmptyConfigurationFoci, 'BadTetrahedralConfig': CipLabelerErrorKind.BadTetrahedralConfig, 'TetrahedralConfigurationMustHave4Carriers': CipLabelerErrorKind.TetrahedralConfigurationMustHave4Carriers, 'DescriptorNotSupportedForAtoms': CipLabelerErrorKind.DescriptorNotSupportedForAtoms, 'InvalidAtomDescriptor': CipLabelerErrorKind.InvalidAtomDescriptor, 'CarrierMismatch': CipLabelerErrorKind.CarrierMismatch, 'BadSp2BondFoci': CipLabelerErrorKind.BadSp2BondFoci, 'BadSp2BondConfig': CipLabelerErrorKind.BadSp2BondConfig, 'IncorrectNumberOfStereoAtoms': CipLabelerErrorKind.IncorrectNumberOfStereoAtoms, 'DescriptorNotSupportedForDoubleBonds': CipLabelerErrorKind.DescriptorNotSupportedForDoubleBonds, 'InvalidBondDescriptor': CipLabelerErrorKind.InvalidBondDescriptor, 'BadAtropisomerBondFoci': CipLabelerErrorKind.BadAtropisomerBondFoci, 'BadAtropisomerBondConfig': CipLabelerErrorKind.BadAtropisomerBondConfig, 'DescriptorNotSupportedForAtropisomerBonds': CipLabelerErrorKind.DescriptorNotSupportedForAtropisomerBonds, 'InvalidInternalState': CipLabelerErrorKind.InvalidInternalState, 'UnsupportedConfiguration': CipLabelerErrorKind.UnsupportedConfiguration, 'InvalidTopology': CipLabelerErrorKind.InvalidTopology, 'AtomProperty': CipLabelerErrorKind.AtomProperty, 'BondValue': CipLabelerErrorKind.BondValue, 'MoleculeProperty': CipLabelerErrorKind.MoleculeProperty, 'Atropisomer': CipLabelerErrorKind.Atropisomer, 'DoubleStereo': CipLabelerErrorKind.DoubleStereo, 'RingFinding': CipLabelerErrorKind.RingFinding, 'Valence': CipLabelerErrorKind.Valence, 'Kekulize': CipLabelerErrorKind.Kekulize, 'PeriodicTable': CipLabelerErrorKind.PeriodicTable})
values = mappingproxy({0: CipLabelerErrorKind.UnsignedPropertyRead, 1: CipLabelerErrorKind.InvalidPropertyKind, 2: CipLabelerErrorKind.AtomIndexOutOfRange, 3: CipLabelerErrorKind.BondIndexOutOfRange, 4: CipLabelerErrorKind.SourceIndexWidthExceeded, 5: CipLabelerErrorKind.BondNotIncident, 6: CipLabelerErrorKind.NonIntegerBondOrder, 7: CipLabelerErrorKind.EdgeEndpointMismatch, 8: CipLabelerErrorKind.TooManyNodes, 9: CipLabelerErrorKind.MaxIterationsExceeded, 10: CipLabelerErrorKind.ControlCCaught, 11: CipLabelerErrorKind.UnexpectedUpEdgeOrdering, 12: CipLabelerErrorKind.NoSequenceRuleProvided, 13: CipLabelerErrorKind.EmptyPairListReference, 14: CipLabelerErrorKind.DescriptorListLengthMismatch, 15: CipLabelerErrorKind.InvalidStereoDescriptor, 16: CipLabelerErrorKind.SubstituentsShouldBeTopologicallyEquivalent, 17: CipLabelerErrorKind.SomethingUnexpected, 18: CipLabelerErrorKind.Rule4bInstanceNotInRuleSet, 19: CipLabelerErrorKind.Rule5NewInstanceNotInRuleSet, 20: CipLabelerErrorKind.ParityVectorsMustHaveSize4, 21: CipLabelerErrorKind.EmptyConfigurationFoci, 22: CipLabelerErrorKind.BadTetrahedralConfig, 23: CipLabelerErrorKind.TetrahedralConfigurationMustHave4Carriers, 24: CipLabelerErrorKind.DescriptorNotSupportedForAtoms, 25: CipLabelerErrorKind.InvalidAtomDescriptor, 26: CipLabelerErrorKind.CarrierMismatch, 27: CipLabelerErrorKind.BadSp2BondFoci, 28: CipLabelerErrorKind.BadSp2BondConfig, 29: CipLabelerErrorKind.IncorrectNumberOfStereoAtoms, 30: CipLabelerErrorKind.DescriptorNotSupportedForDoubleBonds, 31: CipLabelerErrorKind.InvalidBondDescriptor, 32: CipLabelerErrorKind.BadAtropisomerBondFoci, 33: CipLabelerErrorKind.BadAtropisomerBondConfig, 34: CipLabelerErrorKind.DescriptorNotSupportedForAtropisomerBonds, 35: CipLabelerErrorKind.InvalidInternalState, 36: CipLabelerErrorKind.UnsupportedConfiguration, 37: CipLabelerErrorKind.InvalidTopology, 38: CipLabelerErrorKind.AtomProperty, 39: CipLabelerErrorKind.BondValue, 40: CipLabelerErrorKind.MoleculeProperty, 41: CipLabelerErrorKind.Atropisomer, 42: CipLabelerErrorKind.DoubleStereo, 43: CipLabelerErrorKind.RingFinding, 44: CipLabelerErrorKind.Valence, 45: CipLabelerErrorKind.Kekulize, 46: CipLabelerErrorKind.PeriodicTable})
class cosmolkit.CipLabelOptions(*, atoms=Ellipsis, bonds=Ellipsis, max_recursive_iterations=Ellipsis)

Atom/bond selections and recursion limit for CIP assignment.

Members (3)
atoms: tuple[int, ...] | None

Atom identifiers to label, or None for all eligible atoms.

bonds: tuple[int, ...] | None

Bond identifiers to label, or None for all eligible bonds.

max_recursive_iterations: int

Maximum recursive CIP iterations; zero leaves the native limit unrestricted.

exception cosmolkit.CipRankError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CipRankError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (16)
property actual: int | None

Observed value reported by the native check. Applies to CipRankError.ValenceRowCount, CipRankError.InvariantCount. None when this payload is absent.

property atom: int | None

Atom identifier implicated in the failure. Applies to CipRankError.NegativeImplicitHydrogen, CipRankError.AtomMapOutOfRange, CipRankError.InvariantOutOfRange, CipRankError.TooManyNeighbors. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to CipRankError.ValenceRowCount, CipRankError.InvariantCount. None when this payload is absent.

property bond: int | None

Readonly bond payload of the UnsupportedBondOrder error variant; None for other variants.

property degree: int | None

Readonly degree payload of the TooManyNeighbors error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property field: str | None

Readonly field payload of the ValenceRowCount error variant; None for other variants.

property map_number: int | None

Readonly map_number payload of the AtomMapOutOfRange error variant; None for other variants.

property maximum_supported: int | None

Readonly maximum_supported payload of the TooManyNeighbors error variant; None for other variants.

property order: BondOrder | None

Readonly order payload of the UnsupportedBondOrder error variant; None for other variants.

property query_state: QueryStateError | None

“error_payload”} Structured QueryStateError payload of CipRankError.InvalidQueryState; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: MappingValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of CipRankError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property value: int | None

Value rejected or reported by the native operation. Applies to CipRankError.NegativeImplicitHydrogen, CipRankError.InvariantOutOfRange. None when this payload is absent.

property variant: CipRankErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.CipRankErrorKind(value)

Discriminants of CipRankErrorKind.

Members: InvalidTopology, InvalidQueryState, ValenceRowCount, NegativeImplicitHydrogen, AtomMapOutOfRange, InvariantCount, InvariantOutOfRange, TooManyNeighbors, UnsupportedBondOrder, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
AtomMapOutOfRange = CipRankErrorKind.AtomMapOutOfRange
InvalidQueryState = CipRankErrorKind.InvalidQueryState
InvalidTopology = CipRankErrorKind.InvalidTopology
InvariantCount = CipRankErrorKind.InvariantCount
InvariantOutOfRange = CipRankErrorKind.InvariantOutOfRange
NegativeImplicitHydrogen = CipRankErrorKind.NegativeImplicitHydrogen
TooManyNeighbors = CipRankErrorKind.TooManyNeighbors
UnsupportedBondOrder = CipRankErrorKind.UnsupportedBondOrder
ValenceRowCount = CipRankErrorKind.ValenceRowCount
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': CipRankErrorKind.InvalidTopology, 'InvalidQueryState': CipRankErrorKind.InvalidQueryState, 'ValenceRowCount': CipRankErrorKind.ValenceRowCount, 'NegativeImplicitHydrogen': CipRankErrorKind.NegativeImplicitHydrogen, 'AtomMapOutOfRange': CipRankErrorKind.AtomMapOutOfRange, 'InvariantCount': CipRankErrorKind.InvariantCount, 'InvariantOutOfRange': CipRankErrorKind.InvariantOutOfRange, 'TooManyNeighbors': CipRankErrorKind.TooManyNeighbors, 'UnsupportedBondOrder': CipRankErrorKind.UnsupportedBondOrder})
values = mappingproxy({0: CipRankErrorKind.InvalidTopology, 1: CipRankErrorKind.InvalidQueryState, 2: CipRankErrorKind.ValenceRowCount, 3: CipRankErrorKind.NegativeImplicitHydrogen, 4: CipRankErrorKind.AtomMapOutOfRange, 5: CipRankErrorKind.InvariantCount, 6: CipRankErrorKind.InvariantOutOfRange, 7: CipRankErrorKind.TooManyNeighbors, 8: CipRankErrorKind.UnsupportedBondOrder})
exception cosmolkit.CleanupError(*args, **kwargs)

Failure in the cleanup domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CleanupError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property canonical_rank: CanonicalRankError | None

“error_payload”} Structured CanonicalRankError payload of CleanupError.CanonicalRank; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: TopologyValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of CleanupError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of CleanupError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: CleanupErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.CleanupErrorKind(value)

Discriminants of CleanupErrorKind.

Members: InvalidTopology, Valence, CanonicalRank, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
CanonicalRank = CleanupErrorKind.CanonicalRank
InvalidTopology = CleanupErrorKind.InvalidTopology
Valence = CleanupErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': CleanupErrorKind.InvalidTopology, 'Valence': CleanupErrorKind.Valence, 'CanonicalRank': CleanupErrorKind.CanonicalRank})
values = mappingproxy({0: CleanupErrorKind.InvalidTopology, 1: CleanupErrorKind.Valence, 2: CleanupErrorKind.CanonicalRank})
class cosmolkit.CompiledQuery

Compiled native substructure query with its graph and planned atom order.

Members (4)
atom_order: list[int]

Query atom visitation order selected by the native query compiler.

num_atoms: int

Number of query atoms.

num_bonds: int

Number of query bonds.

query: QueryGraph

Query graph retained by the compiled matcher.

class cosmolkit.Conformer2D(id, coordinates)

Owned 2D coordinate rows with a conformer identifier. Reading coordinates returns an independent NumPy array, not mutable molecular storage.

Members (2)
coordinates: numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]

[“numpy”], “type”: “numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]”} Return an independent float64 array of shape (num_atoms, 2), in atom-index order.

Type:

{“role”

Type:

“return_type”, “imports”

id: int

Identifier associated with these coordinate rows.

class cosmolkit.Conformer3D(id, coordinates, is_3d)

Owned three-component coordinate rows and their explicit dimensionality flag. A false is_3d flag describes planar data stored as three-component rows.

Members (3)
coordinates: numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]

[“numpy”], “type”: “numpy.ndarray[tuple[int, int], numpy.dtype[numpy.float64]]”} Return an independent float64 array of shape (num_atoms, 3), in atom-index order.

Type:

{“role”

Type:

“return_type”, “imports”

id: int

Identifier associated with these coordinate rows.

is_3d: bool

Whether these rows are marked as three-dimensional rather than planar.

class cosmolkit.ConformerAlignmentParameters(*, atom_indices=Ellipsis, conformer_ids=Ellipsis, weights=Ellipsis, reflect=Ellipsis, max_iterations=Ellipsis)

Atom selection, conformer selection and numerical settings for aligning stored conformers.

Members (6)
atom_indices: tuple[int, ...] | None

Optional zero-based atom indices used by alignment.

conformer_ids: tuple[int, ...] | None

Optional stored conformer identifiers to align.

max_iterations: int

Maximum number of iterations in the alignment solver.

static new(atom_indices=Ellipsis, conformer_ids=Ellipsis, weights=Ellipsis, reflect=Ellipsis, max_iterations=Ellipsis) → ConformerAlignmentParameters

Create an independent configuration through the native constructor using the supplied field values.

reflect: bool

Allow reflection as part of the alignment transform.

weights: tuple[float, ...] | None

Optional alignment weights in selected-atom order.

class cosmolkit.ConformerAlignmentReport(rmsds)

Ordered RMSD results returned by native conformer alignment.

Members (1)
rmsds: list[float]

RMSD values in the native alignment result order.

exception cosmolkit.ConformerError(*args, **kwargs)

ConformerError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native error domain identifying the conformer subsystem.

property message: str | None

Native failure message for generation or JSON parameter errors; None for variants without a message.

property variant: ConformerErrorKind

Concrete native failure category; payload fields apply only to their corresponding variants.

class cosmolkit.ConformerErrorKind(value)

Discriminants of ConformerErrorKind.

Members: Unsupported, CannotNormalizeZeroLengthVector, GenerationFailed, InvalidEmbedParametersJson, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
CannotNormalizeZeroLengthVector = ConformerErrorKind.CannotNormalizeZeroLengthVector
GenerationFailed = ConformerErrorKind.GenerationFailed
InvalidEmbedParametersJson = ConformerErrorKind.InvalidEmbedParametersJson
Unsupported = ConformerErrorKind.Unsupported
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unsupported': ConformerErrorKind.Unsupported, 'CannotNormalizeZeroLengthVector': ConformerErrorKind.CannotNormalizeZeroLengthVector, 'GenerationFailed': ConformerErrorKind.GenerationFailed, 'InvalidEmbedParametersJson': ConformerErrorKind.InvalidEmbedParametersJson})
values = mappingproxy({0: ConformerErrorKind.Unsupported, 1: ConformerErrorKind.CannotNormalizeZeroLengthVector, 2: ConformerErrorKind.GenerationFailed, 3: ConformerErrorKind.InvalidEmbedParametersJson})
class cosmolkit.ConformerOptimizerCause

Structured cause of conformer optimization failure, preserving its native variant.

Members (3)
construction: DistGeomForceFieldError | None

Force-field construction details for Construction failures; None otherwise.

message: str | None

Native diagnostic message. Present for ConformerOptimizerCause.Input; None when unavailable.

variant: ConformerOptimizerCauseKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.ConformerOptimizerCauseKind(value)

Discriminants of ConformerOptimizerCauseKind.

Members: Input, Construction, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Construction = ConformerOptimizerCauseKind.Construction
Input = ConformerOptimizerCauseKind.Input
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Input': ConformerOptimizerCauseKind.Input, 'Construction': ConformerOptimizerCauseKind.Construction})
values = mappingproxy({0: ConformerOptimizerCauseKind.Input, 1: ConformerOptimizerCauseKind.Construction})
exception cosmolkit.ConformerOptimizerError(*args, **kwargs)

ConformerOptimizerError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property cause: ConformerOptimizerCause

“error_payload”} Structured native cause of conformer optimization failure.

Type:

{“role”

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: ForceFieldKernelError | UffInversionContributionError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.ConformerRmsd(probe_conformer_id, reference_conformer_id, rmsd)

RMSD value associated with explicit probe and reference conformer identifiers.

Members (3)
probe_conformer_id: int

Identifier of the probe conformer.

reference_conformer_id: int

Identifier of the reference conformer.

rmsd: float

Root-mean-square deviation for the associated alignment or conformer pair.

exception cosmolkit.ConformerRunError(*args, **kwargs)

ConformerRunError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: BoundsQueryError | GenerationError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.ConjugationError(*args, **kwargs)

Failure in the conjugation domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ConjugationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property actual: int | None

Readonly actual payload of the ValenceAssignmentLength error variant; None for other variants.

property aromaticity: AromaticityError | None

“error_payload”} Structured AromaticityError payload of ConjugationError.Aromaticity; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property atom: int | None

Atom identifier implicated in the failure. Applies to ConjugationError.InvalidValenceRow, ConjugationError.AtomOutOfRange. None when this payload is absent.

property atom_count: int | None

Readonly atom_count payload of the AtomOutOfRange error variant; None for other variants.

property bond: int | None

Readonly bond payload of the BondOutOfRange error variant; None for other variants.

property bond_count: int | None

Readonly bond_count payload of the BondOutOfRange error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the ValenceAssignmentLength error variant; None for other variants.

property field: str | None

Field whose content or type caused the failure. Applies to ConjugationError.ValenceAssignmentLength, ConjugationError.InvalidValenceRow, ConjugationError.IntegerOverflow. None when this payload is absent.

property source: TopologyValidationError | MappingValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of ConjugationError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of ConjugationError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property value: int | None

Readonly value payload of the InvalidValenceRow error variant; None for other variants.

property variant: ConjugationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ConjugationErrorKind(value)

Discriminants of ConjugationErrorKind.

Members: InvalidTopology, ValenceAssignmentLength, InvalidValenceRow, AtomOutOfRange, BondOutOfRange, IntegerOverflow, Aromaticity, Valence, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
Aromaticity = ConjugationErrorKind.Aromaticity
AtomOutOfRange = ConjugationErrorKind.AtomOutOfRange
BondOutOfRange = ConjugationErrorKind.BondOutOfRange
IntegerOverflow = ConjugationErrorKind.IntegerOverflow
InvalidTopology = ConjugationErrorKind.InvalidTopology
InvalidValenceRow = ConjugationErrorKind.InvalidValenceRow
Valence = ConjugationErrorKind.Valence
ValenceAssignmentLength = ConjugationErrorKind.ValenceAssignmentLength
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': ConjugationErrorKind.InvalidTopology, 'ValenceAssignmentLength': ConjugationErrorKind.ValenceAssignmentLength, 'InvalidValenceRow': ConjugationErrorKind.InvalidValenceRow, 'AtomOutOfRange': ConjugationErrorKind.AtomOutOfRange, 'BondOutOfRange': ConjugationErrorKind.BondOutOfRange, 'IntegerOverflow': ConjugationErrorKind.IntegerOverflow, 'Aromaticity': ConjugationErrorKind.Aromaticity, 'Valence': ConjugationErrorKind.Valence})
values = mappingproxy({0: ConjugationErrorKind.InvalidTopology, 1: ConjugationErrorKind.ValenceAssignmentLength, 2: ConjugationErrorKind.InvalidValenceRow, 3: ConjugationErrorKind.AtomOutOfRange, 4: ConjugationErrorKind.BondOutOfRange, 5: ConjugationErrorKind.IntegerOverflow, 6: ConjugationErrorKind.Aromaticity, 7: ConjugationErrorKind.Valence})
exception cosmolkit.Coordinate2DError(*args, **kwargs)

Failure in the depict domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

Coordinate2DError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property max_id: int | None

Readonly max_id payload of the ConformerIdOverflow error variant; None for other variants.

property source: TopologyValidationError | ValenceError | RingFindingError | LegacyStereoError | Coordinate2DTemplateError | Coordinate2DLayoutError | CoordinateValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: Coordinate2DErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.Coordinate2DErrorKind(value)

Discriminants of Coordinate2DErrorKind.

Members: InvalidTopology, PropertyCache, RingFinding, StereoAssignment, TemplateLoading, Fragment, CoordinateValidation, ConformerIdOverflow, CoordGenUnavailable, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
ConformerIdOverflow = Coordinate2DErrorKind.ConformerIdOverflow
CoordGenUnavailable = Coordinate2DErrorKind.CoordGenUnavailable
CoordinateValidation = Coordinate2DErrorKind.CoordinateValidation
Fragment = Coordinate2DErrorKind.Fragment
InvalidTopology = Coordinate2DErrorKind.InvalidTopology
PropertyCache = Coordinate2DErrorKind.PropertyCache
RingFinding = Coordinate2DErrorKind.RingFinding
StereoAssignment = Coordinate2DErrorKind.StereoAssignment
TemplateLoading = Coordinate2DErrorKind.TemplateLoading
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': Coordinate2DErrorKind.InvalidTopology, 'PropertyCache': Coordinate2DErrorKind.PropertyCache, 'RingFinding': Coordinate2DErrorKind.RingFinding, 'StereoAssignment': Coordinate2DErrorKind.StereoAssignment, 'TemplateLoading': Coordinate2DErrorKind.TemplateLoading, 'Fragment': Coordinate2DErrorKind.Fragment, 'CoordinateValidation': Coordinate2DErrorKind.CoordinateValidation, 'ConformerIdOverflow': Coordinate2DErrorKind.ConformerIdOverflow, 'CoordGenUnavailable': Coordinate2DErrorKind.CoordGenUnavailable})
values = mappingproxy({0: Coordinate2DErrorKind.InvalidTopology, 1: Coordinate2DErrorKind.PropertyCache, 2: Coordinate2DErrorKind.RingFinding, 3: Coordinate2DErrorKind.StereoAssignment, 4: Coordinate2DErrorKind.TemplateLoading, 5: Coordinate2DErrorKind.Fragment, 6: Coordinate2DErrorKind.CoordinateValidation, 7: Coordinate2DErrorKind.ConformerIdOverflow, 8: Coordinate2DErrorKind.CoordGenUnavailable})
class cosmolkit.Coordinate2DInputParams(*, z_policy=Ellipsis)

Policy for importing two-dimensional coordinate rows.

Members (1)
z_policy: CoordinateZPolicy

How to handle a supplied third coordinate when importing 2D positions.

exception cosmolkit.Coordinate2DLayoutError(*args, **kwargs)

Failure in the depict domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

Coordinate2DLayoutError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (12)
property atom: int | None

Atom index involved in the failure. Present for Coordinate2DLayoutError.AtomIndexOutOfRange, Coordinate2DLayoutError.AtomAlreadyEmbedded, Coordinate2DLayoutError.AtomNotEmbedded, Coordinate2DLayoutError.NotEnoughEmbeddedNeighbors, Coordinate2DLayoutError.EmptyAttachment, Coordinate2DLayoutError.InvalidRankProperty, Coordinate2DLayoutError.GeometryNotEnoughNeighbors; None when unavailable.

property atom_count: int | None

Number of atoms available to the operation. Present for Coordinate2DLayoutError.AtomIndexOutOfRange, Coordinate2DLayoutError.AtomCountTooLarge; None when unavailable.

property bond: int | None

Bond index involved in the failure. Present for Coordinate2DLayoutError.CisTransBondInvalid, Coordinate2DLayoutError.CollisionBondInvalid; None when unavailable.

property centre: int | None

Center atom involved in the coordinate-layout failure. Present for Coordinate2DLayoutError.NonTetrahedralNoLigand, Coordinate2DLayoutError.NonTetrahedralLigandOverflow; None when unavailable.

property count: int | None

Count observed when the failure occurred. Present for Coordinate2DLayoutError.NotEnoughEmbeddedNeighbors, Coordinate2DLayoutError.GeometryNotEnoughNeighbors; None when unavailable.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property first: int | None

Readonly first payload of the UndefinedSamplingDistance error variant; None for other variants.

property key: str | None

Readonly key payload of the InvalidRankProperty error variant; None for other variants.

property second: int | None

Readonly second payload of the UndefinedSamplingDistance error variant; None for other variants.

property source: PropertyUIntReadError | SubstructMatchError | PathError | MatrixError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: Coordinate2DLayoutErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.Coordinate2DLayoutErrorKind(value)

Discriminants of Coordinate2DLayoutErrorKind.

Members: AtomIndexOutOfRange, AtomAlreadyEmbedded, AtomNotEmbedded, NotEnoughEmbeddedNeighbors, CoincidentPoints, InvalidAngle, NoCommonAtoms, MismatchedTopology, EmptyAttachment, NonTetrahedralNoLigand, NonTetrahedralLigandOverflow, CisTransBondInvalid, CollisionBondInvalid, UndefinedSamplingDistance, AtomCountTooLarge, InvalidRankProperty, GeometryNotEnoughNeighbors, TemplateMatch, GraphPath, GraphDistance, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (23)
AtomAlreadyEmbedded = Coordinate2DLayoutErrorKind.AtomAlreadyEmbedded
AtomCountTooLarge = Coordinate2DLayoutErrorKind.AtomCountTooLarge
AtomIndexOutOfRange = Coordinate2DLayoutErrorKind.AtomIndexOutOfRange
AtomNotEmbedded = Coordinate2DLayoutErrorKind.AtomNotEmbedded
CisTransBondInvalid = Coordinate2DLayoutErrorKind.CisTransBondInvalid
CoincidentPoints = Coordinate2DLayoutErrorKind.CoincidentPoints
CollisionBondInvalid = Coordinate2DLayoutErrorKind.CollisionBondInvalid
EmptyAttachment = Coordinate2DLayoutErrorKind.EmptyAttachment
GeometryNotEnoughNeighbors = Coordinate2DLayoutErrorKind.GeometryNotEnoughNeighbors
GraphDistance = Coordinate2DLayoutErrorKind.GraphDistance
GraphPath = Coordinate2DLayoutErrorKind.GraphPath
InvalidAngle = Coordinate2DLayoutErrorKind.InvalidAngle
InvalidRankProperty = Coordinate2DLayoutErrorKind.InvalidRankProperty
MismatchedTopology = Coordinate2DLayoutErrorKind.MismatchedTopology
NoCommonAtoms = Coordinate2DLayoutErrorKind.NoCommonAtoms
NonTetrahedralLigandOverflow = Coordinate2DLayoutErrorKind.NonTetrahedralLigandOverflow
NonTetrahedralNoLigand = Coordinate2DLayoutErrorKind.NonTetrahedralNoLigand
NotEnoughEmbeddedNeighbors = Coordinate2DLayoutErrorKind.NotEnoughEmbeddedNeighbors
TemplateMatch = Coordinate2DLayoutErrorKind.TemplateMatch
UndefinedSamplingDistance = Coordinate2DLayoutErrorKind.UndefinedSamplingDistance
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'AtomIndexOutOfRange': Coordinate2DLayoutErrorKind.AtomIndexOutOfRange, 'AtomAlreadyEmbedded': Coordinate2DLayoutErrorKind.AtomAlreadyEmbedded, 'AtomNotEmbedded': Coordinate2DLayoutErrorKind.AtomNotEmbedded, 'NotEnoughEmbeddedNeighbors': Coordinate2DLayoutErrorKind.NotEnoughEmbeddedNeighbors, 'CoincidentPoints': Coordinate2DLayoutErrorKind.CoincidentPoints, 'InvalidAngle': Coordinate2DLayoutErrorKind.InvalidAngle, 'NoCommonAtoms': Coordinate2DLayoutErrorKind.NoCommonAtoms, 'MismatchedTopology': Coordinate2DLayoutErrorKind.MismatchedTopology, 'EmptyAttachment': Coordinate2DLayoutErrorKind.EmptyAttachment, 'NonTetrahedralNoLigand': Coordinate2DLayoutErrorKind.NonTetrahedralNoLigand, 'NonTetrahedralLigandOverflow': Coordinate2DLayoutErrorKind.NonTetrahedralLigandOverflow, 'CisTransBondInvalid': Coordinate2DLayoutErrorKind.CisTransBondInvalid, 'CollisionBondInvalid': Coordinate2DLayoutErrorKind.CollisionBondInvalid, 'UndefinedSamplingDistance': Coordinate2DLayoutErrorKind.UndefinedSamplingDistance, 'AtomCountTooLarge': Coordinate2DLayoutErrorKind.AtomCountTooLarge, 'InvalidRankProperty': Coordinate2DLayoutErrorKind.InvalidRankProperty, 'GeometryNotEnoughNeighbors': Coordinate2DLayoutErrorKind.GeometryNotEnoughNeighbors, 'TemplateMatch': Coordinate2DLayoutErrorKind.TemplateMatch, 'GraphPath': Coordinate2DLayoutErrorKind.GraphPath, 'GraphDistance': Coordinate2DLayoutErrorKind.GraphDistance})
values = mappingproxy({0: Coordinate2DLayoutErrorKind.AtomIndexOutOfRange, 1: Coordinate2DLayoutErrorKind.AtomAlreadyEmbedded, 2: Coordinate2DLayoutErrorKind.AtomNotEmbedded, 3: Coordinate2DLayoutErrorKind.NotEnoughEmbeddedNeighbors, 4: Coordinate2DLayoutErrorKind.CoincidentPoints, 5: Coordinate2DLayoutErrorKind.InvalidAngle, 6: Coordinate2DLayoutErrorKind.NoCommonAtoms, 7: Coordinate2DLayoutErrorKind.MismatchedTopology, 8: Coordinate2DLayoutErrorKind.EmptyAttachment, 9: Coordinate2DLayoutErrorKind.NonTetrahedralNoLigand, 10: Coordinate2DLayoutErrorKind.NonTetrahedralLigandOverflow, 11: Coordinate2DLayoutErrorKind.CisTransBondInvalid, 12: Coordinate2DLayoutErrorKind.CollisionBondInvalid, 13: Coordinate2DLayoutErrorKind.UndefinedSamplingDistance, 14: Coordinate2DLayoutErrorKind.AtomCountTooLarge, 15: Coordinate2DLayoutErrorKind.InvalidRankProperty, 16: Coordinate2DLayoutErrorKind.GeometryNotEnoughNeighbors, 17: Coordinate2DLayoutErrorKind.TemplateMatch, 18: Coordinate2DLayoutErrorKind.GraphPath, 19: Coordinate2DLayoutErrorKind.GraphDistance})
class cosmolkit.Coordinate2DParams(*, coordinate_map=Ellipsis, canonical_orientation=Ellipsis, clear_existing_2d=Ellipsis, flips_per_sample=Ellipsis, samples=Ellipsis, sample_seed=Ellipsis, permute_degree_four=Ellipsis, force_rdkit=Ellipsis, use_ring_templates=Ellipsis, use_path_angle_expansion=Ellipsis)

Frozen detached counterpart of RDKit’s Compute2DCoordParameters.

clear_existing_2d is consumed by the live runtime when this detached result is installed. It deliberately does not affect independent 3D rows.

Members (10)
canonical_orientation: bool

Orient the generated layout canonically.

clear_existing_2d: bool

Replace existing 2D conformers rather than retaining them.

coordinate_map: collections.abc.Mapping[int, tuple[float, ...]]

Fixed atom positions keyed by zero-based atom index.

flips_per_sample: int

Number of rotatable-bond flips attempted for each sampled layout.

force_rdkit: bool

Force the native RDKit-style layout path.

permute_degree_four: bool

Permit degree-four atom neighbor permutations during sampling.

sample_seed: int

Random seed for layout sampling.

samples: int

Number of alternative layouts to sample.

use_path_angle_expansion: bool

Resolve remaining nonbonded clashes using source path-angle expansion.

use_ring_templates: bool

Use the native ring template library during layout.

exception cosmolkit.Coordinate2DTemplateError(*args, **kwargs)

Failure in the depict domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

Coordinate2DTemplateError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Index associated with the failure. Present for Coordinate2DTemplateError.InvalidDefaultRow, Coordinate2DTemplateError.InvalidTopology, Coordinate2DTemplateError.NonElementIdentity, Coordinate2DTemplateError.RingInitialization, Coordinate2DTemplateError.ConnectedComponents; None when unavailable.

property line: int | None

Readonly line payload of the ExternalInvalidSmarts error variant; None for other variants.

property path: str | None

Source path associated with the failure. Present for Coordinate2DTemplateError.ExternalOpen, Coordinate2DTemplateError.ExternalRead, Coordinate2DTemplateError.ExternalInvalidSmarts; None when unavailable.

property row: str | None

Source row associated with the failure. Present for Coordinate2DTemplateError.MissingCoordinates, Coordinate2DTemplateError.ThreeDimensionalCoordinates, Coordinate2DTemplateError.MultipleFragments, Coordinate2DTemplateError.NotRingSystem; None when unavailable.

property source: SmartsParseError | TopologyValidationError | QueryAtomConversionError | RingFindingError | PathError | IoError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: Coordinate2DTemplateErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.Coordinate2DTemplateErrorKind(value)

Discriminants of Coordinate2DTemplateErrorKind.

Members: InvalidDefaultRow, InvalidTopology, NonElementIdentity, RingInitialization, ConnectedComponents, ExternalOpen, ExternalRead, ExternalInvalidSmarts, MissingCoordinates, ThreeDimensionalCoordinates, MultipleFragments, NotRingSystem, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (15)
ConnectedComponents = Coordinate2DTemplateErrorKind.ConnectedComponents
ExternalInvalidSmarts = Coordinate2DTemplateErrorKind.ExternalInvalidSmarts
ExternalOpen = Coordinate2DTemplateErrorKind.ExternalOpen
ExternalRead = Coordinate2DTemplateErrorKind.ExternalRead
InvalidDefaultRow = Coordinate2DTemplateErrorKind.InvalidDefaultRow
InvalidTopology = Coordinate2DTemplateErrorKind.InvalidTopology
MissingCoordinates = Coordinate2DTemplateErrorKind.MissingCoordinates
MultipleFragments = Coordinate2DTemplateErrorKind.MultipleFragments
NonElementIdentity = Coordinate2DTemplateErrorKind.NonElementIdentity
NotRingSystem = Coordinate2DTemplateErrorKind.NotRingSystem
RingInitialization = Coordinate2DTemplateErrorKind.RingInitialization
ThreeDimensionalCoordinates = Coordinate2DTemplateErrorKind.ThreeDimensionalCoordinates
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidDefaultRow': Coordinate2DTemplateErrorKind.InvalidDefaultRow, 'InvalidTopology': Coordinate2DTemplateErrorKind.InvalidTopology, 'NonElementIdentity': Coordinate2DTemplateErrorKind.NonElementIdentity, 'RingInitialization': Coordinate2DTemplateErrorKind.RingInitialization, 'ConnectedComponents': Coordinate2DTemplateErrorKind.ConnectedComponents, 'ExternalOpen': Coordinate2DTemplateErrorKind.ExternalOpen, 'ExternalRead': Coordinate2DTemplateErrorKind.ExternalRead, 'ExternalInvalidSmarts': Coordinate2DTemplateErrorKind.ExternalInvalidSmarts, 'MissingCoordinates': Coordinate2DTemplateErrorKind.MissingCoordinates, 'ThreeDimensionalCoordinates': Coordinate2DTemplateErrorKind.ThreeDimensionalCoordinates, 'MultipleFragments': Coordinate2DTemplateErrorKind.MultipleFragments, 'NotRingSystem': Coordinate2DTemplateErrorKind.NotRingSystem})
values = mappingproxy({0: Coordinate2DTemplateErrorKind.InvalidDefaultRow, 1: Coordinate2DTemplateErrorKind.InvalidTopology, 2: Coordinate2DTemplateErrorKind.NonElementIdentity, 3: Coordinate2DTemplateErrorKind.RingInitialization, 4: Coordinate2DTemplateErrorKind.ConnectedComponents, 5: Coordinate2DTemplateErrorKind.ExternalOpen, 6: Coordinate2DTemplateErrorKind.ExternalRead, 7: Coordinate2DTemplateErrorKind.ExternalInvalidSmarts, 8: Coordinate2DTemplateErrorKind.MissingCoordinates, 9: Coordinate2DTemplateErrorKind.ThreeDimensionalCoordinates, 10: Coordinate2DTemplateErrorKind.MultipleFragments, 11: Coordinate2DTemplateErrorKind.NotRingSystem})
class cosmolkit.Coordinate3DInputParams(*, is_3d=Ellipsis)

Dimensionality metadata for imported three-component coordinates.

Members (1)
is_3d: bool

Mark the imported conformer as three-dimensional.

exception cosmolkit.Coordinate3DReadError(*args, **kwargs)

Failure in the coordinates domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

Coordinate3DReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property conformer_id: int | None

Readonly conformer_id payload of the ConformerNotFound error variant; None for other variants.

property count: int | None

Readonly count payload of the ConformerNotFound error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: Coordinate3DReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.Coordinate3DReadErrorKind(value)

Discriminants of Coordinate3DReadErrorKind.

Members: ConformerNotFound, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
ConformerNotFound = Coordinate3DReadErrorKind.ConformerNotFound
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ConformerNotFound': Coordinate3DReadErrorKind.ConformerNotFound})
values = mappingproxy({0: Coordinate3DReadErrorKind.ConformerNotFound})
class cosmolkit.CoordinateBlock(conformers_2d, conformers_3d, source_coordinate_dim, source_conformer_order)

Detached 2D/3D conformers and source ordering metadata.

Members (4)
conformers_2d: list[Conformer2D]

Independent copies of the stored two-dimensional conformers.

conformers_3d: list[Conformer3D]

Independent copies of the stored three-dimensional conformers.

source_conformer_order: list[CoordinateDimension] | None

Original 2D/3D conformer ordering, or None when not recorded.

source_coordinate_dim: CoordinateDimension | None

Coordinate dimensionality recorded by the source, or None.

exception cosmolkit.CoordinateBlockSelectionError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CoordinateBlockSelectionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property block_number: int | None

Readonly block_number payload of the LaterCoordinateBlock error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: str

Input source name associated with coordinate-block selection failure.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: CoordinateBlockSelectionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.CoordinateBlockSelectionErrorKind(value)

Discriminants of CoordinateBlockSelectionErrorKind.

Members: EmptyDocument, LaterCoordinateBlock, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
EmptyDocument = CoordinateBlockSelectionErrorKind.EmptyDocument
LaterCoordinateBlock = CoordinateBlockSelectionErrorKind.LaterCoordinateBlock
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyDocument': CoordinateBlockSelectionErrorKind.EmptyDocument, 'LaterCoordinateBlock': CoordinateBlockSelectionErrorKind.LaterCoordinateBlock})
values = mappingproxy({0: CoordinateBlockSelectionErrorKind.EmptyDocument, 1: CoordinateBlockSelectionErrorKind.LaterCoordinateBlock})
class cosmolkit.CoordinateDimension(value)

Typed CoordinateDimension values corresponding to the Rust enum.

Members: TwoD, ThreeD, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
ThreeD = CoordinateDimension.ThreeD
TwoD = CoordinateDimension.TwoD
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TwoD': CoordinateDimension.TwoD, 'ThreeD': CoordinateDimension.ThreeD})
values = mappingproxy({0: CoordinateDimension.TwoD, 1: CoordinateDimension.ThreeD})
exception cosmolkit.CoordinateInputError(*args, **kwargs)

Failure in the coordinates domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CoordinateInputError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property actual: int | None

Readonly actual payload of the RowCount error variant; None for other variants.

property column: int | None

Readonly column payload of the NonFinite error variant; None for other variants.

property columns: int | None

Readonly columns payload of the Shape error variant; None for other variants.

property conformer_id: int | None

Readonly conformer_id payload of the ConformerNotFound error variant; None for other variants.

property coordinates: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of CoordinateInputError.InvalidCoordinates; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property count: int | None

Readonly count payload of the ConformerNotFound error variant; None for other variants.

property dimension: str | None

Coordinate or matrix dimension involved in the failure. Applies to CoordinateInputError.RowCount, CoordinateInputError.Shape, CoordinateInputError.NonFinite. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | str | None

Required value reported by the native check. Applies to CoordinateInputError.RowCount, CoordinateInputError.Shape. None when this payload is absent.

property max_id: int | None

Readonly max_id payload of the ConformerIdOverflow error variant; None for other variants.

property row: int | None

Row reported by the native failure. Applies to CoordinateInputError.Shape, CoordinateInputError.NonFinite, CoordinateInputError.NonZeroZ. None when this payload is absent.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | float | None

Value rejected or reported by the native operation. Applies to CoordinateInputError.UnknownZPolicy, CoordinateInputError.NonFinite. None when this payload is absent.

property variant: CoordinateInputErrorKind

Exact Rust error variant, independent of the human-readable message.

property z: float | None

Readonly z payload of the NonZeroZ error variant; None for other variants.

class cosmolkit.CoordinateInputErrorKind(value)

Discriminants of CoordinateInputErrorKind.

Members: UnknownZPolicy, RowCount, Shape, NonFinite, NonZeroZ, ThreeColumnsForbidden, ConformerNotFound, ConformerIdOverflow, InvalidCoordinates, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
ConformerIdOverflow = CoordinateInputErrorKind.ConformerIdOverflow
ConformerNotFound = CoordinateInputErrorKind.ConformerNotFound
InvalidCoordinates = CoordinateInputErrorKind.InvalidCoordinates
NonFinite = CoordinateInputErrorKind.NonFinite
NonZeroZ = CoordinateInputErrorKind.NonZeroZ
RowCount = CoordinateInputErrorKind.RowCount
Shape = CoordinateInputErrorKind.Shape
ThreeColumnsForbidden = CoordinateInputErrorKind.ThreeColumnsForbidden
UnknownZPolicy = CoordinateInputErrorKind.UnknownZPolicy
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnknownZPolicy': CoordinateInputErrorKind.UnknownZPolicy, 'RowCount': CoordinateInputErrorKind.RowCount, 'Shape': CoordinateInputErrorKind.Shape, 'NonFinite': CoordinateInputErrorKind.NonFinite, 'NonZeroZ': CoordinateInputErrorKind.NonZeroZ, 'ThreeColumnsForbidden': CoordinateInputErrorKind.ThreeColumnsForbidden, 'ConformerNotFound': CoordinateInputErrorKind.ConformerNotFound, 'ConformerIdOverflow': CoordinateInputErrorKind.ConformerIdOverflow, 'InvalidCoordinates': CoordinateInputErrorKind.InvalidCoordinates})
values = mappingproxy({0: CoordinateInputErrorKind.UnknownZPolicy, 1: CoordinateInputErrorKind.RowCount, 2: CoordinateInputErrorKind.Shape, 3: CoordinateInputErrorKind.NonFinite, 4: CoordinateInputErrorKind.NonZeroZ, 5: CoordinateInputErrorKind.ThreeColumnsForbidden, 6: CoordinateInputErrorKind.ConformerNotFound, 7: CoordinateInputErrorKind.ConformerIdOverflow, 8: CoordinateInputErrorKind.InvalidCoordinates})
class cosmolkit.CoordinateRmsdParameters(*, probe_conformer_id=Ellipsis, reference_conformer_id=Ellipsis, atom_maps=Ellipsis, weights=Ellipsis, max_matches=Ellipsis, symmetrize_conjugated_terminal_groups=Ellipsis)

Atom mappings, weights and conformer selection for RMSD without moving coordinates.

Members (7)
atom_maps: tuple[tuple[AlignmentAtomMap, ...], ...]

Candidate probe-to-reference atom mappings; an empty collection requests native match enumeration.

max_matches: int

Maximum number of candidate atom mappings considered.

static new(probe_conformer_id=Ellipsis, reference_conformer_id=Ellipsis, atom_maps=Ellipsis, weights=Ellipsis, max_matches=Ellipsis, symmetrize_conjugated_terminal_groups=Ellipsis) → CoordinateRmsdParameters

Create an independent configuration through the native constructor using the supplied field values.

probe_conformer_id: int

Probe conformer identifier; -1 selects the native default conformer.

reference_conformer_id: int

Reference conformer identifier; -1 selects the native default conformer.

symmetrize_conjugated_terminal_groups: bool

Treat conjugated terminal groups symmetrically when selecting matches.

weights: tuple[float, ...] | None

Optional alignment weights in atom-map order.

exception cosmolkit.CoordinateValidationError(*args, **kwargs)

Failure in the coordinates domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CoordinateValidationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property atom: int | None

Atom index involved in the failure. Present for CoordinateValidationError.AtomIndexOverflow, CoordinateValidationError.NonFiniteCoordinate; None when unavailable.

property atom_count: int | None

Readonly atom_count payload of the RowCount error variant; None for other variants.

property axis: str | None

Readonly axis payload of the NonFiniteCoordinate error variant; None for other variants.

property conformer: int | None

Conformer identifier associated with the failure. Present for CoordinateValidationError.RowCount, CoordinateValidationError.NonFiniteCoordinate; None when unavailable.

property dimension: str | None

Coordinate dimension associated with the failure. Present for CoordinateValidationError.RowCount, CoordinateValidationError.DuplicateConformerId, CoordinateValidationError.NonFiniteCoordinate; None when unavailable.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected_three_d: int | None

Readonly expected_three_d payload of the SourceConformerOrder error variant; None for other variants.

property expected_two_d: int | None

Readonly expected_two_d payload of the SourceConformerOrder error variant; None for other variants.

property id: int | None

Identifier associated with the failed validation. Present for CoordinateValidationError.Missing3DConformer, CoordinateValidationError.DuplicateConformerId; None when unavailable.

property max_id: int | None

Readonly max_id payload of the ConformerIdOverflow error variant; None for other variants.

property rows: int | None

Readonly rows payload of the RowCount error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property three_d: int | None

Readonly three_d payload of the SourceConformerOrder error variant; None for other variants.

property two_d: int | None

Readonly two_d payload of the SourceConformerOrder error variant; None for other variants.

property variant: CoordinateValidationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.CoordinateValidationErrorKind(value)

Discriminants of CoordinateValidationErrorKind.

Members: AtomIndexOverflow, Missing3DConformer, ConformerIdOverflow, RowCount, MissingSourceConformerOrder, SourceConformerOrder, DuplicateConformerId, NonFiniteCoordinate, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
AtomIndexOverflow = CoordinateValidationErrorKind.AtomIndexOverflow
ConformerIdOverflow = CoordinateValidationErrorKind.ConformerIdOverflow
DuplicateConformerId = CoordinateValidationErrorKind.DuplicateConformerId
Missing3DConformer = CoordinateValidationErrorKind.Missing3DConformer
MissingSourceConformerOrder = CoordinateValidationErrorKind.MissingSourceConformerOrder
NonFiniteCoordinate = CoordinateValidationErrorKind.NonFiniteCoordinate
RowCount = CoordinateValidationErrorKind.RowCount
SourceConformerOrder = CoordinateValidationErrorKind.SourceConformerOrder
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'AtomIndexOverflow': CoordinateValidationErrorKind.AtomIndexOverflow, 'Missing3DConformer': CoordinateValidationErrorKind.Missing3DConformer, 'ConformerIdOverflow': CoordinateValidationErrorKind.ConformerIdOverflow, 'RowCount': CoordinateValidationErrorKind.RowCount, 'MissingSourceConformerOrder': CoordinateValidationErrorKind.MissingSourceConformerOrder, 'SourceConformerOrder': CoordinateValidationErrorKind.SourceConformerOrder, 'DuplicateConformerId': CoordinateValidationErrorKind.DuplicateConformerId, 'NonFiniteCoordinate': CoordinateValidationErrorKind.NonFiniteCoordinate})
values = mappingproxy({0: CoordinateValidationErrorKind.AtomIndexOverflow, 1: CoordinateValidationErrorKind.Missing3DConformer, 2: CoordinateValidationErrorKind.ConformerIdOverflow, 3: CoordinateValidationErrorKind.RowCount, 4: CoordinateValidationErrorKind.MissingSourceConformerOrder, 5: CoordinateValidationErrorKind.SourceConformerOrder, 6: CoordinateValidationErrorKind.DuplicateConformerId, 7: CoordinateValidationErrorKind.NonFiniteCoordinate})
class cosmolkit.CoordinateZPolicy(value)

Typed CoordinateZPolicy values corresponding to the Rust enum.

Members: Ignore, RequireZero, Error, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
Error = CoordinateZPolicy.Error
Ignore = CoordinateZPolicy.Ignore
RequireZero = CoordinateZPolicy.RequireZero
static from_name(value) → CoordinateZPolicy

Parse the canonical coordinate-Z policy name; reject unknown names.

name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Ignore': CoordinateZPolicy.Ignore, 'RequireZero': CoordinateZPolicy.RequireZero, 'Error': CoordinateZPolicy.Error})
values = mappingproxy({0: CoordinateZPolicy.Ignore, 1: CoordinateZPolicy.RequireZero, 2: CoordinateZPolicy.Error})
class cosmolkit.CrippenTotals(logp, molar_refractivity)

Molecular Crippen logP and molar refractivity totals.

Members (2)
logp: float

Crippen estimate of the octanol/water partition coefficient logarithm.

molar_refractivity: float

Crippen molecular refractivity estimate.

exception cosmolkit.CrystalffTorsionPreferencesError(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CrystalffTorsionPreferencesError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property aid2: int | None

Readonly aid2 payload of the MissingCentralBond error variant; None for other variants.

property aid3: int | None

Readonly aid3 payload of the MissingCentralBond error variant; None for other variants.

property constant_name: str | None

Named parameter-table constant involved in the failure. Applies to CrystalffTorsionPreferencesError.InvalidParameterSourceFormat, CrystalffTorsionPreferencesError.UnsupportedEscapeSequence, CrystalffTorsionPreferencesError.UnterminatedQuotedLiteral, CrystalffTorsionPreferencesError.TrailingEscape. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property escape: str | None

Readonly escape payload of the UnsupportedEscapeSequence error variant; None for other variants.

property line: str | None

Source line involved in the failure. Applies to CrystalffTorsionPreferencesError.MissingSmartsPattern, CrystalffTorsionPreferencesError.IncompleteParameterLine, CrystalffTorsionPreferencesError.InvalidIntegerToken, CrystalffTorsionPreferencesError.InvalidFloatToken. None when this payload is absent.

property matching: SubstructMatchError | None

“error_payload”} Structured native error payload. Present for CrystalffTorsionPreferencesError.Match; None when unavailable.

Type:

{“role”

property prepared_target: QueryMatchContextError | None

“error_payload”} Structured native error payload. Present for CrystalffTorsionPreferencesError.PreparedTarget; None when unavailable.

Type:

{“role”

property reason: str | None

Native explanation for rejecting the operation. Applies to CrystalffTorsionPreferencesError.QueryBuildFailed, CrystalffTorsionPreferencesError.RingInfoUnavailable. None when this payload is absent.

property smarts: str | None

SMARTS expression implicated in the parsing or query failure. Applies to CrystalffTorsionPreferencesError.QueryBuildFailed, CrystalffTorsionPreferencesError.MissingCentralBond. None when this payload is absent.

property source: PropertyUIntReadError | AtomPropertyError | PropertyIntReadError | TopologyValidationError | RingFindingError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property token: str | None

Input token rejected by the parser. Applies to CrystalffTorsionPreferencesError.InvalidIntegerToken, CrystalffTorsionPreferencesError.InvalidFloatToken. None when this payload is absent.

property variant: CrystalffTorsionPreferencesErrorKind

Exact Rust error variant, independent of the human-readable message.

property version: int | None

Readonly version payload of the InvalidExperimentalTorsionVersion error variant; None for other variants.

class cosmolkit.CrystalffTorsionPreferencesErrorKind(value)

Discriminants of CrystalffTorsionPreferencesErrorKind.

Members: InvalidExperimentalTorsionVersion, MissingSmartsPattern, IncompleteParameterLine, InvalidIntegerToken, InvalidFloatToken, InvalidParameterSourceFormat, UnsupportedEscapeSequence, UnterminatedQuotedLiteral, TrailingEscape, EmptyMolecule, PreparedTarget, Match, QueryBuildFailed, RingInfoUnavailable, MissingCentralBond, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (18)
EmptyMolecule = CrystalffTorsionPreferencesErrorKind.EmptyMolecule
IncompleteParameterLine = CrystalffTorsionPreferencesErrorKind.IncompleteParameterLine
InvalidExperimentalTorsionVersion = CrystalffTorsionPreferencesErrorKind.InvalidExperimentalTorsionVersion
InvalidFloatToken = CrystalffTorsionPreferencesErrorKind.InvalidFloatToken
InvalidIntegerToken = CrystalffTorsionPreferencesErrorKind.InvalidIntegerToken
InvalidParameterSourceFormat = CrystalffTorsionPreferencesErrorKind.InvalidParameterSourceFormat
Match = CrystalffTorsionPreferencesErrorKind.Match
MissingCentralBond = CrystalffTorsionPreferencesErrorKind.MissingCentralBond
MissingSmartsPattern = CrystalffTorsionPreferencesErrorKind.MissingSmartsPattern
PreparedTarget = CrystalffTorsionPreferencesErrorKind.PreparedTarget
QueryBuildFailed = CrystalffTorsionPreferencesErrorKind.QueryBuildFailed
RingInfoUnavailable = CrystalffTorsionPreferencesErrorKind.RingInfoUnavailable
TrailingEscape = CrystalffTorsionPreferencesErrorKind.TrailingEscape
UnsupportedEscapeSequence = CrystalffTorsionPreferencesErrorKind.UnsupportedEscapeSequence
UnterminatedQuotedLiteral = CrystalffTorsionPreferencesErrorKind.UnterminatedQuotedLiteral
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidExperimentalTorsionVersion': CrystalffTorsionPreferencesErrorKind.InvalidExperimentalTorsionVersion, 'MissingSmartsPattern': CrystalffTorsionPreferencesErrorKind.MissingSmartsPattern, 'IncompleteParameterLine': CrystalffTorsionPreferencesErrorKind.IncompleteParameterLine, 'InvalidIntegerToken': CrystalffTorsionPreferencesErrorKind.InvalidIntegerToken, 'InvalidFloatToken': CrystalffTorsionPreferencesErrorKind.InvalidFloatToken, 'InvalidParameterSourceFormat': CrystalffTorsionPreferencesErrorKind.InvalidParameterSourceFormat, 'UnsupportedEscapeSequence': CrystalffTorsionPreferencesErrorKind.UnsupportedEscapeSequence, 'UnterminatedQuotedLiteral': CrystalffTorsionPreferencesErrorKind.UnterminatedQuotedLiteral, 'TrailingEscape': CrystalffTorsionPreferencesErrorKind.TrailingEscape, 'EmptyMolecule': CrystalffTorsionPreferencesErrorKind.EmptyMolecule, 'PreparedTarget': CrystalffTorsionPreferencesErrorKind.PreparedTarget, 'Match': CrystalffTorsionPreferencesErrorKind.Match, 'QueryBuildFailed': CrystalffTorsionPreferencesErrorKind.QueryBuildFailed, 'RingInfoUnavailable': CrystalffTorsionPreferencesErrorKind.RingInfoUnavailable, 'MissingCentralBond': CrystalffTorsionPreferencesErrorKind.MissingCentralBond})
values = mappingproxy({0: CrystalffTorsionPreferencesErrorKind.InvalidExperimentalTorsionVersion, 1: CrystalffTorsionPreferencesErrorKind.MissingSmartsPattern, 2: CrystalffTorsionPreferencesErrorKind.IncompleteParameterLine, 3: CrystalffTorsionPreferencesErrorKind.InvalidIntegerToken, 4: CrystalffTorsionPreferencesErrorKind.InvalidFloatToken, 5: CrystalffTorsionPreferencesErrorKind.InvalidParameterSourceFormat, 6: CrystalffTorsionPreferencesErrorKind.UnsupportedEscapeSequence, 7: CrystalffTorsionPreferencesErrorKind.UnterminatedQuotedLiteral, 8: CrystalffTorsionPreferencesErrorKind.TrailingEscape, 9: CrystalffTorsionPreferencesErrorKind.EmptyMolecule, 10: CrystalffTorsionPreferencesErrorKind.PreparedTarget, 11: CrystalffTorsionPreferencesErrorKind.Match, 12: CrystalffTorsionPreferencesErrorKind.QueryBuildFailed, 13: CrystalffTorsionPreferencesErrorKind.RingInfoUnavailable, 14: CrystalffTorsionPreferencesErrorKind.MissingCentralBond})
class cosmolkit.CxCoordinateSelection

Coordinate selection for CXSMILES: Auto, TwoD(id), or ThreeD(id).

Members (4)
Auto = <cosmolkit.CxCoordinateSelection object>
static ThreeD(id) → CxCoordinateSelection

Select a stored three-dimensional conformer by its dimension-scoped identifier.

static TwoD(id) → CxCoordinateSelection

Select a stored two-dimensional layout by its dimension-scoped identifier.

id: int | None

Dimension-scoped coordinate identifier, or None for Auto selection.

exception cosmolkit.CxParseError(*args, **kwargs)

CxParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property message: str

Original CXSMILES parser explanation.

property offset: int

Byte offset of the CXSMILES parsing failure.

exception cosmolkit.CxQueryLoweringError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CxQueryLoweringError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (11)
property actual: int | None

Readonly actual payload of the CoordinateCount error variant; None for other variants.

property atom: int | None

Atom index involved in the failure. Present for CxQueryLoweringError.BondAtomMismatch, CxQueryLoweringError.WedgeAtomMismatch; None when unavailable.

property bond: int | None

Bond index involved in the failure. Present for CxQueryLoweringError.BondAtomMismatch, CxQueryLoweringError.WedgeAtomMismatch; None when unavailable.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the CoordinateCount error variant; None for other variants.

property index: int | None

Index associated with the failure. Present for CxQueryLoweringError.AtomIndex, CxQueryLoweringError.BondIndex; None when unavailable.

property message: str | None

Native diagnostic message. Present for CxQueryLoweringError.InvalidGraph; None when unavailable.

property record: str | None

Readonly record payload of the UnsupportedRecord error variant; None for other variants.

property source: StereoGroupError | CxStereoGroupMergeError | PropertyUIntReadError | BondValueError | AtomPropertyError | PropertyStringError | MoleculePropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: CxQueryLoweringErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.CxQueryLoweringErrorKind(value)

Discriminants of CxQueryLoweringErrorKind.

Members: StereoGroup, StereoGroupMerge, Numeric, BondProperty, AtomProperty, Property, MoleculeProperty, AtomIndex, BondIndex, CoordinateCount, BondAtomMismatch, WedgeAtomMismatch, UnsupportedRecord, InvalidGraph, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (17)
AtomIndex = CxQueryLoweringErrorKind.AtomIndex
AtomProperty = CxQueryLoweringErrorKind.AtomProperty
BondAtomMismatch = CxQueryLoweringErrorKind.BondAtomMismatch
BondIndex = CxQueryLoweringErrorKind.BondIndex
BondProperty = CxQueryLoweringErrorKind.BondProperty
CoordinateCount = CxQueryLoweringErrorKind.CoordinateCount
InvalidGraph = CxQueryLoweringErrorKind.InvalidGraph
MoleculeProperty = CxQueryLoweringErrorKind.MoleculeProperty
Numeric = CxQueryLoweringErrorKind.Numeric
Property = CxQueryLoweringErrorKind.Property
StereoGroup = CxQueryLoweringErrorKind.StereoGroup
StereoGroupMerge = CxQueryLoweringErrorKind.StereoGroupMerge
UnsupportedRecord = CxQueryLoweringErrorKind.UnsupportedRecord
WedgeAtomMismatch = CxQueryLoweringErrorKind.WedgeAtomMismatch
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': CxQueryLoweringErrorKind.StereoGroup, 'StereoGroupMerge': CxQueryLoweringErrorKind.StereoGroupMerge, 'Numeric': CxQueryLoweringErrorKind.Numeric, 'BondProperty': CxQueryLoweringErrorKind.BondProperty, 'AtomProperty': CxQueryLoweringErrorKind.AtomProperty, 'Property': CxQueryLoweringErrorKind.Property, 'MoleculeProperty': CxQueryLoweringErrorKind.MoleculeProperty, 'AtomIndex': CxQueryLoweringErrorKind.AtomIndex, 'BondIndex': CxQueryLoweringErrorKind.BondIndex, 'CoordinateCount': CxQueryLoweringErrorKind.CoordinateCount, 'BondAtomMismatch': CxQueryLoweringErrorKind.BondAtomMismatch, 'WedgeAtomMismatch': CxQueryLoweringErrorKind.WedgeAtomMismatch, 'UnsupportedRecord': CxQueryLoweringErrorKind.UnsupportedRecord, 'InvalidGraph': CxQueryLoweringErrorKind.InvalidGraph})
values = mappingproxy({0: CxQueryLoweringErrorKind.StereoGroup, 1: CxQueryLoweringErrorKind.StereoGroupMerge, 2: CxQueryLoweringErrorKind.Numeric, 3: CxQueryLoweringErrorKind.BondProperty, 4: CxQueryLoweringErrorKind.AtomProperty, 5: CxQueryLoweringErrorKind.Property, 6: CxQueryLoweringErrorKind.MoleculeProperty, 7: CxQueryLoweringErrorKind.AtomIndex, 8: CxQueryLoweringErrorKind.BondIndex, 9: CxQueryLoweringErrorKind.CoordinateCount, 10: CxQueryLoweringErrorKind.BondAtomMismatch, 11: CxQueryLoweringErrorKind.WedgeAtomMismatch, 12: CxQueryLoweringErrorKind.UnsupportedRecord, 13: CxQueryLoweringErrorKind.InvalidGraph})
class cosmolkit.CxSmilesFields

Bit mask selecting CXSMILES extension fields; combine constants with the bitwise OR operator.

Members (19)
ALL = <cosmolkit.CxSmilesFields object>
ALL_BUT_COORDS = <cosmolkit.CxSmilesFields object>
ATOM_LABELS = <cosmolkit.CxSmilesFields object>
ATOM_PROPS = <cosmolkit.CxSmilesFields object>
BOND_ATROPISOMER = <cosmolkit.CxSmilesFields object>
BOND_CFG = <cosmolkit.CxSmilesFields object>
COORDINATE_BONDS = <cosmolkit.CxSmilesFields object>
COORDS = <cosmolkit.CxSmilesFields object>
ENHANCED_STEREO = <cosmolkit.CxSmilesFields object>
HYDROGEN_BONDS = <cosmolkit.CxSmilesFields object>
LINKNODES = <cosmolkit.CxSmilesFields object>
MOLFILE_VALUES = <cosmolkit.CxSmilesFields object>
NONE = <cosmolkit.CxSmilesFields object>
POLYMER = <cosmolkit.CxSmilesFields object>
RADICALS = <cosmolkit.CxSmilesFields object>
SGROUPS = <cosmolkit.CxSmilesFields object>
ZERO_BONDS = <cosmolkit.CxSmilesFields object>
bits: int

Integer representation of this option mask.

contains(other) → bool

Whether every bit in the supplied mask is present.

class cosmolkit.CxSmilesWriteParams(*, smiles=Ellipsis, fields=Ellipsis, coordinate_selection=Ellipsis)

Options for detached CXSMILES writing.

Members (3)
coordinate_selection: CxCoordinateSelection

Stored coordinate set to write in the CX extension.

fields: CxSmilesFields

CX extension fields to include in the output.

smiles: SmilesWriteParams

Base SMILES formatting and stereochemistry options.

exception cosmolkit.CxStereoGroupMergeError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

CxStereoGroupMergeError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property actual: PropertyValueKind | None

Readonly actual payload of the TrackerPropertyType error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property groups: int | None

Readonly groups payload of the TrackerCount error variant; None for other variants.

property hashes: int | None

Readonly hashes payload of the TrackerCount error variant; None for other variants.

property source: StereoGroupError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: CxStereoGroupMergeErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.CxStereoGroupMergeErrorKind(value)

Discriminants of CxStereoGroupMergeErrorKind.

Members: StereoGroup, TrackerPropertyType, TrackerCount, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
StereoGroup = CxStereoGroupMergeErrorKind.StereoGroup
TrackerCount = CxStereoGroupMergeErrorKind.TrackerCount
TrackerPropertyType = CxStereoGroupMergeErrorKind.TrackerPropertyType
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': CxStereoGroupMergeErrorKind.StereoGroup, 'TrackerPropertyType': CxStereoGroupMergeErrorKind.TrackerPropertyType, 'TrackerCount': CxStereoGroupMergeErrorKind.TrackerCount})
values = mappingproxy({0: CxStereoGroupMergeErrorKind.StereoGroup, 1: CxStereoGroupMergeErrorKind.TrackerPropertyType, 2: CxStereoGroupMergeErrorKind.TrackerCount})
class cosmolkit.DenseMatrix

Readonly dense square matrix with native row/column indexing.

Members (3)
dimension: int

Number of rows and columns in the square matrix.

get(row, column) → float | None

Return the matrix entry, or None when either index is out of range.

values: list[float]

Independent flat list of matrix entries in native storage order.

exception cosmolkit.DescriptorError(*args, **kwargs)

Failure in the descriptors domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

DescriptorError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (18)
property actual: int | None

Observed count or value. Present for DescriptorError.InvalidHallKierContributionRows, DescriptorError.InvalidCrippenOptionalRows, DescriptorError.InvalidValenceRows; None when unavailable.

property actual_rows: int | None

Readonly actual_rows payload of the InvalidConnectivityPath error variant; None for other variants.

property bin_prop_len: int | None

Readonly bin_prop_len payload of the MismatchedBinArrays error variant; None for other variants.

property bins_len: int | None

Readonly bins_len payload of the MismatchedBinArrays error variant; None for other variants.

property cell: str | None

Readonly cell payload of the CrippenParamNumeric error variant; None for other variants.

property contribs_len: int | None

Readonly contribs_len payload of the MismatchedBinArrays error variant; None for other variants.

property detail: str | None

Readonly detail payload of the Unsupported error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Expected count or value. Present for DescriptorError.InvalidCrippenOptionalRows, DescriptorError.InvalidValenceRows; None when unavailable.

property expected_rows: int | None

Readonly expected_rows payload of the InvalidConnectivityPath error variant; None for other variants.

property field: str | None

Input field associated with the failure. Present for DescriptorError.MissingFinalHydrogenState, DescriptorError.CrippenParamNumeric, DescriptorError.InvalidCrippenOptionalRows, DescriptorError.CountOverflow, DescriptorError.InvalidValenceRows; None when unavailable.

property function: str | None

Descriptor function reporting the failure. Present for DescriptorError.TopologyEdit, DescriptorError.InvalidConnectivityPath, DescriptorError.InvalidTopology, DescriptorError.Path, DescriptorError.MissingComputedScalar, DescriptorError.MissingLabuteHydrogens, DescriptorError.MissingLabuteAsa, DescriptorError.MissingCrippenMrContributions, DescriptorError.MissingCrippenMr, DescriptorError.Hydrogens, DescriptorError.CountOverflow, DescriptorError.Valence, DescriptorError.InvalidValenceRows, DescriptorError.Unsupported, DescriptorError.Ring, DescriptorError.Search, DescriptorError.Stereo; None when unavailable.

property include_sulfur_phosphorus: bool | None

Readonly include_sulfur_phosphorus payload of the MissingComputedScalar error variant; None for other variants.

property minimum: int | None

Readonly minimum payload of the InvalidHallKierContributionRows error variant; None for other variants.

property row: int | None

Readonly row payload of the MissingCrippenDefaultPattern error variant; None for other variants.

property source: TopologyEditError | TopologyValidationError | PathError | HydrogenError | ValenceError | RingFindingError | DescriptorSearchCause | LegacyStereoError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: DescriptorErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.DescriptorErrorKind(value)

Discriminants of DescriptorErrorKind.

Members: TopologyEdit, MissingFinalHydrogenState, InvalidConnectivityPath, InvalidTopology, Path, InvalidHallKierContributionRows, MissingComputedScalar, MissingLabuteHydrogens, MissingLabuteAsa, MismatchedBinArrays, CrippenParamNumeric, MissingCrippenMrContributions, MissingCrippenMr, InvalidCrippenOptionalRows, MissingCrippenDefaultPattern, Hydrogens, CountOverflow, Valence, InvalidValenceRows, Unsupported, Ring, Search, Stereo, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (26)
CountOverflow = DescriptorErrorKind.CountOverflow
CrippenParamNumeric = DescriptorErrorKind.CrippenParamNumeric
Hydrogens = DescriptorErrorKind.Hydrogens
InvalidConnectivityPath = DescriptorErrorKind.InvalidConnectivityPath
InvalidCrippenOptionalRows = DescriptorErrorKind.InvalidCrippenOptionalRows
InvalidHallKierContributionRows = DescriptorErrorKind.InvalidHallKierContributionRows
InvalidTopology = DescriptorErrorKind.InvalidTopology
InvalidValenceRows = DescriptorErrorKind.InvalidValenceRows
MismatchedBinArrays = DescriptorErrorKind.MismatchedBinArrays
MissingComputedScalar = DescriptorErrorKind.MissingComputedScalar
MissingCrippenDefaultPattern = DescriptorErrorKind.MissingCrippenDefaultPattern
MissingCrippenMr = DescriptorErrorKind.MissingCrippenMr
MissingCrippenMrContributions = DescriptorErrorKind.MissingCrippenMrContributions
MissingFinalHydrogenState = DescriptorErrorKind.MissingFinalHydrogenState
MissingLabuteAsa = DescriptorErrorKind.MissingLabuteAsa
MissingLabuteHydrogens = DescriptorErrorKind.MissingLabuteHydrogens
Path = DescriptorErrorKind.Path
Ring = DescriptorErrorKind.Ring
Search = DescriptorErrorKind.Search
Stereo = DescriptorErrorKind.Stereo
TopologyEdit = DescriptorErrorKind.TopologyEdit
Unsupported = DescriptorErrorKind.Unsupported
Valence = DescriptorErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TopologyEdit': DescriptorErrorKind.TopologyEdit, 'MissingFinalHydrogenState': DescriptorErrorKind.MissingFinalHydrogenState, 'InvalidConnectivityPath': DescriptorErrorKind.InvalidConnectivityPath, 'InvalidTopology': DescriptorErrorKind.InvalidTopology, 'Path': DescriptorErrorKind.Path, 'InvalidHallKierContributionRows': DescriptorErrorKind.InvalidHallKierContributionRows, 'MissingComputedScalar': DescriptorErrorKind.MissingComputedScalar, 'MissingLabuteHydrogens': DescriptorErrorKind.MissingLabuteHydrogens, 'MissingLabuteAsa': DescriptorErrorKind.MissingLabuteAsa, 'MismatchedBinArrays': DescriptorErrorKind.MismatchedBinArrays, 'CrippenParamNumeric': DescriptorErrorKind.CrippenParamNumeric, 'MissingCrippenMrContributions': DescriptorErrorKind.MissingCrippenMrContributions, 'MissingCrippenMr': DescriptorErrorKind.MissingCrippenMr, 'InvalidCrippenOptionalRows': DescriptorErrorKind.InvalidCrippenOptionalRows, 'MissingCrippenDefaultPattern': DescriptorErrorKind.MissingCrippenDefaultPattern, 'Hydrogens': DescriptorErrorKind.Hydrogens, 'CountOverflow': DescriptorErrorKind.CountOverflow, 'Valence': DescriptorErrorKind.Valence, 'InvalidValenceRows': DescriptorErrorKind.InvalidValenceRows, 'Unsupported': DescriptorErrorKind.Unsupported, 'Ring': DescriptorErrorKind.Ring, 'Search': DescriptorErrorKind.Search, 'Stereo': DescriptorErrorKind.Stereo})
values = mappingproxy({0: DescriptorErrorKind.TopologyEdit, 1: DescriptorErrorKind.MissingFinalHydrogenState, 2: DescriptorErrorKind.InvalidConnectivityPath, 3: DescriptorErrorKind.InvalidTopology, 4: DescriptorErrorKind.Path, 5: DescriptorErrorKind.InvalidHallKierContributionRows, 6: DescriptorErrorKind.MissingComputedScalar, 7: DescriptorErrorKind.MissingLabuteHydrogens, 8: DescriptorErrorKind.MissingLabuteAsa, 9: DescriptorErrorKind.MismatchedBinArrays, 10: DescriptorErrorKind.CrippenParamNumeric, 11: DescriptorErrorKind.MissingCrippenMrContributions, 12: DescriptorErrorKind.MissingCrippenMr, 13: DescriptorErrorKind.InvalidCrippenOptionalRows, 14: DescriptorErrorKind.MissingCrippenDefaultPattern, 15: DescriptorErrorKind.Hydrogens, 16: DescriptorErrorKind.CountOverflow, 17: DescriptorErrorKind.Valence, 18: DescriptorErrorKind.InvalidValenceRows, 19: DescriptorErrorKind.Unsupported, 20: DescriptorErrorKind.Ring, 21: DescriptorErrorKind.Search, 22: DescriptorErrorKind.Stereo})
exception cosmolkit.DescriptorReadError(*args, **kwargs)

Failure in the descriptors domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

DescriptorReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: DescriptorError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: DescriptorReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.DescriptorReadErrorKind(value)

Discriminants of DescriptorReadErrorKind.

Members: MissingPreparedValence, CachePoisoned, MissingInitializedRings, Algorithm, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
Algorithm = DescriptorReadErrorKind.Algorithm
CachePoisoned = DescriptorReadErrorKind.CachePoisoned
MissingInitializedRings = DescriptorReadErrorKind.MissingInitializedRings
MissingPreparedValence = DescriptorReadErrorKind.MissingPreparedValence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingPreparedValence': DescriptorReadErrorKind.MissingPreparedValence, 'CachePoisoned': DescriptorReadErrorKind.CachePoisoned, 'MissingInitializedRings': DescriptorReadErrorKind.MissingInitializedRings, 'Algorithm': DescriptorReadErrorKind.Algorithm})
values = mappingproxy({0: DescriptorReadErrorKind.MissingPreparedValence, 1: DescriptorReadErrorKind.CachePoisoned, 2: DescriptorReadErrorKind.MissingInitializedRings, 3: DescriptorReadErrorKind.Algorithm})
exception cosmolkit.DescriptorSearchCause(*args, **kwargs)

Failure in the descriptors domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

DescriptorSearchCause is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: SmartsParseError | SubstructMatchError | QueryMatchContextError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: DescriptorSearchCauseKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.DescriptorSearchCauseKind(value)

Discriminants of DescriptorSearchCauseKind.

Members: Compile, Match, Context, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Compile = DescriptorSearchCauseKind.Compile
Context = DescriptorSearchCauseKind.Context
Match = DescriptorSearchCauseKind.Match
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Compile': DescriptorSearchCauseKind.Compile, 'Match': DescriptorSearchCauseKind.Match, 'Context': DescriptorSearchCauseKind.Context})
values = mappingproxy({0: DescriptorSearchCauseKind.Compile, 1: DescriptorSearchCauseKind.Match, 2: DescriptorSearchCauseKind.Context})
exception cosmolkit.DispatchedUffOptimizationError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

DispatchedUffOptimizationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: AutomaticForceFieldConstructionError | UffThreadCountError | ThreadCountError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: DispatchedUffOptimizationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.DispatchedUffOptimizationErrorKind(value)

Discriminants of DispatchedUffOptimizationErrorKind.

Members: Construction, ThreadCount, ThreadObservation, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Construction = DispatchedUffOptimizationErrorKind.Construction
ThreadCount = DispatchedUffOptimizationErrorKind.ThreadCount
ThreadObservation = DispatchedUffOptimizationErrorKind.ThreadObservation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Construction': DispatchedUffOptimizationErrorKind.Construction, 'ThreadCount': DispatchedUffOptimizationErrorKind.ThreadCount, 'ThreadObservation': DispatchedUffOptimizationErrorKind.ThreadObservation})
values = mappingproxy({0: DispatchedUffOptimizationErrorKind.Construction, 1: DispatchedUffOptimizationErrorKind.ThreadCount, 2: DispatchedUffOptimizationErrorKind.ThreadObservation})
class cosmolkit.DistanceMatrix3dParams(*, conformer_id=Ellipsis, use_atom_weights=Ellipsis)

Conformer selection and diagonal weighting for Cartesian distance matrices.

Members (2)
conformer_id: int | None

Stored 3D conformer identifier, or None for default selection.

use_atom_weights: bool

Set diagonal entries using the native atomic-number weighting.

class cosmolkit.DistanceMatrixParams(*, use_bond_order=Ellipsis, use_atom_weights=Ellipsis)

Public options for a full-molecule topological distance matrix.

Active atom and bond subsets remain detached implementation APIs because they do not describe an ordinary single-molecule query projection.

Members (2)
use_atom_weights: bool

Set diagonal entries using the native atomic-number weighting.

use_bond_order: bool

Weight topological path lengths by reciprocal bond order.

class cosmolkit.DistGeomForceFieldError

Distance-geometry force-field construction diagnostic.

Members (4)
index: int | None

Index reported by the failing native check. Applies to DistGeomForceFieldError.IndexOverflow. None when this payload is absent.

inversion: UffInversionContributionError | None

Structured native error payload. Present for DistGeomForceFieldError.Inversion; None when unavailable.

kernel: ForceFieldKernelError | None

Structured native error payload. Present for DistGeomForceFieldError.Kernel; None when unavailable.

variant: DistGeomForceFieldErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.DistGeomForceFieldErrorKind(value)

Discriminants of DistGeomForceFieldErrorKind.

Members: Kernel, Inversion, IndexOverflow, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
IndexOverflow = DistGeomForceFieldErrorKind.IndexOverflow
Inversion = DistGeomForceFieldErrorKind.Inversion
Kernel = DistGeomForceFieldErrorKind.Kernel
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Kernel': DistGeomForceFieldErrorKind.Kernel, 'Inversion': DistGeomForceFieldErrorKind.Inversion, 'IndexOverflow': DistGeomForceFieldErrorKind.IndexOverflow})
values = mappingproxy({0: DistGeomForceFieldErrorKind.Kernel, 1: DistGeomForceFieldErrorKind.Inversion, 2: DistGeomForceFieldErrorKind.IndexOverflow})
exception cosmolkit.DoubleBondStereoError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

DoubleBondStereoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (20)
property actual: int | None

Observed value reported by the native check. Applies to DoubleBondStereoError.RankCount, DoubleBondStereoError.RingRowCount. None when this payload is absent.

property atom: int | None

Atom identifier implicated in the failure. Applies to DoubleBondStereoError.UnsignedPropertyOverflow, DoubleBondStereoError.InvalidPropertyKind, DoubleBondStereoError.NumericPropertyRead, DoubleBondStereoError.AtomOutOfRange. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to DoubleBondStereoError.AtomOutOfRange, DoubleBondStereoError.RankCount. None when this payload is absent.

property bond: int | None

Bond index involved in the failure. Present for DoubleBondStereoError.UnsignedPropertyOverflow, DoubleBondStereoError.InvalidPropertyKind, DoubleBondStereoError.NumericPropertyRead, DoubleBondStereoError.BondOutOfRange, DoubleBondStereoError.NotDoubleBond, DoubleBondStereoError.UndefinedStereo, DoubleBondStereoError.UnsupportedStereo, DoubleBondStereoError.InvalidEndpointDegree, DoubleBondStereoError.StereoReferenceRequired, DoubleBondStereoError.StereoReferenceNotNeighbor, DoubleBondStereoError.StereoReferenceIsOppositeEndpoint, DoubleBondStereoError.ControllingAtomMismatch, DoubleBondStereoError.ControllingSlotOverflow; None when unavailable.

property bond_count: int | None

Readonly bond_count payload of the BondOutOfRange error variant; None for other variants.

property degree: int | None

Neighbor count reported by the native check. Applies to DoubleBondStereoError.InvalidEndpointDegree, DoubleBondStereoError.ControllingSlotOverflow. None when this payload is absent.

property dimension: str | None

Readonly dimension payload of the RingRowCount error variant; None for other variants.

property direction: BondDirection | None

Readonly direction payload of the InvalidDirection error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property endpoint: str | None

Bond endpoint associated with the stereo failure. Present for DoubleBondStereoError.InvalidEndpointDegree, DoubleBondStereoError.StereoReferenceNotNeighbor, DoubleBondStereoError.StereoReferenceIsOppositeEndpoint, DoubleBondStereoError.ControllingAtomMismatch, DoubleBondStereoError.ControllingSlotOverflow; None when unavailable.

property expected: int | None

Readonly expected payload of the RingRowCount error variant; None for other variants.

property kind: PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to DoubleBondStereoError.InvalidPropertyKind. None when this payload is absent.

Type:

{“role”

property order: BondOrder | None

Bond order associated with the failure. Present for DoubleBondStereoError.NotDoubleBond; None when unavailable.

property property: str | None

Property name involved in the failure. Applies to DoubleBondStereoError.UnsignedPropertyOverflow, DoubleBondStereoError.InvalidPropertyKind, DoubleBondStereoError.NumericPropertyRead. None when this payload is absent.

property reference: int | None

Stereo or structural reference implicated in the failure. Applies to DoubleBondStereoError.StereoReferenceNotNeighbor, DoubleBondStereoError.StereoReferenceIsOppositeEndpoint, DoubleBondStereoError.ControllingAtomMismatch. None when this payload is absent.

property source: RingFindingError | PropertyIntReadError | TopologyValidationError | BondValueError | CoordinateValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stereo: BondStereo | None

Bond stereo value rejected by this failure; None for other variants.

property value: int | None

Readonly value payload of the UnsignedPropertyOverflow error variant; None for other variants.

property variant: DoubleBondStereoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.DoubleBondStereoErrorKind(value)

Discriminants of DoubleBondStereoErrorKind.

Members: Rings, UnsignedPropertyOverflow, InvalidPropertyKind, NumericPropertyRead, InvalidTopology, BondValue, BondOutOfRange, AtomOutOfRange, NotDoubleBond, UndefinedStereo, UnsupportedStereo, InvalidEndpointDegree, InvalidDirection, RankCount, RingInfoNotInitialized, RingRowCount, InvalidConformer, StereoReferenceRequired, StereoReferenceNotNeighbor, StereoReferenceIsOppositeEndpoint, ControllingAtomMismatch, ControllingSlotOverflow, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (25)
AtomOutOfRange = DoubleBondStereoErrorKind.AtomOutOfRange
BondOutOfRange = DoubleBondStereoErrorKind.BondOutOfRange
BondValue = DoubleBondStereoErrorKind.BondValue
ControllingAtomMismatch = DoubleBondStereoErrorKind.ControllingAtomMismatch
ControllingSlotOverflow = DoubleBondStereoErrorKind.ControllingSlotOverflow
InvalidConformer = DoubleBondStereoErrorKind.InvalidConformer
InvalidDirection = DoubleBondStereoErrorKind.InvalidDirection
InvalidEndpointDegree = DoubleBondStereoErrorKind.InvalidEndpointDegree
InvalidPropertyKind = DoubleBondStereoErrorKind.InvalidPropertyKind
InvalidTopology = DoubleBondStereoErrorKind.InvalidTopology
NotDoubleBond = DoubleBondStereoErrorKind.NotDoubleBond
NumericPropertyRead = DoubleBondStereoErrorKind.NumericPropertyRead
RankCount = DoubleBondStereoErrorKind.RankCount
RingInfoNotInitialized = DoubleBondStereoErrorKind.RingInfoNotInitialized
RingRowCount = DoubleBondStereoErrorKind.RingRowCount
Rings = DoubleBondStereoErrorKind.Rings
StereoReferenceIsOppositeEndpoint = DoubleBondStereoErrorKind.StereoReferenceIsOppositeEndpoint
StereoReferenceNotNeighbor = DoubleBondStereoErrorKind.StereoReferenceNotNeighbor
StereoReferenceRequired = DoubleBondStereoErrorKind.StereoReferenceRequired
UndefinedStereo = DoubleBondStereoErrorKind.UndefinedStereo
UnsignedPropertyOverflow = DoubleBondStereoErrorKind.UnsignedPropertyOverflow
UnsupportedStereo = DoubleBondStereoErrorKind.UnsupportedStereo
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Rings': DoubleBondStereoErrorKind.Rings, 'UnsignedPropertyOverflow': DoubleBondStereoErrorKind.UnsignedPropertyOverflow, 'InvalidPropertyKind': DoubleBondStereoErrorKind.InvalidPropertyKind, 'NumericPropertyRead': DoubleBondStereoErrorKind.NumericPropertyRead, 'InvalidTopology': DoubleBondStereoErrorKind.InvalidTopology, 'BondValue': DoubleBondStereoErrorKind.BondValue, 'BondOutOfRange': DoubleBondStereoErrorKind.BondOutOfRange, 'AtomOutOfRange': DoubleBondStereoErrorKind.AtomOutOfRange, 'NotDoubleBond': DoubleBondStereoErrorKind.NotDoubleBond, 'UndefinedStereo': DoubleBondStereoErrorKind.UndefinedStereo, 'UnsupportedStereo': DoubleBondStereoErrorKind.UnsupportedStereo, 'InvalidEndpointDegree': DoubleBondStereoErrorKind.InvalidEndpointDegree, 'InvalidDirection': DoubleBondStereoErrorKind.InvalidDirection, 'RankCount': DoubleBondStereoErrorKind.RankCount, 'RingInfoNotInitialized': DoubleBondStereoErrorKind.RingInfoNotInitialized, 'RingRowCount': DoubleBondStereoErrorKind.RingRowCount, 'InvalidConformer': DoubleBondStereoErrorKind.InvalidConformer, 'StereoReferenceRequired': DoubleBondStereoErrorKind.StereoReferenceRequired, 'StereoReferenceNotNeighbor': DoubleBondStereoErrorKind.StereoReferenceNotNeighbor, 'StereoReferenceIsOppositeEndpoint': DoubleBondStereoErrorKind.StereoReferenceIsOppositeEndpoint, 'ControllingAtomMismatch': DoubleBondStereoErrorKind.ControllingAtomMismatch, 'ControllingSlotOverflow': DoubleBondStereoErrorKind.ControllingSlotOverflow})
values = mappingproxy({0: DoubleBondStereoErrorKind.Rings, 1: DoubleBondStereoErrorKind.UnsignedPropertyOverflow, 2: DoubleBondStereoErrorKind.InvalidPropertyKind, 3: DoubleBondStereoErrorKind.NumericPropertyRead, 4: DoubleBondStereoErrorKind.InvalidTopology, 5: DoubleBondStereoErrorKind.BondValue, 6: DoubleBondStereoErrorKind.BondOutOfRange, 7: DoubleBondStereoErrorKind.AtomOutOfRange, 8: DoubleBondStereoErrorKind.NotDoubleBond, 9: DoubleBondStereoErrorKind.UndefinedStereo, 10: DoubleBondStereoErrorKind.UnsupportedStereo, 11: DoubleBondStereoErrorKind.InvalidEndpointDegree, 12: DoubleBondStereoErrorKind.InvalidDirection, 13: DoubleBondStereoErrorKind.RankCount, 14: DoubleBondStereoErrorKind.RingInfoNotInitialized, 15: DoubleBondStereoErrorKind.RingRowCount, 16: DoubleBondStereoErrorKind.InvalidConformer, 17: DoubleBondStereoErrorKind.StereoReferenceRequired, 18: DoubleBondStereoErrorKind.StereoReferenceNotNeighbor, 19: DoubleBondStereoErrorKind.StereoReferenceIsOppositeEndpoint, 20: DoubleBondStereoErrorKind.ControllingAtomMismatch, 21: DoubleBondStereoErrorKind.ControllingSlotOverflow})
exception cosmolkit.DoubleLexicalReadError(*args, **kwargs)

DoubleLexicalReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property consumed: int

Number of input bytes consumed before conversion failed.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property kind: DoubleLexicalReadErrorKind

“error_payload”} Native floating-point lexical conversion failure category.

Type:

{“role”

property state: SourceNumericStreamState

“error_payload”} Native numeric stream flags at the point of failure.

Type:

{“role”

property value_bits: int | None

Optional IEEE-754 bits of the value retained by the failed conversion.

class cosmolkit.DoubleLexicalReadErrorKind(value)

Typed DoubleLexicalReadErrorKind values corresponding to the Rust enum.

Members: Syntax, TrailingByte, Overflow, FloatingEnvironmentNotModeled, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
FloatingEnvironmentNotModeled = DoubleLexicalReadErrorKind.FloatingEnvironmentNotModeled
Overflow = DoubleLexicalReadErrorKind.Overflow
Syntax = DoubleLexicalReadErrorKind.Syntax
TrailingByte = DoubleLexicalReadErrorKind.TrailingByte
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Syntax': DoubleLexicalReadErrorKind.Syntax, 'TrailingByte': DoubleLexicalReadErrorKind.TrailingByte, 'Overflow': DoubleLexicalReadErrorKind.Overflow, 'FloatingEnvironmentNotModeled': DoubleLexicalReadErrorKind.FloatingEnvironmentNotModeled})
values = mappingproxy({0: DoubleLexicalReadErrorKind.Syntax, 1: DoubleLexicalReadErrorKind.TrailingByte, 2: DoubleLexicalReadErrorKind.Overflow, 3: DoubleLexicalReadErrorKind.FloatingEnvironmentNotModeled})
exception cosmolkit.DrawingError(*args, **kwargs)

Failure in the depict domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

DrawingError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (14)
property actual: int | None

Readonly actual payload of the StateRows error variant; None for other variants.

property atom_count: int | None

Readonly atom_count payload of the VariationIndex error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the StateRows error variant; None for other variants.

property field: str | None

Field whose content or type caused the failure. Applies to DrawingError.StateRows, DrawingError.DataFieldDouble. None when this payload is absent.

property group: int | None

Readonly group payload of the DataFieldDouble error variant; None for other variants.

property height: int | None

Height reported by the failed native dimension check. Applies to DrawingError.InvalidDimensions, DrawingError.PixmapAllocation. None when this payload is absent.

property index: int | None

Readonly index payload of the VariationIndex error variant; None for other variants.

property reason: str | None

Readonly reason payload of the HydrogenAppend error variant; None for other variants.

property row: int | None

Readonly row payload of the HydrogenAppend error variant; None for other variants.

property source: PropertyValueError | TopologyValidationError | CoordinateValidationError | MappingValidationError | KekulizeError | HydrogenError | WedgeError | ValenceError | Coordinate2DError | FromUtf8Error | SvgParseError | IoError | Utf8Error | ExternalError | PropertyStringError | UnsignedStreamArrayError | DoubleLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: DrawingErrorKind

Exact Rust error variant, independent of the human-readable message.

property width: int | None

Width reported by the failing native check. Applies to DrawingError.InvalidDimensions, DrawingError.PixmapAllocation. None when this payload is absent.

class cosmolkit.DrawingErrorKind(value)

Discriminants of DrawingErrorKind.

Members: Property, Topology, Coordinates, Mapping, Kekulize, Hydrogen, Wedge, Valence, CoordinateGeneration, StateRows, HydrogenAppend, InvalidDimensions, SvgTextProjection, SvgParse, PixmapAllocation, PngEncode, PropertyString, VariationArray, VariationIndex, DataFieldDouble, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (23)
CoordinateGeneration = DrawingErrorKind.CoordinateGeneration
Coordinates = DrawingErrorKind.Coordinates
DataFieldDouble = DrawingErrorKind.DataFieldDouble
Hydrogen = DrawingErrorKind.Hydrogen
HydrogenAppend = DrawingErrorKind.HydrogenAppend
InvalidDimensions = DrawingErrorKind.InvalidDimensions
Kekulize = DrawingErrorKind.Kekulize
Mapping = DrawingErrorKind.Mapping
PixmapAllocation = DrawingErrorKind.PixmapAllocation
PngEncode = DrawingErrorKind.PngEncode
Property = DrawingErrorKind.Property
PropertyString = DrawingErrorKind.PropertyString
StateRows = DrawingErrorKind.StateRows
SvgParse = DrawingErrorKind.SvgParse
SvgTextProjection = DrawingErrorKind.SvgTextProjection
Topology = DrawingErrorKind.Topology
Valence = DrawingErrorKind.Valence
VariationArray = DrawingErrorKind.VariationArray
VariationIndex = DrawingErrorKind.VariationIndex
Wedge = DrawingErrorKind.Wedge
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Property': DrawingErrorKind.Property, 'Topology': DrawingErrorKind.Topology, 'Coordinates': DrawingErrorKind.Coordinates, 'Mapping': DrawingErrorKind.Mapping, 'Kekulize': DrawingErrorKind.Kekulize, 'Hydrogen': DrawingErrorKind.Hydrogen, 'Wedge': DrawingErrorKind.Wedge, 'Valence': DrawingErrorKind.Valence, 'CoordinateGeneration': DrawingErrorKind.CoordinateGeneration, 'StateRows': DrawingErrorKind.StateRows, 'HydrogenAppend': DrawingErrorKind.HydrogenAppend, 'InvalidDimensions': DrawingErrorKind.InvalidDimensions, 'SvgTextProjection': DrawingErrorKind.SvgTextProjection, 'SvgParse': DrawingErrorKind.SvgParse, 'PixmapAllocation': DrawingErrorKind.PixmapAllocation, 'PngEncode': DrawingErrorKind.PngEncode, 'PropertyString': DrawingErrorKind.PropertyString, 'VariationArray': DrawingErrorKind.VariationArray, 'VariationIndex': DrawingErrorKind.VariationIndex, 'DataFieldDouble': DrawingErrorKind.DataFieldDouble})
values = mappingproxy({0: DrawingErrorKind.Property, 1: DrawingErrorKind.Topology, 2: DrawingErrorKind.Coordinates, 3: DrawingErrorKind.Mapping, 4: DrawingErrorKind.Kekulize, 5: DrawingErrorKind.Hydrogen, 6: DrawingErrorKind.Wedge, 7: DrawingErrorKind.Valence, 8: DrawingErrorKind.CoordinateGeneration, 9: DrawingErrorKind.StateRows, 10: DrawingErrorKind.HydrogenAppend, 11: DrawingErrorKind.InvalidDimensions, 12: DrawingErrorKind.SvgTextProjection, 13: DrawingErrorKind.SvgParse, 14: DrawingErrorKind.PixmapAllocation, 15: DrawingErrorKind.PngEncode, 16: DrawingErrorKind.PropertyString, 17: DrawingErrorKind.VariationArray, 18: DrawingErrorKind.VariationIndex, 19: DrawingErrorKind.DataFieldDouble})
exception cosmolkit.DrawingWriteError(*args, **kwargs)

Failure in the depict domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

DrawingWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property path: pathlib.Path | None

Filesystem path involved in the operation. Applies to DrawingWriteError.Io. None when this payload is absent.

property source: DrawingError | IoError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: DrawingWriteErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.DrawingWriteErrorKind(value)

Discriminants of DrawingWriteErrorKind.

Members: Drawing, Io, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Drawing = DrawingWriteErrorKind.Drawing
Io = DrawingWriteErrorKind.Io
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Drawing': DrawingWriteErrorKind.Drawing, 'Io': DrawingWriteErrorKind.Io})
values = mappingproxy({0: DrawingWriteErrorKind.Drawing, 1: DrawingWriteErrorKind.Io})
class cosmolkit.Element

Chemical element identified by atomic number, with value equality and hashing. DUMMY represents atomic number zero. Use from_symbol or from_atomic_number to look up a value; an unrecognized symbol or number returns None.

Members (123)
AC = <cosmolkit.Element object>
AG = <cosmolkit.Element object>
AL = <cosmolkit.Element object>
AM = <cosmolkit.Element object>
AR = <cosmolkit.Element object>
AS = <cosmolkit.Element object>
AT = <cosmolkit.Element object>
AU = <cosmolkit.Element object>
B = <cosmolkit.Element object>
BA = <cosmolkit.Element object>
BE = <cosmolkit.Element object>
BH = <cosmolkit.Element object>
BI = <cosmolkit.Element object>
BK = <cosmolkit.Element object>
BR = <cosmolkit.Element object>
C = <cosmolkit.Element object>
CA = <cosmolkit.Element object>
CD = <cosmolkit.Element object>
CE = <cosmolkit.Element object>
CF = <cosmolkit.Element object>
CL = <cosmolkit.Element object>
CM = <cosmolkit.Element object>
CN = <cosmolkit.Element object>
CO = <cosmolkit.Element object>
CR = <cosmolkit.Element object>
CS = <cosmolkit.Element object>
CU = <cosmolkit.Element object>
DB = <cosmolkit.Element object>
DS = <cosmolkit.Element object>
DUMMY = <cosmolkit.Element object>
DY = <cosmolkit.Element object>
ER = <cosmolkit.Element object>
ES = <cosmolkit.Element object>
EU = <cosmolkit.Element object>
F = <cosmolkit.Element object>
FE = <cosmolkit.Element object>
FL = <cosmolkit.Element object>
FM = <cosmolkit.Element object>
FR = <cosmolkit.Element object>
GA = <cosmolkit.Element object>
GD = <cosmolkit.Element object>
GE = <cosmolkit.Element object>
H = <cosmolkit.Element object>
HE = <cosmolkit.Element object>
HF = <cosmolkit.Element object>
HG = <cosmolkit.Element object>
HO = <cosmolkit.Element object>
HS = <cosmolkit.Element object>
I = <cosmolkit.Element object>
IN = <cosmolkit.Element object>
IR = <cosmolkit.Element object>
K = <cosmolkit.Element object>
KR = <cosmolkit.Element object>
LA = <cosmolkit.Element object>
LI = <cosmolkit.Element object>
LR = <cosmolkit.Element object>
LU = <cosmolkit.Element object>
LV = <cosmolkit.Element object>
MC = <cosmolkit.Element object>
MD = <cosmolkit.Element object>
MG = <cosmolkit.Element object>
MN = <cosmolkit.Element object>
MO = <cosmolkit.Element object>
MT = <cosmolkit.Element object>
N = <cosmolkit.Element object>
NA = <cosmolkit.Element object>
NB = <cosmolkit.Element object>
ND = <cosmolkit.Element object>
NE = <cosmolkit.Element object>
NH = <cosmolkit.Element object>
NI = <cosmolkit.Element object>
NO = <cosmolkit.Element object>
NP = <cosmolkit.Element object>
O = <cosmolkit.Element object>
OG = <cosmolkit.Element object>
OS = <cosmolkit.Element object>
P = <cosmolkit.Element object>
PA = <cosmolkit.Element object>
PB = <cosmolkit.Element object>
PD = <cosmolkit.Element object>
PM = <cosmolkit.Element object>
PO = <cosmolkit.Element object>
PR = <cosmolkit.Element object>
PT = <cosmolkit.Element object>
PU = <cosmolkit.Element object>
RA = <cosmolkit.Element object>
RB = <cosmolkit.Element object>
RE = <cosmolkit.Element object>
RF = <cosmolkit.Element object>
RG = <cosmolkit.Element object>
RH = <cosmolkit.Element object>
RN = <cosmolkit.Element object>
RU = <cosmolkit.Element object>
S = <cosmolkit.Element object>
SB = <cosmolkit.Element object>
SC = <cosmolkit.Element object>
SE = <cosmolkit.Element object>
SG = <cosmolkit.Element object>
SI = <cosmolkit.Element object>
SM = <cosmolkit.Element object>
SN = <cosmolkit.Element object>
SR = <cosmolkit.Element object>
TA = <cosmolkit.Element object>
TB = <cosmolkit.Element object>
TC = <cosmolkit.Element object>
TE = <cosmolkit.Element object>
TH = <cosmolkit.Element object>
TI = <cosmolkit.Element object>
TL = <cosmolkit.Element object>
TM = <cosmolkit.Element object>
TS = <cosmolkit.Element object>
U = <cosmolkit.Element object>
V = <cosmolkit.Element object>
W = <cosmolkit.Element object>
XE = <cosmolkit.Element object>
Y = <cosmolkit.Element object>
YB = <cosmolkit.Element object>
ZN = <cosmolkit.Element object>
ZR = <cosmolkit.Element object>
atomic_number: int

Atomic number (proton count), or zero for DUMMY.

static from_atomic_number(atomic_number) → Element | None

Look up an atomic number, including zero for DUMMY; return None if it is unknown.

static from_symbol(symbol) → Element | None

Look up a case-sensitive element symbol such as “Cl”; return None if it is unknown.

symbol: str

Canonical chemical symbol, preserving element-name capitalization.

class cosmolkit.ElementInfo

Readonly periodic-table metadata for an element, including native valence and radius data.

Members (8)
atomic_number: int

Atomic number of the element.

atomic_weight: float

Standard atomic weight from the native periodic table.

element: Element

Element represented by this periodic-table row.

outer_electrons: int

Number of outer-shell electrons in the native periodic table.

period: int

Periodic-table period number.

rb0: float

RDKit-defined Rb0 bond radius in angstroms.

symbol: str

Conventional chemical element symbol.

valences: list[int]

Allowed valence entries from the native table, retaining any native sentinel values.

class cosmolkit.EmbedFailureCause(value)

Typed EmbedFailureCause values corresponding to the Rust enum.

Members: InitialCoords, FirstMinimization, CheckTetrahedralCenters, CheckChiralCenters, MinimizeFourthDimension, EtkMinimization, FinalChiralBounds, FinalCenterInVolume, LinearDoubleBond, BadDoubleBondStereo, CheckChiralCenters2, ExceededTimeout, Minimization, KtermViolation, Clash, EndOfEnum, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (19)
BadDoubleBondStereo = EmbedFailureCause.BadDoubleBondStereo
CheckChiralCenters = EmbedFailureCause.CheckChiralCenters
CheckChiralCenters2 = EmbedFailureCause.CheckChiralCenters2
CheckTetrahedralCenters = EmbedFailureCause.CheckTetrahedralCenters
Clash = EmbedFailureCause.Clash
EndOfEnum = EmbedFailureCause.EndOfEnum
EtkMinimization = EmbedFailureCause.EtkMinimization
ExceededTimeout = EmbedFailureCause.ExceededTimeout
FinalCenterInVolume = EmbedFailureCause.FinalCenterInVolume
FinalChiralBounds = EmbedFailureCause.FinalChiralBounds
FirstMinimization = EmbedFailureCause.FirstMinimization
InitialCoords = EmbedFailureCause.InitialCoords
KtermViolation = EmbedFailureCause.KtermViolation
LinearDoubleBond = EmbedFailureCause.LinearDoubleBond
Minimization = EmbedFailureCause.Minimization
MinimizeFourthDimension = EmbedFailureCause.MinimizeFourthDimension
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InitialCoords': EmbedFailureCause.InitialCoords, 'FirstMinimization': EmbedFailureCause.FirstMinimization, 'CheckTetrahedralCenters': EmbedFailureCause.CheckTetrahedralCenters, 'CheckChiralCenters': EmbedFailureCause.CheckChiralCenters, 'MinimizeFourthDimension': EmbedFailureCause.MinimizeFourthDimension, 'EtkMinimization': EmbedFailureCause.EtkMinimization, 'FinalChiralBounds': EmbedFailureCause.FinalChiralBounds, 'FinalCenterInVolume': EmbedFailureCause.FinalCenterInVolume, 'LinearDoubleBond': EmbedFailureCause.LinearDoubleBond, 'BadDoubleBondStereo': EmbedFailureCause.BadDoubleBondStereo, 'CheckChiralCenters2': EmbedFailureCause.CheckChiralCenters2, 'ExceededTimeout': EmbedFailureCause.ExceededTimeout, 'Minimization': EmbedFailureCause.Minimization, 'KtermViolation': EmbedFailureCause.KtermViolation, 'Clash': EmbedFailureCause.Clash, 'EndOfEnum': EmbedFailureCause.EndOfEnum})
values = mappingproxy({0: EmbedFailureCause.InitialCoords, 1: EmbedFailureCause.FirstMinimization, 2: EmbedFailureCause.CheckTetrahedralCenters, 3: EmbedFailureCause.CheckChiralCenters, 4: EmbedFailureCause.MinimizeFourthDimension, 5: EmbedFailureCause.EtkMinimization, 6: EmbedFailureCause.FinalChiralBounds, 7: EmbedFailureCause.FinalCenterInVolume, 8: EmbedFailureCause.LinearDoubleBond, 9: EmbedFailureCause.BadDoubleBondStereo, 10: EmbedFailureCause.CheckChiralCenters2, 11: EmbedFailureCause.ExceededTimeout, 12: EmbedFailureCause.Minimization, 13: EmbedFailureCause.KtermViolation, 14: EmbedFailureCause.Clash, 15: EmbedFailureCause.EndOfEnum})
exception cosmolkit.EmbedFailureCountError(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

EmbedFailureCountError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property available: int | None

Readonly available payload of the MissingCounter error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Readonly index payload of the MissingCounter error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: EmbedFailureCountErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.EmbedFailureCountErrorKind(value)

Discriminants of EmbedFailureCountErrorKind.

Members: InvalidCause, MissingCounter, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
InvalidCause = EmbedFailureCountErrorKind.InvalidCause
MissingCounter = EmbedFailureCountErrorKind.MissingCounter
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidCause': EmbedFailureCountErrorKind.InvalidCause, 'MissingCounter': EmbedFailureCountErrorKind.MissingCounter})
values = mappingproxy({0: EmbedFailureCountErrorKind.InvalidCause, 1: EmbedFailureCountErrorKind.MissingCounter})
class cosmolkit.EmbedMoleculeResult(molecule, conf_id, params, termination=Ellipsis)

Single-conformer embedding result retaining the output molecule, optional generated ID and execution diagnostics.

Members (8)
conf_id: int | None

Generated conformer identifier, or None when no conformer was generated.

failure_count(cause) → int | None

Return the count for one failure cause, or None when tracking was disabled; invalid causes raise EmbedFailureCountError.

failure_counts: tuple[int, ...] | None

Readonly counts in EmbedFailureCause order, or None when tracking was disabled.

failures_tracked: bool

Whether failure-stage counters were enabled for this run.

molecule: Molecule

Output molecule as a copy-on-write value; editing it does not alter this result.

ok: bool

Whether a conformer identifier was produced by this single-conformer run.

params: EmbedParams

Independent configuration value carrying this run’s diagnostics; modifying it does not change the result.

termination: EmbedTermination

completed, timed out or interrupted; inspect generated IDs separately.

Type:

Reason embedding stopped

class cosmolkit.EmbedMultipleConfsResult(molecule, conf_ids, requested_num_confs, params, termination=Ellipsis)

Multi-conformer embedding result retaining successful IDs, the requested count and execution diagnostics.

Members (9)
conf_ids: list[int]

Identifiers of successfully generated conformers; failed attempts are not conformer IDs.

failure_count(cause) → int | None

Return the count for one failure cause, or None when tracking was disabled; invalid causes raise EmbedFailureCountError.

failure_counts: tuple[int, ...] | None

Readonly counts in EmbedFailureCause order, or None when tracking was disabled.

failures_tracked: bool

Whether failure-stage counters were enabled for this run.

generated_count: int

Number of successfully generated conformer IDs, not the number requested or attempted.

molecule: Molecule

Output molecule as a copy-on-write value; editing it does not alter this result.

params: EmbedParams

Independent configuration value carrying this run’s diagnostics; modifying it does not change the result.

requested_num_confs: int

Number of conformers requested, which may exceed the generated count after pruning or failure.

termination: EmbedTermination

completed, timed out or interrupted; inspect generated IDs separately.

Type:

Reason embedding stopped

class cosmolkit.EmbedParams(*, max_iterations=Ellipsis, num_threads=Ellipsis, random_seed=Ellipsis, clear_conformers=Ellipsis, use_random_coords=Ellipsis, box_size_mult=Ellipsis, rand_neg_eig=Ellipsis, num_zero_fail=Ellipsis, optimizer_force_tol=Ellipsis, ignore_smoothing_failures=Ellipsis, enforce_chirality=Ellipsis, use_exp_torsion_angle_prefs=Ellipsis, use_basic_knowledge=Ellipsis, verbose=Ellipsis, basin_thresh=Ellipsis, prune_rms_thresh=Ellipsis, only_heavy_atoms_for_rms=Ellipsis, et_version=Ellipsis, embed_fragments_separately=Ellipsis, use_small_ring_torsions=Ellipsis, use_macrocycle_torsions=Ellipsis, use_macrocycle14config=Ellipsis, timeout=Ellipsis, force_trans_amides=Ellipsis, use_symmetry_for_pruning=Ellipsis, bounds_mat_force_scaling=Ellipsis, track_failures=Ellipsis, enable_sequential_random_seeds=Ellipsis, symmetrize_conjugated_terminal_groups_for_pruning=Ellipsis, coord_map=Ellipsis, cpci=Ellipsis)

Distance-geometry embedding options with native presets and optional coordinate constraints. Set fields before execution; result objects carry execution diagnostics separately.

Members (43)
basin_thresh: float

Basin threshold used by the distance-geometry force field.

bounds_mat_force_scaling: float

Scale the bounds-matrix contribution to the embedding force field.

box_size_mult: float

Random-coordinate box scaling; negative values specify a fixed box side length by magnitude.

clear_conformers: bool

Remove existing conformers from the output before adding generated conformers.

coord_map: collections.abc.Mapping[int, tuple[float, ...]] | None

Readonly atom-index to three-dimensional coordinate constraints, or None. Replace the whole field to edit.

cpci: collections.abc.Mapping[tuple[int, int], float] | None

Readonly atom-pair to custom Coulomb-like interaction strengths, or None. Replace the whole field to edit.

static dg() → EmbedParams

Create parameters using the native dg embedding preset; subsequent field edits affect this configuration only.

embed_fragments_separately: bool

Embed disconnected molecular fragments separately.

enable_sequential_random_seeds: bool

Advance seeds sequentially across conformer generation attempts.

enforce_chirality: bool

Enforce the molecule’s specified chirality during embedding.

et_version: int

Experimental torsion parameter-set version, not the ETKDG preset number.

static etdg() → EmbedParams

Create parameters using the native etdg embedding preset; subsequent field edits affect this configuration only.

static etdg_v2() → EmbedParams

Create parameters using the native etdg_v2 embedding preset; subsequent field edits affect this configuration only.

static etkdg() → EmbedParams

Create parameters using the native etkdg embedding preset; subsequent field edits affect this configuration only.

static etkdg_v2() → EmbedParams

Create parameters using the native etkdg_v2 embedding preset; subsequent field edits affect this configuration only.

static etkdg_v3() → EmbedParams

Create parameters using the native etkdg_v3 embedding preset; subsequent field edits affect this configuration only.

failures: list[int]

Copy of recorded failure-stage counters; execution results also expose failure_counts directly.

force_trans_amides: bool

Favor trans amide conformations during embedding.

ignore_smoothing_failures: bool

Continue embedding when triangle smoothing fails.

static kdg() → EmbedParams

Create parameters using the native kdg embedding preset; subsequent field edits affect this configuration only.

max_iterations: int

Maximum embedding attempts per conformer; zero selects the algorithm’s automatic limit.

static new() → EmbedParams

Create distance-geometry parameters using the native constructor defaults.

num_threads: int

Number of embedding threads; zero requests the available hardware threads.

num_zero_fail: int

Number of zero eigenvalues at which embedding is rejected.

only_heavy_atoms_for_rms: bool

Use only heavy atoms when computing pruning RMS differences.

optimizer_force_tol: float

Force convergence tolerance for distance-geometry optimization.

prune_rms_thresh: float

RMS threshold for pruning similar conformers; a negative value disables pruning.

rand_neg_eig: bool

Use random coordinates for components associated with negative eigenvalues.

random_seed: int

Random-number seed; a negative value requests an unseeded run.

static sr_etkdg_v3() → EmbedParams

Create parameters using the native sr_etkdg_v3 embedding preset; subsequent field edits affect this configuration only.

symmetrize_conjugated_terminal_groups_for_pruning: bool

Treat conjugated terminal groups symmetrically during RMS pruning.

timeout: int

Embedding timeout in seconds; zero disables the timeout.

to_json() → str

Serialize the native JSON-supported embedding options; this is not a complete execution-state archive.

track_failures: bool

Collect counts of failed embedding stages in the returned diagnostics.

use_basic_knowledge: bool

Apply basic geometric knowledge, including preferred planar arrangements.

use_exp_torsion_angle_prefs: bool

Apply experimental torsion-angle preferences.

use_macrocycle14config: bool

Apply macrocycle-specific 1-4 distance-bound treatment.

use_macrocycle_torsions: bool

Include macrocycle torsion preferences.

use_random_coords: bool

Start from random Cartesian coordinates instead of distance-matrix eigenvectors.

use_small_ring_torsions: bool

Include small-ring torsion preferences.

use_symmetry_for_pruning: bool

Account for molecular symmetry when pruning similar conformers.

verbose: bool

Enable verbose embedding diagnostics.

with_json(json) → EmbedParams

Return an independent configuration updated from JSON using the native parameter parser.

exception cosmolkit.EmbedSeedError(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

EmbedSeedError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Readonly index payload of the ResultInvariant error variant; None for other variants.

property seed: int

Random seed associated with the failed embedding seed validation.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: int | None

Readonly value payload of the ResultInvariant error variant; None for other variants.

property variant: EmbedSeedErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.EmbedSeedErrorKind(value)

Discriminants of EmbedSeedErrorKind.

Members: InvalidRandomSeed, ResultInvariant, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
InvalidRandomSeed = EmbedSeedErrorKind.InvalidRandomSeed
ResultInvariant = EmbedSeedErrorKind.ResultInvariant
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidRandomSeed': EmbedSeedErrorKind.InvalidRandomSeed, 'ResultInvariant': EmbedSeedErrorKind.ResultInvariant})
values = mappingproxy({0: EmbedSeedErrorKind.InvalidRandomSeed, 1: EmbedSeedErrorKind.ResultInvariant})
class cosmolkit.EmbedTermination(value)

Typed EmbedTermination values corresponding to the Rust enum.

Members: Completed, TimedOut, Interrupted, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
Completed = EmbedTermination.Completed
Interrupted = EmbedTermination.Interrupted
TimedOut = EmbedTermination.TimedOut
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Completed': EmbedTermination.Completed, 'TimedOut': EmbedTermination.TimedOut, 'Interrupted': EmbedTermination.Interrupted})
values = mappingproxy({0: EmbedTermination.Completed, 1: EmbedTermination.TimedOut, 2: EmbedTermination.Interrupted})
class cosmolkit.EntityKind(value)

Typed EntityKind values corresponding to the Rust enum.

Members: Unknown, Polymer, NonPolymer, Branched, Water, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (8)
Branched = EntityKind.Branched
NonPolymer = EntityKind.NonPolymer
Polymer = EntityKind.Polymer
Unknown = EntityKind.Unknown
Water = EntityKind.Water
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unknown': EntityKind.Unknown, 'Polymer': EntityKind.Polymer, 'NonPolymer': EntityKind.NonPolymer, 'Branched': EntityKind.Branched, 'Water': EntityKind.Water})
values = mappingproxy({0: EntityKind.Unknown, 1: EntityKind.Polymer, 2: EntityKind.NonPolymer, 3: EntityKind.Branched, 4: EntityKind.Water})
class cosmolkit.EntitySourceIds(source_entity_id)

Entity identifier retained from the source structure file.

Members (1)
source_entity_id: str

Entity identifier used by the original structure file.

exception cosmolkit.EnumerationError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

EnumerationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (21)
property atom: int | None

Readonly atom payload of the InvalidFlipperAtom error variant; None for other variants.

property atom_property: AtomPropertyError | None

“error_payload”} Structured native error payload. Present for EnumerationError.AtomProperty; None when unavailable.

Type:

{“role”

property bit_count: int | None

Readonly bit_count payload of the RandomBitsSource error variant; None for other variants.

property bond: int | None

Readonly bond payload of the InvalidFlipperBond error variant; None for other variants.

property bond_property: BondValueError | None

“error_payload”} Structured native error payload. Present for EnumerationError.BondProperty; None when unavailable.

Type:

{“role”

property coordinates: CoordinateValidationError | None

“error_payload”} Structured native error payload. Present for EnumerationError.Coordinates; None when unavailable.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property double_bond: DoubleBondStereoError | None

“error_payload”} Structured native error payload. Present for EnumerationError.DoubleBond; None when unavailable.

Type:

{“role”

property embedding: GenerationError | None

“error_payload”} Structured GenerationError payload of EnumerationError.Embedding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property hydrogens: HydrogenError | None

“error_payload”} Hydrogen count or hydrogen-related payload reported by the native check. Applies to EnumerationError.Hydrogens. None when this payload is absent.

Type:

{“role”

property message: str | None

Readonly message payload of the RandomBitsSource error variant; None for other variants.

property molecule_property: MoleculePropertyError | None

“error_payload”} Structured native error payload. Present for EnumerationError.MoleculeProperty; None when unavailable.

Type:

{“role”

property potential_stereo: PotentialStereoError | None

“error_payload”} Structured native error payload. Present for EnumerationError.PotentialStereo; None when unavailable.

Type:

{“role”

property rings: RingFindingError | None

“error_payload”} Structured native error payload. Present for EnumerationError.Rings; None when unavailable.

Type:

{“role”

property smiles_write: SmilesParseError | None

“error_payload”} Structured native error payload. Present for EnumerationError.SmilesWrite; None when unavailable.

Type:

{“role”

property source: StereoGroupError | TopologyEditError | CoordinateValidationError | AtomPropertyError | BondValueError | MoleculePropertyError | PropertyIntReadError | PropertyULongReadError | PropertyUIntReadError | PropertyValueError | RequiredPropertyStringError | PropertyStringError | LegacyStereoError | PotentialStereoError | ParserStereoOrderError | StereoOrderError | SmilesStereoError | AtropisomerError | RingFindingError | ParserCarrierError | KekulizeError | SanitizeError | HydrogenError | ValenceError | ConjugationError | HybridizationError | TopologyValidationError | TemplateAttachmentOrderError | MappingValidationError | CanonicalRankError | DoubleBondStereoError | BoundsMatrixError | UffBoundsError | MatrixError | ForceFieldKernelError | UffInversionContributionError | CxQueryLoweringError | QueryGraphError | ThreadCountError | MoleculeFragmentsFailure | UffBuilderError | IoError | PoisonError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stereo: LegacyStereoError | None

“error_payload”} Structured native error payload. Present for EnumerationError.Stereo; None when unavailable.

Type:

{“role”

property topology: TopologyValidationError | None

“error_payload”} Structured native error payload. Present for EnumerationError.Topology; None when unavailable.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of EnumerationError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: EnumerationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.EnumerationErrorKind(value)

Discriminants of EnumerationErrorKind.

Members: Valence, Rings, Stereo, DoubleBond, SmilesWrite, PotentialStereo, Hydrogens, Embedding, AtomProperty, BondProperty, MoleculeProperty, Topology, Coordinates, InvalidFlipperAtom, InvalidFlipperBond, RandomBitsSource, RandomSourcePoisoned, EmbeddingCoordinates, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (21)
AtomProperty = EnumerationErrorKind.AtomProperty
BondProperty = EnumerationErrorKind.BondProperty
Coordinates = EnumerationErrorKind.Coordinates
DoubleBond = EnumerationErrorKind.DoubleBond
Embedding = EnumerationErrorKind.Embedding
EmbeddingCoordinates = EnumerationErrorKind.EmbeddingCoordinates
Hydrogens = EnumerationErrorKind.Hydrogens
InvalidFlipperAtom = EnumerationErrorKind.InvalidFlipperAtom
InvalidFlipperBond = EnumerationErrorKind.InvalidFlipperBond
MoleculeProperty = EnumerationErrorKind.MoleculeProperty
PotentialStereo = EnumerationErrorKind.PotentialStereo
RandomBitsSource = EnumerationErrorKind.RandomBitsSource
RandomSourcePoisoned = EnumerationErrorKind.RandomSourcePoisoned
Rings = EnumerationErrorKind.Rings
SmilesWrite = EnumerationErrorKind.SmilesWrite
Stereo = EnumerationErrorKind.Stereo
Topology = EnumerationErrorKind.Topology
Valence = EnumerationErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Valence': EnumerationErrorKind.Valence, 'Rings': EnumerationErrorKind.Rings, 'Stereo': EnumerationErrorKind.Stereo, 'DoubleBond': EnumerationErrorKind.DoubleBond, 'SmilesWrite': EnumerationErrorKind.SmilesWrite, 'PotentialStereo': EnumerationErrorKind.PotentialStereo, 'Hydrogens': EnumerationErrorKind.Hydrogens, 'Embedding': EnumerationErrorKind.Embedding, 'AtomProperty': EnumerationErrorKind.AtomProperty, 'BondProperty': EnumerationErrorKind.BondProperty, 'MoleculeProperty': EnumerationErrorKind.MoleculeProperty, 'Topology': EnumerationErrorKind.Topology, 'Coordinates': EnumerationErrorKind.Coordinates, 'InvalidFlipperAtom': EnumerationErrorKind.InvalidFlipperAtom, 'InvalidFlipperBond': EnumerationErrorKind.InvalidFlipperBond, 'RandomBitsSource': EnumerationErrorKind.RandomBitsSource, 'RandomSourcePoisoned': EnumerationErrorKind.RandomSourcePoisoned, 'EmbeddingCoordinates': EnumerationErrorKind.EmbeddingCoordinates})
values = mappingproxy({0: EnumerationErrorKind.Valence, 1: EnumerationErrorKind.Rings, 2: EnumerationErrorKind.Stereo, 3: EnumerationErrorKind.DoubleBond, 4: EnumerationErrorKind.SmilesWrite, 5: EnumerationErrorKind.PotentialStereo, 6: EnumerationErrorKind.Hydrogens, 7: EnumerationErrorKind.Embedding, 8: EnumerationErrorKind.AtomProperty, 9: EnumerationErrorKind.BondProperty, 10: EnumerationErrorKind.MoleculeProperty, 11: EnumerationErrorKind.Topology, 12: EnumerationErrorKind.Coordinates, 13: EnumerationErrorKind.InvalidFlipperAtom, 14: EnumerationErrorKind.InvalidFlipperBond, 15: EnumerationErrorKind.RandomBitsSource, 16: EnumerationErrorKind.RandomSourcePoisoned, 17: EnumerationErrorKind.EmbeddingCoordinates})
exception cosmolkit.EnumerationRunError(*args, **kwargs)

EnumerationRunError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: EnumerationError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.ExternalError(*args, **kwargs)

ExternalError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: IoError | Utf8Error | FromUtf8Error | ExternalError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.FeatureSpec

Read-only public feature declaration from the compiled Rust facade.

Members (3)
category: str

Category assigned to this feature declaration.

docs: str

Documentation text retained by the canonical feature declaration.

name: str

Canonical public feature name.

class cosmolkit.FeatureSpecIter

Iterator over the compiled feature declarations in native declaration order.

class cosmolkit.Fingerprint

Immutable bit fingerprint with an explicit bit-index capacity. on_bits() returns the set positions; to_numpy() expands bits to an independent uint8 array. Similarity and bit operations use native values.

Members (6)
static from_on_bits(n_bits, on_bits) → Fingerprint

Construct a bit fingerprint of n_bits positions from the supplied set-bit indices; invalid indices raise FingerprintError.

get_bit(bit) → bool

Read the bit at a zero-based index; out-of-range indices raise FingerprintError.

n_bits: int

Size of the fingerprint’s bit index space, not the number of set bits.

on_bits: list[int]

Return set-bit indices in increasing order.

tanimoto(other) → float

Calculate Tanimoto similarity to another fingerprint using the native size and empty-fingerprint rules.

to_numpy() → numpy.ndarray[tuple[int], numpy.dtype[numpy.uint8]]

Return an independent uint8 array with one entry per fingerprint bit. Shape is (n_bits,); entries are 0 or 1 in increasing bit-index order.

class cosmolkit.FingerprintAdditionalOutput

Mutable native fingerprint provenance collector. Allocate the desired outputs before passing it to fingerprint generation.

Members (12)
allocate_atom_counts() → None

Enable collection of per-atom contribution counts.

allocate_atom_to_bits() → None

Enable collection of contributing bit identifiers per atom.

allocate_atoms_per_bit() → None

Enable collection of participating atom sets per bit.

allocate_bit_info_map() → None

Enable collection of generator-specific bit provenance tuples.

allocate_bit_paths() → None

Enable collection of contributing paths per bit.

atom_counts: list[int] | None

Per-atom feature contribution counts, or None when not collected.

atom_to_bits: list[list[int]] | None

Contributing fingerprint bit identifiers for each atom, or None when not collected.

atoms_per_bit: dict[int, list[list[int]]] | None

Bit identifiers mapped to participating atom sets, or None when not collected.

bit_info_map: dict[int, list[tuple[int, int]]] | None

Bit identifiers mapped to native feature descriptors (center/radius or atom-pair endpoints, depending on the generator), or None when not collected.

bit_paths: dict[int, list[list[int]]] | None

Bit identifiers mapped to contributing native paths, or None when not collected.

static default() → FingerprintAdditionalOutput

Create a collector using the native default allocation policy.

static new() → FingerprintAdditionalOutput

Create an empty additional-output collector; enable individual outputs before fingerprint generation.

class cosmolkit.FingerprintBatch(values)

Ordered, immutable collection of optional Fingerprint values.

None retains a missing result at its original position. len() counts all records. Integer indexing returns a record; slices, index sequences and boolean masks return a new collection. Selections preserve order and duplicate indices.

Members (2)
len: int

Number of records, including missing (None) records.

to_numpy() → numpy.ndarray[tuple[int, int], numpy.dtype[numpy.uint8]]

Return an independent uint8 matrix of shape (number_of_records, n_bits). Rows retain batch order; columns are increasing bit indices, containing 0 or 1. None rows and unequal widths raise FingerprintBatchError rather than silently dropping records or padding fingerprints.

exception cosmolkit.FingerprintBatchError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

FingerprintBatchError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property actual: int | None

Readonly actual payload of the WidthMismatch error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the WidthMismatch error variant; None for other variants.

property index: int

Zero-based row containing a missing fingerprint or incompatible width.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: FingerprintBatchErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.FingerprintBatchErrorKind(value)

Discriminants of FingerprintBatchErrorKind.

Members: MissingRow, WidthMismatch, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
MissingRow = FingerprintBatchErrorKind.MissingRow
WidthMismatch = FingerprintBatchErrorKind.WidthMismatch
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingRow': FingerprintBatchErrorKind.MissingRow, 'WidthMismatch': FingerprintBatchErrorKind.WidthMismatch})
values = mappingproxy({0: FingerprintBatchErrorKind.MissingRow, 1: FingerprintBatchErrorKind.WidthMismatch})
exception cosmolkit.FingerprintError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

FingerprintError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (13)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property factor: int | None

Readonly factor payload of the InvalidFoldFactor error variant; None for other variants.

property index: int | None

Readonly index payload of the SparseIndexOutOfRange error variant; None for other variants.

property left: int | None

Readonly left payload of the BitLengthMismatch error variant; None for other variants.

property n_bits: int | None

Readonly n_bits payload of the InvalidFoldFactor error variant; None for other variants.

property reason: str | None

Readonly reason payload of the InvalidArguments error variant; None for other variants.

property right: int | None

Readonly right payload of the BitLengthMismatch error variant; None for other variants.

property site: str | None

Readonly site payload of the UndefinedArithmetic error variant; None for other variants.

property size: int | None

Readonly size payload of the SparseIndexOutOfRange error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: float | None

Readonly value payload of the RangeError error variant; None for other variants.

property variant: FingerprintErrorKind

Exact Rust error variant, independent of the human-readable message.

property what: str | None

Readonly what payload of the PreconditionViolation error variant; None for other variants.

class cosmolkit.FingerprintErrorKind(value)

Discriminants of FingerprintErrorKind.

Members: EmptyFingerprint, Unsupported, SparseIndexOutOfRange, BitLengthMismatch, InvalidFoldFactor, RangeError, UndefinedArithmetic, PreconditionViolation, InvalidArguments, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
BitLengthMismatch = FingerprintErrorKind.BitLengthMismatch
EmptyFingerprint = FingerprintErrorKind.EmptyFingerprint
InvalidArguments = FingerprintErrorKind.InvalidArguments
InvalidFoldFactor = FingerprintErrorKind.InvalidFoldFactor
PreconditionViolation = FingerprintErrorKind.PreconditionViolation
RangeError = FingerprintErrorKind.RangeError
SparseIndexOutOfRange = FingerprintErrorKind.SparseIndexOutOfRange
UndefinedArithmetic = FingerprintErrorKind.UndefinedArithmetic
Unsupported = FingerprintErrorKind.Unsupported
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyFingerprint': FingerprintErrorKind.EmptyFingerprint, 'Unsupported': FingerprintErrorKind.Unsupported, 'SparseIndexOutOfRange': FingerprintErrorKind.SparseIndexOutOfRange, 'BitLengthMismatch': FingerprintErrorKind.BitLengthMismatch, 'InvalidFoldFactor': FingerprintErrorKind.InvalidFoldFactor, 'RangeError': FingerprintErrorKind.RangeError, 'UndefinedArithmetic': FingerprintErrorKind.UndefinedArithmetic, 'PreconditionViolation': FingerprintErrorKind.PreconditionViolation, 'InvalidArguments': FingerprintErrorKind.InvalidArguments})
values = mappingproxy({0: FingerprintErrorKind.EmptyFingerprint, 1: FingerprintErrorKind.Unsupported, 2: FingerprintErrorKind.SparseIndexOutOfRange, 3: FingerprintErrorKind.BitLengthMismatch, 4: FingerprintErrorKind.InvalidFoldFactor, 5: FingerprintErrorKind.RangeError, 6: FingerprintErrorKind.UndefinedArithmetic, 7: FingerprintErrorKind.PreconditionViolation, 8: FingerprintErrorKind.InvalidArguments})
exception cosmolkit.FingerprintJsonError(*args, **kwargs)

FingerprintJsonError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property component: str | None

Coordinate component involved in the failure. Applies to FingerprintJsonError.UnsupportedComponent. None when this payload is absent.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property invalid: str | None

Explanation of invalid fingerprint configuration; None for other variants.

property source: SerdeJsonError | None

“error_source”} Actual underlying JSON parse error, identical to __cause__, or None.

Type:

{“role”

property source_type: str | None

Native source type reported by the failed conversion. Applies to FingerprintJsonError.UnsupportedComponent. None when this payload is absent.

property variant: FingerprintJsonErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.FingerprintJsonErrorKind(value)

Discriminants of FingerprintJsonErrorKind.

Members: Parse, Invalid, UnsupportedComponent, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Invalid = FingerprintJsonErrorKind.Invalid
Parse = FingerprintJsonErrorKind.Parse
UnsupportedComponent = FingerprintJsonErrorKind.UnsupportedComponent
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Parse': FingerprintJsonErrorKind.Parse, 'Invalid': FingerprintJsonErrorKind.Invalid, 'UnsupportedComponent': FingerprintJsonErrorKind.UnsupportedComponent})
values = mappingproxy({0: FingerprintJsonErrorKind.Parse, 1: FingerprintJsonErrorKind.Invalid, 2: FingerprintJsonErrorKind.UnsupportedComponent})
exception cosmolkit.FingerprintPreparationError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

FingerprintPreparationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: RingFindingError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: FingerprintPreparationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.FingerprintPreparationErrorKind(value)

Discriminants of FingerprintPreparationErrorKind.

Members: MissingPreparedValence, RingPreparation, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
MissingPreparedValence = FingerprintPreparationErrorKind.MissingPreparedValence
RingPreparation = FingerprintPreparationErrorKind.RingPreparation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingPreparedValence': FingerprintPreparationErrorKind.MissingPreparedValence, 'RingPreparation': FingerprintPreparationErrorKind.RingPreparation})
values = mappingproxy({0: FingerprintPreparationErrorKind.MissingPreparedValence, 1: FingerprintPreparationErrorKind.RingPreparation})
exception cosmolkit.FingerprintWorkerError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

FingerprintWorkerError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: ThreadCountError | IoError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: FingerprintWorkerErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.FingerprintWorkerErrorKind(value)

Discriminants of FingerprintWorkerErrorKind.

Members: ThreadCount, ThreadSpawn, Panic, Protocol, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
Panic = FingerprintWorkerErrorKind.Panic
Protocol = FingerprintWorkerErrorKind.Protocol
ThreadCount = FingerprintWorkerErrorKind.ThreadCount
ThreadSpawn = FingerprintWorkerErrorKind.ThreadSpawn
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ThreadCount': FingerprintWorkerErrorKind.ThreadCount, 'ThreadSpawn': FingerprintWorkerErrorKind.ThreadSpawn, 'Panic': FingerprintWorkerErrorKind.Panic, 'Protocol': FingerprintWorkerErrorKind.Protocol})
values = mappingproxy({0: FingerprintWorkerErrorKind.ThreadCount, 1: FingerprintWorkerErrorKind.ThreadSpawn, 2: FingerprintWorkerErrorKind.Panic, 3: FingerprintWorkerErrorKind.Protocol})
class cosmolkit.ForceFieldAngleConstraintParams(*, relative, min_angle_deg, max_angle_deg, force_constant)

Required angle restraint inputs; no implicit numerical defaults.

Members (4)
force_constant: float

Force constant multiplying the restraint penalty.

max_angle_deg: float

Upper bond-angle bound in degrees.

min_angle_deg: float

Lower bond-angle bound in degrees.

relative: bool

Interpret restraint bounds relative to the initial geometry instead of as absolute values.

class cosmolkit.ForceFieldAngleIndexArgument(value)

Typed ForceFieldAngleIndexArgument values corresponding to the Rust enum.

Members: First, Second, Third, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
First = ForceFieldAngleIndexArgument.First
Second = ForceFieldAngleIndexArgument.Second
Third = ForceFieldAngleIndexArgument.Third
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'First': ForceFieldAngleIndexArgument.First, 'Second': ForceFieldAngleIndexArgument.Second, 'Third': ForceFieldAngleIndexArgument.Third})
values = mappingproxy({0: ForceFieldAngleIndexArgument.First, 1: ForceFieldAngleIndexArgument.Second, 2: ForceFieldAngleIndexArgument.Third})
class cosmolkit.ForceFieldAngleRangeBound(value)

Typed ForceFieldAngleRangeBound values corresponding to the Rust enum.

Members: Minimum, Maximum, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Maximum = ForceFieldAngleRangeBound.Maximum
Minimum = ForceFieldAngleRangeBound.Minimum
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Minimum': ForceFieldAngleRangeBound.Minimum, 'Maximum': ForceFieldAngleRangeBound.Maximum})
values = mappingproxy({0: ForceFieldAngleRangeBound.Minimum, 1: ForceFieldAngleRangeBound.Maximum})
class cosmolkit.ForceFieldBondIndexArgument(value)

Typed ForceFieldBondIndexArgument values corresponding to the Rust enum.

Members: First, Second, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
First = ForceFieldBondIndexArgument.First
Second = ForceFieldBondIndexArgument.Second
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'First': ForceFieldBondIndexArgument.First, 'Second': ForceFieldBondIndexArgument.Second})
values = mappingproxy({0: ForceFieldBondIndexArgument.First, 1: ForceFieldBondIndexArgument.Second})
exception cosmolkit.ForceFieldConstructionError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ForceFieldConstructionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: UffBuilderError | NonbondedAssemblyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: ForceFieldConstructionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ForceFieldConstructionErrorKind(value)

Discriminants of ForceFieldConstructionErrorKind.

Members: Builder, Nonbonded, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Builder = ForceFieldConstructionErrorKind.Builder
Nonbonded = ForceFieldConstructionErrorKind.Nonbonded
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Builder': ForceFieldConstructionErrorKind.Builder, 'Nonbonded': ForceFieldConstructionErrorKind.Nonbonded})
values = mappingproxy({0: ForceFieldConstructionErrorKind.Builder, 1: ForceFieldConstructionErrorKind.Nonbonded})
class cosmolkit.ForceFieldDistanceConstraintParams(*, relative, min_distance, max_distance, force_constant)

Required distance restraint inputs; no implicit numerical defaults.

Members (4)
force_constant: float

Force constant multiplying the restraint penalty.

max_distance: float

Upper distance bound in angstroms.

min_distance: float

Lower distance bound in angstroms.

relative: bool

Interpret restraint bounds relative to the initial geometry instead of as absolute values.

class cosmolkit.ForceFieldEnergyGradient

Energy and per-atom Cartesian gradient evaluated by a persistent native force field.

Members (2)
energy: float

Evaluated force-field energy.

gradient: list[list[float]]

Independent list of Cartesian gradient triples in atom order.

exception cosmolkit.ForceFieldError(*args, **kwargs)

ForceFieldError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property actual: int | None

Observed size or index reported by the native failure, or None when inapplicable.

property atom_index: int | None

Atom index implicated in the failure, or None for failures without an atom.

property component: int | None

Coordinate component implicated in the failure, or None when inapplicable.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property expected: int | None

Required size reported by the native failure, or None when inapplicable.

property kind: MolecularForceFieldErrorKind

Typed native persistent-force-field failure category.

property requested: int | None

Requested conformer identifier when relevant, otherwise None.

property source: MmffMolPropertiesError | MmffBuilderError | UffParameterError | UffBuilderError | ForceFieldKernelError | None

“error_source”} Actual underlying exception, identical to __cause__.

Type:

{“role”

class cosmolkit.ForceFieldIndexArgument(value)

Typed ForceFieldIndexArgument values corresponding to the Rust enum.

Members: I, J, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
I = ForceFieldIndexArgument.I
J = ForceFieldIndexArgument.J
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'I': ForceFieldIndexArgument.I, 'J': ForceFieldIndexArgument.J})
values = mappingproxy({0: ForceFieldIndexArgument.I, 1: ForceFieldIndexArgument.J})
exception cosmolkit.ForceFieldKernelError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ForceFieldKernelError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (11)
property argument: ForceFieldIndexArgument | ForceFieldBondIndexArgument | ForceFieldAngleIndexArgument | ForceFieldTorsionIndexArgument | None

“error_payload”} Argument rejected by the native operation. Applies to ForceFieldKernelError.IndexOutOfRange, ForceFieldKernelError.BondIndexOutOfRange, ForceFieldKernelError.AngleIndexOutOfRange, ForceFieldKernelError.TorsionIndexOutOfRange. None when this payload is absent.

Type:

{“role”

property bound: ForceFieldAngleRangeBound | None

“error_payload”} Bound involved in the failed constraint check. Applies to ForceFieldKernelError.AngleOutOfRange. None when this payload is absent.

Type:

{“role”

property buffer_len: int | None

Buffer length used by the failed range check. Applies to ForceFieldKernelError.TorsionAddressOutsideDefinedSource, ForceFieldKernelError.OopAddressOutsideDefinedSource. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Index reported by the failing native check. Applies to ForceFieldKernelError.IndexOutOfRange, ForceFieldKernelError.BondIndexOutOfRange, ForceFieldKernelError.AngleIndexOutOfRange, ForceFieldKernelError.TorsionIndexOutOfRange, ForceFieldKernelError.BadFixedPoint, ForceFieldKernelError.OopAddressOutsideDefinedSource, ForceFieldKernelError.TorsionAddressOutsideDefinedSource. None when this payload is absent.

property num_points: int | None

Readonly num_points payload of the PositionCountMismatch error variant; None for other variants.

property order: int | None

Bond order associated with the failure. Present for ForceFieldKernelError.AngleBadOrder, ForceFieldKernelError.TorsionBadOrder; None when unavailable.

property position_count: int | None

Readonly position_count payload of the PositionCountMismatch error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property upper_bound: int | None

Upper bound used by the failed range check. Applies to ForceFieldKernelError.IndexOutOfRange, ForceFieldKernelError.BadFixedPoint, ForceFieldKernelError.BondIndexOutOfRange, ForceFieldKernelError.AngleIndexOutOfRange, ForceFieldKernelError.TorsionIndexOutOfRange. None when this payload is absent.

property variant: ForceFieldKernelErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ForceFieldKernelErrorKind(value)

Discriminants of ForceFieldKernelErrorKind.

Members: NoPoints, NoDistanceMatrix, MatrixSizeMismatch, NotInitialized, BadBounds, BadBondOrder, PositionCountMismatch, IndexOutOfRange, BondIndexOutOfRange, AngleDegeneratePoints, AngleIndexOutOfRange, AngleBadOrder, TorsionIndexOutOfRange, TorsionDegeneratePoints, TorsionBadHybridizations, TorsionBadOrder, AngleOutOfRange, AngleBoundsOrder, PackedAngleBoundsOrder, TorsionBoundsOrder, BadIndex, OptimizerBadTolerance, OptimizerBadDirection, BadFixedPoint, TransferPostcondition, OopParametersMissing, TorsionParametersOutsideDefinedSource, TorsionAddressOutsideDefinedSource, OopAddressOutsideDefinedSource, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (32)
AngleBadOrder = ForceFieldKernelErrorKind.AngleBadOrder
AngleBoundsOrder = ForceFieldKernelErrorKind.AngleBoundsOrder
AngleDegeneratePoints = ForceFieldKernelErrorKind.AngleDegeneratePoints
AngleIndexOutOfRange = ForceFieldKernelErrorKind.AngleIndexOutOfRange
AngleOutOfRange = ForceFieldKernelErrorKind.AngleOutOfRange
BadBondOrder = ForceFieldKernelErrorKind.BadBondOrder
BadBounds = ForceFieldKernelErrorKind.BadBounds
BadFixedPoint = ForceFieldKernelErrorKind.BadFixedPoint
BadIndex = ForceFieldKernelErrorKind.BadIndex
BondIndexOutOfRange = ForceFieldKernelErrorKind.BondIndexOutOfRange
IndexOutOfRange = ForceFieldKernelErrorKind.IndexOutOfRange
MatrixSizeMismatch = ForceFieldKernelErrorKind.MatrixSizeMismatch
NoDistanceMatrix = ForceFieldKernelErrorKind.NoDistanceMatrix
NoPoints = ForceFieldKernelErrorKind.NoPoints
NotInitialized = ForceFieldKernelErrorKind.NotInitialized
OopAddressOutsideDefinedSource = ForceFieldKernelErrorKind.OopAddressOutsideDefinedSource
OopParametersMissing = ForceFieldKernelErrorKind.OopParametersMissing
OptimizerBadDirection = ForceFieldKernelErrorKind.OptimizerBadDirection
OptimizerBadTolerance = ForceFieldKernelErrorKind.OptimizerBadTolerance
PackedAngleBoundsOrder = ForceFieldKernelErrorKind.PackedAngleBoundsOrder
PositionCountMismatch = ForceFieldKernelErrorKind.PositionCountMismatch
TorsionAddressOutsideDefinedSource = ForceFieldKernelErrorKind.TorsionAddressOutsideDefinedSource
TorsionBadHybridizations = ForceFieldKernelErrorKind.TorsionBadHybridizations
TorsionBadOrder = ForceFieldKernelErrorKind.TorsionBadOrder
TorsionBoundsOrder = ForceFieldKernelErrorKind.TorsionBoundsOrder
TorsionDegeneratePoints = ForceFieldKernelErrorKind.TorsionDegeneratePoints
TorsionIndexOutOfRange = ForceFieldKernelErrorKind.TorsionIndexOutOfRange
TorsionParametersOutsideDefinedSource = ForceFieldKernelErrorKind.TorsionParametersOutsideDefinedSource
TransferPostcondition = ForceFieldKernelErrorKind.TransferPostcondition
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NoPoints': ForceFieldKernelErrorKind.NoPoints, 'NoDistanceMatrix': ForceFieldKernelErrorKind.NoDistanceMatrix, 'MatrixSizeMismatch': ForceFieldKernelErrorKind.MatrixSizeMismatch, 'NotInitialized': ForceFieldKernelErrorKind.NotInitialized, 'BadBounds': ForceFieldKernelErrorKind.BadBounds, 'BadBondOrder': ForceFieldKernelErrorKind.BadBondOrder, 'PositionCountMismatch': ForceFieldKernelErrorKind.PositionCountMismatch, 'IndexOutOfRange': ForceFieldKernelErrorKind.IndexOutOfRange, 'BondIndexOutOfRange': ForceFieldKernelErrorKind.BondIndexOutOfRange, 'AngleDegeneratePoints': ForceFieldKernelErrorKind.AngleDegeneratePoints, 'AngleIndexOutOfRange': ForceFieldKernelErrorKind.AngleIndexOutOfRange, 'AngleBadOrder': ForceFieldKernelErrorKind.AngleBadOrder, 'TorsionIndexOutOfRange': ForceFieldKernelErrorKind.TorsionIndexOutOfRange, 'TorsionDegeneratePoints': ForceFieldKernelErrorKind.TorsionDegeneratePoints, 'TorsionBadHybridizations': ForceFieldKernelErrorKind.TorsionBadHybridizations, 'TorsionBadOrder': ForceFieldKernelErrorKind.TorsionBadOrder, 'AngleOutOfRange': ForceFieldKernelErrorKind.AngleOutOfRange, 'AngleBoundsOrder': ForceFieldKernelErrorKind.AngleBoundsOrder, 'PackedAngleBoundsOrder': ForceFieldKernelErrorKind.PackedAngleBoundsOrder, 'TorsionBoundsOrder': ForceFieldKernelErrorKind.TorsionBoundsOrder, 'BadIndex': ForceFieldKernelErrorKind.BadIndex, 'OptimizerBadTolerance': ForceFieldKernelErrorKind.OptimizerBadTolerance, 'OptimizerBadDirection': ForceFieldKernelErrorKind.OptimizerBadDirection, 'BadFixedPoint': ForceFieldKernelErrorKind.BadFixedPoint, 'TransferPostcondition': ForceFieldKernelErrorKind.TransferPostcondition, 'OopParametersMissing': ForceFieldKernelErrorKind.OopParametersMissing, 'TorsionParametersOutsideDefinedSource': ForceFieldKernelErrorKind.TorsionParametersOutsideDefinedSource, 'TorsionAddressOutsideDefinedSource': ForceFieldKernelErrorKind.TorsionAddressOutsideDefinedSource, 'OopAddressOutsideDefinedSource': ForceFieldKernelErrorKind.OopAddressOutsideDefinedSource})
values = mappingproxy({0: ForceFieldKernelErrorKind.NoPoints, 1: ForceFieldKernelErrorKind.NoDistanceMatrix, 2: ForceFieldKernelErrorKind.MatrixSizeMismatch, 3: ForceFieldKernelErrorKind.NotInitialized, 4: ForceFieldKernelErrorKind.BadBounds, 5: ForceFieldKernelErrorKind.BadBondOrder, 6: ForceFieldKernelErrorKind.PositionCountMismatch, 7: ForceFieldKernelErrorKind.IndexOutOfRange, 8: ForceFieldKernelErrorKind.BondIndexOutOfRange, 9: ForceFieldKernelErrorKind.AngleDegeneratePoints, 10: ForceFieldKernelErrorKind.AngleIndexOutOfRange, 11: ForceFieldKernelErrorKind.AngleBadOrder, 12: ForceFieldKernelErrorKind.TorsionIndexOutOfRange, 13: ForceFieldKernelErrorKind.TorsionDegeneratePoints, 14: ForceFieldKernelErrorKind.TorsionBadHybridizations, 15: ForceFieldKernelErrorKind.TorsionBadOrder, 16: ForceFieldKernelErrorKind.AngleOutOfRange, 17: ForceFieldKernelErrorKind.AngleBoundsOrder, 18: ForceFieldKernelErrorKind.PackedAngleBoundsOrder, 19: ForceFieldKernelErrorKind.TorsionBoundsOrder, 20: ForceFieldKernelErrorKind.BadIndex, 21: ForceFieldKernelErrorKind.OptimizerBadTolerance, 22: ForceFieldKernelErrorKind.OptimizerBadDirection, 23: ForceFieldKernelErrorKind.BadFixedPoint, 24: ForceFieldKernelErrorKind.TransferPostcondition, 25: ForceFieldKernelErrorKind.OopParametersMissing, 26: ForceFieldKernelErrorKind.TorsionParametersOutsideDefinedSource, 27: ForceFieldKernelErrorKind.TorsionAddressOutsideDefinedSource, 28: ForceFieldKernelErrorKind.OopAddressOutsideDefinedSource})
class cosmolkit.ForceFieldMinimizeOutcome

Persistent force-field minimization outcome with convergence, iteration count and final energy.

Members (3)
converged: bool

Whether minimization reached the requested convergence criteria.

energy: float

Evaluated force-field energy.

iterations: int

Number of minimization iterations performed.

class cosmolkit.ForceFieldMinimizeParams(*, max_iterations=Ellipsis, force_tolerance=Ellipsis, energy_tolerance=Ellipsis)

Iteration limit and numerical tolerances for persistent force-field minimization.

Members (3)
energy_tolerance: float

Energy tolerance forwarded to the source-compatible minimizer; its current algorithm does not use this criterion.

force_tolerance: float

Force convergence tolerance passed to the native minimizer.

max_iterations: int

Maximum number of minimizer iterations.

class cosmolkit.ForceFieldPositionConstraintParams(*, max_displacement, force_constant)

Required position restraint inputs; no implicit numerical defaults.

Members (2)
force_constant: float

Force constant multiplying the restraint penalty.

max_displacement: float

Maximum displacement from the restrained initial position, in angstroms.

class cosmolkit.ForceFieldTorsionConstraintParams(*, relative, min_dihedral_deg, max_dihedral_deg, force_constant)

Required torsion restraint inputs; no implicit numerical defaults.

Members (4)
force_constant: float

Force constant multiplying the restraint penalty.

max_dihedral_deg: float

Upper dihedral-angle bound in degrees.

min_dihedral_deg: float

Lower dihedral-angle bound in degrees.

relative: bool

Interpret restraint bounds relative to the initial geometry instead of as absolute values.

class cosmolkit.ForceFieldTorsionIndexArgument(value)

Typed ForceFieldTorsionIndexArgument values corresponding to the Rust enum.

Members: First, Second, Third, Fourth, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
First = ForceFieldTorsionIndexArgument.First
Fourth = ForceFieldTorsionIndexArgument.Fourth
Second = ForceFieldTorsionIndexArgument.Second
Third = ForceFieldTorsionIndexArgument.Third
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'First': ForceFieldTorsionIndexArgument.First, 'Second': ForceFieldTorsionIndexArgument.Second, 'Third': ForceFieldTorsionIndexArgument.Third, 'Fourth': ForceFieldTorsionIndexArgument.Fourth})
values = mappingproxy({0: ForceFieldTorsionIndexArgument.First, 1: ForceFieldTorsionIndexArgument.Second, 2: ForceFieldTorsionIndexArgument.Third, 3: ForceFieldTorsionIndexArgument.Fourth})
exception cosmolkit.FragmentCoordinateViewError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

FragmentCoordinateViewError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property actual: int | None

Observed value reported by the native check. Applies to FragmentCoordinateViewError.KernelCoordinateRowCount, FragmentCoordinateViewError.KernelCoordinateRowWidth. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the KernelCoordinateRowCount error variant; None for other variants.

property id: int

Identifier involved in the native failure. Applies to FragmentCoordinateViewError.SelectedConformerMissing, FragmentCoordinateViewError.SelectedConformerDuplicated, FragmentCoordinateViewError.KernelCoordinateRowCount, FragmentCoordinateViewError.KernelCoordinateRowWidth.

property row: int | None

Readonly row payload of the KernelCoordinateRowWidth error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: FragmentCoordinateViewErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.FragmentCoordinateViewErrorKind(value)

Discriminants of FragmentCoordinateViewErrorKind.

Members: SelectedConformerMissing, SelectedConformerDuplicated, KernelCoordinateRowCount, KernelCoordinateRowWidth, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
KernelCoordinateRowCount = FragmentCoordinateViewErrorKind.KernelCoordinateRowCount
KernelCoordinateRowWidth = FragmentCoordinateViewErrorKind.KernelCoordinateRowWidth
SelectedConformerDuplicated = FragmentCoordinateViewErrorKind.SelectedConformerDuplicated
SelectedConformerMissing = FragmentCoordinateViewErrorKind.SelectedConformerMissing
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SelectedConformerMissing': FragmentCoordinateViewErrorKind.SelectedConformerMissing, 'SelectedConformerDuplicated': FragmentCoordinateViewErrorKind.SelectedConformerDuplicated, 'KernelCoordinateRowCount': FragmentCoordinateViewErrorKind.KernelCoordinateRowCount, 'KernelCoordinateRowWidth': FragmentCoordinateViewErrorKind.KernelCoordinateRowWidth})
values = mappingproxy({0: FragmentCoordinateViewErrorKind.SelectedConformerMissing, 1: FragmentCoordinateViewErrorKind.SelectedConformerDuplicated, 2: FragmentCoordinateViewErrorKind.KernelCoordinateRowCount, 3: FragmentCoordinateViewErrorKind.KernelCoordinateRowWidth})
class cosmolkit.FragmentCxSmilesWriteParams(*, atoms, cx=Ellipsis, bonds=Ellipsis, atom_symbols=Ellipsis, bond_symbols=Ellipsis)

Fragment selection with explicit CX fields and dimension-scoped coordinates.

Members (5)
atom_symbols: tuple[str, ...] | None

Optional replacement symbols indexed by original molecule atom index.

atoms: tuple[int, ...]

Original molecule atom indices included in the fragment.

bond_symbols: tuple[str, ...] | None

Optional replacement symbols indexed by original molecule bond index.

bonds: tuple[int, ...] | None

Optional original bond indices; None includes bonds between selected atoms.

cx: CxSmilesWriteParams

CXSMILES formatting, extension fields and coordinate selection.

class cosmolkit.FragmentSmilesWriteParams(*, atoms, smiles=Ellipsis, bonds=Ellipsis, atom_symbols=Ellipsis, bond_symbols=Ellipsis)

Original-index fragment selection; symbol arrays are indexed by the full molecule.

Members (5)
atom_symbols: tuple[str, ...] | None

Optional replacement symbols indexed by original molecule atom index.

atoms: tuple[int, ...]

Original molecule atom indices included in the fragment.

bond_symbols: tuple[str, ...] | None

Optional replacement symbols indexed by original molecule bond index.

bonds: tuple[int, ...] | None

None selects all bonds between selected atoms; Some(empty) selects no bonds.

smiles: SmilesWriteParams

SMILES formatting and stereochemistry options.

exception cosmolkit.FragmentWriteInputError(*args, **kwargs)

Failure in the smiles domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

FragmentWriteInputError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (14)
property atom_count: int | None

Number of atoms available to the operation. Present for FragmentWriteInputError.RootAtomOutOfRange, FragmentWriteInputError.AtomOutOfRange, FragmentWriteInputError.ValenceAssignmentLengthMismatch; None when unavailable.

property atom_index: int | None

Atom index involved in the failure. Present for FragmentWriteInputError.RootAtomOutOfRange, FragmentWriteInputError.RootAtomNotSelected, FragmentWriteInputError.AtomOutOfRange, FragmentWriteInputError.RootAtomRequiresSingleFragment; None when unavailable.

property bond_count: int | None

Readonly bond_count payload of the BondOutOfRange error variant; None for other variants.

property bond_index: int | None

Readonly bond_index payload of the BondOutOfRange error variant; None for other variants.

property detail: str | None

Additional native diagnostic detail. Present for FragmentWriteInputError.InvalidTopology; None when unavailable.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Expected count or value. Present for FragmentWriteInputError.AtomSymbolsTooShort, FragmentWriteInputError.BondSymbolsTooShort; None when unavailable.

property explicit_len: int | None

Readonly explicit_len payload of the ValenceAssignmentLengthMismatch error variant; None for other variants.

property fragment_count: int | None

Readonly fragment_count payload of the RootAtomRequiresSingleFragment error variant; None for other variants.

property implicit_len: int | None

Readonly implicit_len payload of the ValenceAssignmentLengthMismatch error variant; None for other variants.

property len: int | None

Length of the invalid span or collection. Present for FragmentWriteInputError.AtomSymbolsTooShort, FragmentWriteInputError.BondSymbolsTooShort; None when unavailable.

property source: StereoGroupError | ValenceError | RingFindingError | LegacyStereoError | CanonicalRankError | SmilesParseError | PropertyStringError | AtomPropertyError | BondValueError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: FragmentWriteInputErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.FragmentWriteInputErrorKind(value)

Discriminants of FragmentWriteInputErrorKind.

Members: StereoGroup, NoAtomsProvided, RootAtomOutOfRange, RootAtomNotSelected, AtomSymbolsTooShort, BondSymbolsTooShort, AtomOutOfRange, BondOutOfRange, RootAtomRequiresSingleFragment, InvalidTopology, ValenceAssignmentLengthMismatch, Valence, Ring, Stereo, Rank, Writer, CipProperty, AtomProperty, StereoBond, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (22)
AtomOutOfRange = FragmentWriteInputErrorKind.AtomOutOfRange
AtomProperty = FragmentWriteInputErrorKind.AtomProperty
AtomSymbolsTooShort = FragmentWriteInputErrorKind.AtomSymbolsTooShort
BondOutOfRange = FragmentWriteInputErrorKind.BondOutOfRange
BondSymbolsTooShort = FragmentWriteInputErrorKind.BondSymbolsTooShort
CipProperty = FragmentWriteInputErrorKind.CipProperty
InvalidTopology = FragmentWriteInputErrorKind.InvalidTopology
NoAtomsProvided = FragmentWriteInputErrorKind.NoAtomsProvided
Rank = FragmentWriteInputErrorKind.Rank
Ring = FragmentWriteInputErrorKind.Ring
RootAtomNotSelected = FragmentWriteInputErrorKind.RootAtomNotSelected
RootAtomOutOfRange = FragmentWriteInputErrorKind.RootAtomOutOfRange
RootAtomRequiresSingleFragment = FragmentWriteInputErrorKind.RootAtomRequiresSingleFragment
Stereo = FragmentWriteInputErrorKind.Stereo
StereoBond = FragmentWriteInputErrorKind.StereoBond
StereoGroup = FragmentWriteInputErrorKind.StereoGroup
Valence = FragmentWriteInputErrorKind.Valence
ValenceAssignmentLengthMismatch = FragmentWriteInputErrorKind.ValenceAssignmentLengthMismatch
Writer = FragmentWriteInputErrorKind.Writer
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': FragmentWriteInputErrorKind.StereoGroup, 'NoAtomsProvided': FragmentWriteInputErrorKind.NoAtomsProvided, 'RootAtomOutOfRange': FragmentWriteInputErrorKind.RootAtomOutOfRange, 'RootAtomNotSelected': FragmentWriteInputErrorKind.RootAtomNotSelected, 'AtomSymbolsTooShort': FragmentWriteInputErrorKind.AtomSymbolsTooShort, 'BondSymbolsTooShort': FragmentWriteInputErrorKind.BondSymbolsTooShort, 'AtomOutOfRange': FragmentWriteInputErrorKind.AtomOutOfRange, 'BondOutOfRange': FragmentWriteInputErrorKind.BondOutOfRange, 'RootAtomRequiresSingleFragment': FragmentWriteInputErrorKind.RootAtomRequiresSingleFragment, 'InvalidTopology': FragmentWriteInputErrorKind.InvalidTopology, 'ValenceAssignmentLengthMismatch': FragmentWriteInputErrorKind.ValenceAssignmentLengthMismatch, 'Valence': FragmentWriteInputErrorKind.Valence, 'Ring': FragmentWriteInputErrorKind.Ring, 'Stereo': FragmentWriteInputErrorKind.Stereo, 'Rank': FragmentWriteInputErrorKind.Rank, 'Writer': FragmentWriteInputErrorKind.Writer, 'CipProperty': FragmentWriteInputErrorKind.CipProperty, 'AtomProperty': FragmentWriteInputErrorKind.AtomProperty, 'StereoBond': FragmentWriteInputErrorKind.StereoBond})
values = mappingproxy({0: FragmentWriteInputErrorKind.StereoGroup, 1: FragmentWriteInputErrorKind.NoAtomsProvided, 2: FragmentWriteInputErrorKind.RootAtomOutOfRange, 3: FragmentWriteInputErrorKind.RootAtomNotSelected, 4: FragmentWriteInputErrorKind.AtomSymbolsTooShort, 5: FragmentWriteInputErrorKind.BondSymbolsTooShort, 6: FragmentWriteInputErrorKind.AtomOutOfRange, 7: FragmentWriteInputErrorKind.BondOutOfRange, 8: FragmentWriteInputErrorKind.RootAtomRequiresSingleFragment, 9: FragmentWriteInputErrorKind.InvalidTopology, 10: FragmentWriteInputErrorKind.ValenceAssignmentLengthMismatch, 11: FragmentWriteInputErrorKind.Valence, 12: FragmentWriteInputErrorKind.Ring, 13: FragmentWriteInputErrorKind.Stereo, 14: FragmentWriteInputErrorKind.Rank, 15: FragmentWriteInputErrorKind.Writer, 16: FragmentWriteInputErrorKind.CipProperty, 17: FragmentWriteInputErrorKind.AtomProperty, 18: FragmentWriteInputErrorKind.StereoBond})
exception cosmolkit.FromUtf8Error(*args, **kwargs)

FromUtf8Error is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
as_bytes(*args, **kwargs) → bytes

Return an independent bytes object containing the original undecodable input.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property utf8_error: Utf8Error

“error_payload”} UTF-8 validation details retained with the original byte input.

Type:

{“role”

exception cosmolkit.FullCopyComponentError(*args, **kwargs)

Failure in the fragments domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

FullCopyComponentError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (14)
property actual: int | None

Readonly actual payload of the AtomMaskSize error variant; None for other variants.

property conformer_id: int | None

Readonly conformer_id payload of the MissingCoordinateRow error variant; None for other variants.

property coordinate_validation: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of FullCopyComponentError.CoordinateValidation; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the AtomMaskSize error variant; None for other variants.

property mapping_validation: MappingValidationError | None

“error_payload”} Structured MappingValidationError payload of FullCopyComponentError.MappingValidation; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property row: int | None

Readonly row payload of the AddedAtomRow error variant; None for other variants.

property source: StereoGroupError | CoordinateValidationError | MoleculePropertyError | AtomPropertyError | TemplateAttachmentOrderError | UIntLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property source_row: int | None

Readonly source_row payload of the MissingCoordinateRow error variant; None for other variants.

property source_text: PropertyStringError | None

“error_payload”} Structured PropertyStringError payload of FullCopyComponentError.SourceText; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source_uint: PropertyUIntReadError | None

“error_payload”} Structured PropertyUIntReadError payload of FullCopyComponentError.SourceUInt; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property topology_edit: TopologyEditError | None

“error_payload”} Structured TopologyEditError payload of FullCopyComponentError.TopologyEdit; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: FullCopyComponentErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.FullCopyComponentErrorKind(value)

Discriminants of FullCopyComponentErrorKind.

Members: SourceUInt, SourceText, TopologyEdit, MappingValidation, CoordinateValidation, AtomMaskSize, AddedAtomRow, MissingCoordinateRow, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
AddedAtomRow = FullCopyComponentErrorKind.AddedAtomRow
AtomMaskSize = FullCopyComponentErrorKind.AtomMaskSize
CoordinateValidation = FullCopyComponentErrorKind.CoordinateValidation
MappingValidation = FullCopyComponentErrorKind.MappingValidation
MissingCoordinateRow = FullCopyComponentErrorKind.MissingCoordinateRow
SourceText = FullCopyComponentErrorKind.SourceText
SourceUInt = FullCopyComponentErrorKind.SourceUInt
TopologyEdit = FullCopyComponentErrorKind.TopologyEdit
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SourceUInt': FullCopyComponentErrorKind.SourceUInt, 'SourceText': FullCopyComponentErrorKind.SourceText, 'TopologyEdit': FullCopyComponentErrorKind.TopologyEdit, 'MappingValidation': FullCopyComponentErrorKind.MappingValidation, 'CoordinateValidation': FullCopyComponentErrorKind.CoordinateValidation, 'AtomMaskSize': FullCopyComponentErrorKind.AtomMaskSize, 'AddedAtomRow': FullCopyComponentErrorKind.AddedAtomRow, 'MissingCoordinateRow': FullCopyComponentErrorKind.MissingCoordinateRow})
values = mappingproxy({0: FullCopyComponentErrorKind.SourceUInt, 1: FullCopyComponentErrorKind.SourceText, 2: FullCopyComponentErrorKind.TopologyEdit, 3: FullCopyComponentErrorKind.MappingValidation, 4: FullCopyComponentErrorKind.CoordinateValidation, 5: FullCopyComponentErrorKind.AtomMaskSize, 6: FullCopyComponentErrorKind.AddedAtomRow, 7: FullCopyComponentErrorKind.MissingCoordinateRow})
class cosmolkit.FunctionStatus

Native implementation status with optional parity reference and difference explanation.

Members (4)
Experimental = Experimental
Native = Native
explanation: str | None

Declared explanation of parity differences, or None for other statuses.

reference: str | None

Upstream parity reference recorded by the declaration, or None for native/experimental status.

exception cosmolkit.GenerationError(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

GenerationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (25)
property atom_count: int | None

Readonly atom_count payload of the CoordinateMapIndex error variant; None for other variants.

property atom_index: int | None

Atom index involved in the native failure. Applies to GenerationError.CoordinateMapIndex, GenerationError.CoordinateMapNonFinite. None when this payload is absent.

property atropisomer: AtropisomerError | None

“error_payload”} Structured native error payload. Present for GenerationError.Atropisomer; None when unavailable.

Type:

{“role”

property bounds: BoundsMatrixError | None

“error_payload”} Structured BoundsMatrixError payload of GenerationError.Bounds; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property conjugation: ConjugationError | None

“error_payload”} Structured native error payload. Present for GenerationError.Conjugation; None when unavailable.

Type:

{“role”

property coordinates: CoordinateValidationError | None

“error_payload”} Structured native error payload. Present for GenerationError.Coordinates; None when unavailable.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property force_field: ConformerOptimizerError | None

“error_payload”} Structured ConformerOptimizerError payload of GenerationError.ForceField; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property fragments: MoleculeFragmentsError | None

“error_payload”} Structured native error payload. Present for GenerationError.Fragments; None when unavailable.

Type:

{“role”

property generation_failed: GenerationFailure | None

“error_payload”} Structured GenerationFailure payload of GenerationError.GenerationFailed; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property hybridization: HybridizationError | None

“error_payload”} Structured native error payload. Present for GenerationError.Hybridization; None when unavailable.

Type:

{“role”

property hydrogens: MissingExplicitHydrogensError | None

“error_payload”} Structured MissingExplicitHydrogensError payload of GenerationError.Hydrogens; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property implementation: str | None

Readonly implementation payload of the UnsupportedImplementation error variant; None for other variants.

property message: str | None

Detailed native diagnostic message. Applies to GenerationError.Input. None when this payload is absent.

property numeric: ConformerError | None

“error_payload”} Structured ConformerError payload of GenerationError.Numeric; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property pruning: PruningError | None

“error_payload”} Structured PruningError payload of GenerationError.Pruning; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property rings: RingFindingError | None

“error_payload”} Structured native error payload. Present for GenerationError.Rings; None when unavailable.

Type:

{“role”

property seed: EmbedSeedError | None

“error_payload”} Structured EmbedSeedError payload of GenerationError.Seed; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | TopologyEditError | CoordinateValidationError | AtomPropertyError | BondValueError | MoleculePropertyError | PropertyIntReadError | PropertyULongReadError | PropertyUIntReadError | PropertyValueError | RequiredPropertyStringError | PropertyStringError | LegacyStereoError | PotentialStereoError | ParserStereoOrderError | StereoOrderError | SmilesStereoError | AtropisomerError | RingFindingError | ParserCarrierError | KekulizeError | SanitizeError | HydrogenError | ValenceError | ConjugationError | HybridizationError | TopologyValidationError | TemplateAttachmentOrderError | MappingValidationError | CanonicalRankError | DoubleBondStereoError | BoundsMatrixError | UffBoundsError | MatrixError | ForceFieldKernelError | UffInversionContributionError | CxQueryLoweringError | QueryGraphError | ThreadCountError | MoleculeFragmentsFailure | UffBuilderError | IoError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stereo: LegacyStereoError | None

“error_payload”} Structured native error payload. Present for GenerationError.Stereo; None when unavailable.

Type:

{“role”

property thread_count: ThreadCountError | None

“error_payload”} Structured ThreadCountError payload of GenerationError.ThreadCount; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property topology: TopologyValidationError | None

“error_payload”} Structured native error payload. Present for GenerationError.Topology; None when unavailable.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of GenerationError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: GenerationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.GenerationErrorKind(value)

Discriminants of GenerationErrorKind.

Members: Topology, Coordinates, Valence, Rings, Conjugation, Hybridization, Stereo, Fragments, Hydrogens, Pruning, Seed, GenerationFailed, Atropisomer, Bounds, ForceField, Numeric, ThreadCount, WorkerLaunch, Input, CoordinateMapIndex, CoordinateMapNonFinite, UnsupportedImplementation, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (25)
Atropisomer = GenerationErrorKind.Atropisomer
Bounds = GenerationErrorKind.Bounds
Conjugation = GenerationErrorKind.Conjugation
CoordinateMapIndex = GenerationErrorKind.CoordinateMapIndex
CoordinateMapNonFinite = GenerationErrorKind.CoordinateMapNonFinite
Coordinates = GenerationErrorKind.Coordinates
ForceField = GenerationErrorKind.ForceField
Fragments = GenerationErrorKind.Fragments
GenerationFailed = GenerationErrorKind.GenerationFailed
Hybridization = GenerationErrorKind.Hybridization
Hydrogens = GenerationErrorKind.Hydrogens
Input = GenerationErrorKind.Input
Numeric = GenerationErrorKind.Numeric
Pruning = GenerationErrorKind.Pruning
Rings = GenerationErrorKind.Rings
Seed = GenerationErrorKind.Seed
Stereo = GenerationErrorKind.Stereo
ThreadCount = GenerationErrorKind.ThreadCount
Topology = GenerationErrorKind.Topology
UnsupportedImplementation = GenerationErrorKind.UnsupportedImplementation
Valence = GenerationErrorKind.Valence
WorkerLaunch = GenerationErrorKind.WorkerLaunch
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Topology': GenerationErrorKind.Topology, 'Coordinates': GenerationErrorKind.Coordinates, 'Valence': GenerationErrorKind.Valence, 'Rings': GenerationErrorKind.Rings, 'Conjugation': GenerationErrorKind.Conjugation, 'Hybridization': GenerationErrorKind.Hybridization, 'Stereo': GenerationErrorKind.Stereo, 'Fragments': GenerationErrorKind.Fragments, 'Hydrogens': GenerationErrorKind.Hydrogens, 'Pruning': GenerationErrorKind.Pruning, 'Seed': GenerationErrorKind.Seed, 'GenerationFailed': GenerationErrorKind.GenerationFailed, 'Atropisomer': GenerationErrorKind.Atropisomer, 'Bounds': GenerationErrorKind.Bounds, 'ForceField': GenerationErrorKind.ForceField, 'Numeric': GenerationErrorKind.Numeric, 'ThreadCount': GenerationErrorKind.ThreadCount, 'WorkerLaunch': GenerationErrorKind.WorkerLaunch, 'Input': GenerationErrorKind.Input, 'CoordinateMapIndex': GenerationErrorKind.CoordinateMapIndex, 'CoordinateMapNonFinite': GenerationErrorKind.CoordinateMapNonFinite, 'UnsupportedImplementation': GenerationErrorKind.UnsupportedImplementation})
values = mappingproxy({0: GenerationErrorKind.Topology, 1: GenerationErrorKind.Coordinates, 2: GenerationErrorKind.Valence, 3: GenerationErrorKind.Rings, 4: GenerationErrorKind.Conjugation, 5: GenerationErrorKind.Hybridization, 6: GenerationErrorKind.Stereo, 7: GenerationErrorKind.Fragments, 8: GenerationErrorKind.Hydrogens, 9: GenerationErrorKind.Pruning, 10: GenerationErrorKind.Seed, 11: GenerationErrorKind.GenerationFailed, 12: GenerationErrorKind.Atropisomer, 13: GenerationErrorKind.Bounds, 14: GenerationErrorKind.ForceField, 15: GenerationErrorKind.Numeric, 16: GenerationErrorKind.ThreadCount, 17: GenerationErrorKind.WorkerLaunch, 18: GenerationErrorKind.Input, 19: GenerationErrorKind.CoordinateMapIndex, 20: GenerationErrorKind.CoordinateMapNonFinite, 21: GenerationErrorKind.UnsupportedImplementation})
exception cosmolkit.GenerationFailure(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

GenerationFailure is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: BoundsMatrixError | UffBoundsError | MatrixError | ValenceError | PropertyUIntReadError | AtomPropertyError | PropertyIntReadError | TopologyValidationError | RingFindingError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology_bounds: GraphBoundsError | None

“error_payload”} Structured GraphBoundsError payload of GenerationFailure.TopologyBounds; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property torsion_preferences: CrystalffTorsionPreferencesError | None

“error_payload”} Structured CrystalffTorsionPreferencesError payload of GenerationFailure.TorsionPreferences; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: GenerationFailureKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.GenerationFailureKind(value)

Discriminants of GenerationFailureKind.

Members: TopologyBounds, TorsionPreferences, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
TopologyBounds = GenerationFailureKind.TopologyBounds
TorsionPreferences = GenerationFailureKind.TorsionPreferences
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TopologyBounds': GenerationFailureKind.TopologyBounds, 'TorsionPreferences': GenerationFailureKind.TorsionPreferences})
values = mappingproxy({0: GenerationFailureKind.TopologyBounds, 1: GenerationFailureKind.TorsionPreferences})
exception cosmolkit.GraphBoundsError(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

GraphBoundsError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property atomic_number: int | None

Atomic number involved in the failed chemistry operation. Applies to GraphBoundsError.AtomicNumber. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property message: str | None

Detailed native diagnostic message. Applies to GraphBoundsError.InvalidBounds, GraphBoundsError.Detail, GraphBoundsError.Input. None when this payload is absent.

property source: BoundsMatrixError | UffBoundsError | MatrixError | ValenceError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: GraphBoundsErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.GraphBoundsErrorKind(value)

Discriminants of GraphBoundsErrorKind.

Members: Bounds, Uff, Matrix, Valence, InvalidBounds, Detail, Input, AtomicNumber, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
AtomicNumber = GraphBoundsErrorKind.AtomicNumber
Bounds = GraphBoundsErrorKind.Bounds
Detail = GraphBoundsErrorKind.Detail
Input = GraphBoundsErrorKind.Input
InvalidBounds = GraphBoundsErrorKind.InvalidBounds
Matrix = GraphBoundsErrorKind.Matrix
Uff = GraphBoundsErrorKind.Uff
Valence = GraphBoundsErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Bounds': GraphBoundsErrorKind.Bounds, 'Uff': GraphBoundsErrorKind.Uff, 'Matrix': GraphBoundsErrorKind.Matrix, 'Valence': GraphBoundsErrorKind.Valence, 'InvalidBounds': GraphBoundsErrorKind.InvalidBounds, 'Detail': GraphBoundsErrorKind.Detail, 'Input': GraphBoundsErrorKind.Input, 'AtomicNumber': GraphBoundsErrorKind.AtomicNumber})
values = mappingproxy({0: GraphBoundsErrorKind.Bounds, 1: GraphBoundsErrorKind.Uff, 2: GraphBoundsErrorKind.Matrix, 3: GraphBoundsErrorKind.Valence, 4: GraphBoundsErrorKind.InvalidBounds, 5: GraphBoundsErrorKind.Detail, 6: GraphBoundsErrorKind.Input, 7: GraphBoundsErrorKind.AtomicNumber})
class cosmolkit.Hybridization(value)

Typed Hybridization values corresponding to the Rust enum.

Members: Unspecified, S, Sp, Sp2, Sp3, Sp2d, Sp3d, Sp3d2, Other, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (20)
OTHER = Hybridization.Other
Other = Hybridization.Other
S = Hybridization.S
SP = Hybridization.Sp
SP2 = Hybridization.Sp2
SP2D = Hybridization.Sp2d
SP3 = Hybridization.Sp3
SP3D = Hybridization.Sp3d
SP3D2 = Hybridization.Sp3d2
Sp = Hybridization.Sp
Sp2 = Hybridization.Sp2
Sp2d = Hybridization.Sp2d
Sp3 = Hybridization.Sp3
Sp3d = Hybridization.Sp3d
Sp3d2 = Hybridization.Sp3d2
UNSPECIFIED = Hybridization.Unspecified
Unspecified = Hybridization.Unspecified
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unspecified': Hybridization.Unspecified, 'UNSPECIFIED': Hybridization.Unspecified, 'S': Hybridization.S, 'Sp': Hybridization.Sp, 'SP': Hybridization.Sp, 'Sp2': Hybridization.Sp2, 'SP2': Hybridization.Sp2, 'Sp3': Hybridization.Sp3, 'SP3': Hybridization.Sp3, 'Sp2d': Hybridization.Sp2d, 'SP2D': Hybridization.Sp2d, 'Sp3d': Hybridization.Sp3d, 'SP3D': Hybridization.Sp3d, 'Sp3d2': Hybridization.Sp3d2, 'SP3D2': Hybridization.Sp3d2, 'Other': Hybridization.Other, 'OTHER': Hybridization.Other})
values = mappingproxy({0: Hybridization.Unspecified, 1: Hybridization.S, 2: Hybridization.Sp, 3: Hybridization.Sp2, 4: Hybridization.Sp3, 5: Hybridization.Sp2d, 6: Hybridization.Sp3d, 7: Hybridization.Sp3d2, 8: Hybridization.Other})
exception cosmolkit.HybridizationError(*args, **kwargs)

Failure in the hybridization domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

HybridizationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (11)
property actual: int | None

Observed value reported by the native check. Applies to HybridizationError.ConjugatedBondAssignmentLength, HybridizationError.ValenceAssignmentLength. None when this payload is absent.

property atom: int | None

Atom identifier implicated in the failure. Applies to HybridizationError.InvalidValenceRow, HybridizationError.IntegerOverflow. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Required value reported by the native check. Applies to HybridizationError.ConjugatedBondAssignmentLength, HybridizationError.ValenceAssignmentLength. None when this payload is absent.

property field: str | None

Field whose content or type caused the failure. Applies to HybridizationError.ValenceAssignmentLength, HybridizationError.InvalidValenceRow, HybridizationError.IntegerOverflow. None when this payload is absent.

property source: TopologyValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of HybridizationError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of HybridizationError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property value: int | None

Readonly value payload of the InvalidValenceRow error variant; None for other variants.

property variant: HybridizationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.HybridizationErrorKind(value)

Discriminants of HybridizationErrorKind.

Members: ConjugatedBondAssignmentLength, InvalidTopology, ValenceAssignmentLength, InvalidValenceRow, IntegerOverflow, Valence, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
ConjugatedBondAssignmentLength = HybridizationErrorKind.ConjugatedBondAssignmentLength
IntegerOverflow = HybridizationErrorKind.IntegerOverflow
InvalidTopology = HybridizationErrorKind.InvalidTopology
InvalidValenceRow = HybridizationErrorKind.InvalidValenceRow
Valence = HybridizationErrorKind.Valence
ValenceAssignmentLength = HybridizationErrorKind.ValenceAssignmentLength
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ConjugatedBondAssignmentLength': HybridizationErrorKind.ConjugatedBondAssignmentLength, 'InvalidTopology': HybridizationErrorKind.InvalidTopology, 'ValenceAssignmentLength': HybridizationErrorKind.ValenceAssignmentLength, 'InvalidValenceRow': HybridizationErrorKind.InvalidValenceRow, 'IntegerOverflow': HybridizationErrorKind.IntegerOverflow, 'Valence': HybridizationErrorKind.Valence})
values = mappingproxy({0: HybridizationErrorKind.ConjugatedBondAssignmentLength, 1: HybridizationErrorKind.InvalidTopology, 2: HybridizationErrorKind.ValenceAssignmentLength, 3: HybridizationErrorKind.InvalidValenceRow, 4: HybridizationErrorKind.IntegerOverflow, 5: HybridizationErrorKind.Valence})
exception cosmolkit.HydrogenError(*args, **kwargs)

Failure in the hydrogens domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

HydrogenError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (30)
property actual: int | None

Readonly actual payload of the ValenceAssignmentLength error variant; None for other variants.

property actual_rows: int | None

Readonly actual_rows payload of the InvalidPropertyList error variant; None for other variants.

property addition: int | None

Hydrogen addition-plan entry that failed, or None when unavailable.

property atom: int | None

Atom identifier implicated in the failure. Applies to HydrogenError.OnlyOnAtomOutOfRange, HydrogenError.InvalidRemovalCandidate, HydrogenError.ExplicitHydrogenOverflow. None when this payload is absent.

property atom_count: int | None

Readonly atom_count payload of the OnlyOnAtomOutOfRange error variant; None for other variants.

property bond: int | None

Readonly bond payload of the InvalidStereoTransition error variant; None for other variants.

property conformer: int | None

Readonly conformer payload of the CoordinatePlacement error variant; None for other variants.

property coordinates: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of HydrogenError.InvalidCoordinates; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property current: int | None

Readonly current payload of the ExplicitHydrogenOverflow error variant; None for other variants.

property dimension: str | None

Readonly dimension payload of the CoordinatePlacement error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the ValenceAssignmentLength error variant; None for other variants.

property expected_rows: int | None

Readonly expected_rows payload of the InvalidPropertyList error variant; None for other variants.

property field: str | None

Readonly field payload of the ValenceAssignmentLength error variant; None for other variants.

property mapping: MappingValidationError | None

“error_payload”} Structured MappingValidationError payload of HydrogenError.InvalidMapping; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property name: str | None

Name associated with the rejected value or property list. Applies to HydrogenError.InvalidPropertyList. None when this payload is absent.

property operation: str | None

Readonly operation payload of the Unsupported error variant; None for other variants.

property position: int | None

Readonly position payload of the InvalidRemovalCandidate error variant; None for other variants.

property query_state: QueryStateError | None

“error_payload”} Structured QueryStateError payload of HydrogenError.InvalidQueryState; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property reason: str | None

Native explanation for rejecting the operation. Applies to HydrogenError.Unsupported, HydrogenError.InvalidAdditionPlan, HydrogenError.InvalidRemovalCandidate, HydrogenError.InvalidStereoTransition, HydrogenError.CoordinatePlacement. None when this payload is absent.

property sanitize: SanitizeError | None

“error_payload”} Structured SanitizeError payload of HydrogenError.Sanitize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoOrderError | AtomPropertyError | BondValueError | MoleculePropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stage: str | None

Readonly stage payload of the MissingSourceState error variant; None for other variants.

property state: str | None

Readonly state payload of the MissingSourceState error variant; None for other variants.

property target: SdfPropertyListTarget | None

“error_payload”} Target value or index implicated in the failure. Applies to HydrogenError.InvalidPropertyList. None when this payload is absent.

Type:

{“role”

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of HydrogenError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property topology_edit: TopologyEditError | None

“error_payload”} Structured TopologyEditError payload of HydrogenError.TopologyEdit; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of HydrogenError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: HydrogenErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.HydrogenErrorKind(value)

Discriminants of HydrogenErrorKind.

Members: StereoOrder, BondProperty, AtomProperty, InvalidTopology, InvalidCoordinates, TopologyEdit, InvalidMapping, InvalidQueryState, InvalidProperty, InvalidPropertyList, Unsupported, OnlyOnAtomOutOfRange, InvalidAdditionPlan, InvalidRemovalCandidate, MissingSourceState, ValenceAssignmentLength, ExplicitHydrogenOverflow, InvalidStereoTransition, CoordinatePlacement, Valence, Sanitize, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (24)
AtomProperty = HydrogenErrorKind.AtomProperty
BondProperty = HydrogenErrorKind.BondProperty
CoordinatePlacement = HydrogenErrorKind.CoordinatePlacement
ExplicitHydrogenOverflow = HydrogenErrorKind.ExplicitHydrogenOverflow
InvalidAdditionPlan = HydrogenErrorKind.InvalidAdditionPlan
InvalidCoordinates = HydrogenErrorKind.InvalidCoordinates
InvalidMapping = HydrogenErrorKind.InvalidMapping
InvalidProperty = HydrogenErrorKind.InvalidProperty
InvalidPropertyList = HydrogenErrorKind.InvalidPropertyList
InvalidQueryState = HydrogenErrorKind.InvalidQueryState
InvalidRemovalCandidate = HydrogenErrorKind.InvalidRemovalCandidate
InvalidStereoTransition = HydrogenErrorKind.InvalidStereoTransition
InvalidTopology = HydrogenErrorKind.InvalidTopology
MissingSourceState = HydrogenErrorKind.MissingSourceState
OnlyOnAtomOutOfRange = HydrogenErrorKind.OnlyOnAtomOutOfRange
Sanitize = HydrogenErrorKind.Sanitize
StereoOrder = HydrogenErrorKind.StereoOrder
TopologyEdit = HydrogenErrorKind.TopologyEdit
Unsupported = HydrogenErrorKind.Unsupported
Valence = HydrogenErrorKind.Valence
ValenceAssignmentLength = HydrogenErrorKind.ValenceAssignmentLength
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoOrder': HydrogenErrorKind.StereoOrder, 'BondProperty': HydrogenErrorKind.BondProperty, 'AtomProperty': HydrogenErrorKind.AtomProperty, 'InvalidTopology': HydrogenErrorKind.InvalidTopology, 'InvalidCoordinates': HydrogenErrorKind.InvalidCoordinates, 'TopologyEdit': HydrogenErrorKind.TopologyEdit, 'InvalidMapping': HydrogenErrorKind.InvalidMapping, 'InvalidQueryState': HydrogenErrorKind.InvalidQueryState, 'InvalidProperty': HydrogenErrorKind.InvalidProperty, 'InvalidPropertyList': HydrogenErrorKind.InvalidPropertyList, 'Unsupported': HydrogenErrorKind.Unsupported, 'OnlyOnAtomOutOfRange': HydrogenErrorKind.OnlyOnAtomOutOfRange, 'InvalidAdditionPlan': HydrogenErrorKind.InvalidAdditionPlan, 'InvalidRemovalCandidate': HydrogenErrorKind.InvalidRemovalCandidate, 'MissingSourceState': HydrogenErrorKind.MissingSourceState, 'ValenceAssignmentLength': HydrogenErrorKind.ValenceAssignmentLength, 'ExplicitHydrogenOverflow': HydrogenErrorKind.ExplicitHydrogenOverflow, 'InvalidStereoTransition': HydrogenErrorKind.InvalidStereoTransition, 'CoordinatePlacement': HydrogenErrorKind.CoordinatePlacement, 'Valence': HydrogenErrorKind.Valence, 'Sanitize': HydrogenErrorKind.Sanitize})
values = mappingproxy({0: HydrogenErrorKind.StereoOrder, 1: HydrogenErrorKind.BondProperty, 2: HydrogenErrorKind.AtomProperty, 3: HydrogenErrorKind.InvalidTopology, 4: HydrogenErrorKind.InvalidCoordinates, 5: HydrogenErrorKind.TopologyEdit, 6: HydrogenErrorKind.InvalidMapping, 7: HydrogenErrorKind.InvalidQueryState, 8: HydrogenErrorKind.InvalidProperty, 9: HydrogenErrorKind.InvalidPropertyList, 10: HydrogenErrorKind.Unsupported, 11: HydrogenErrorKind.OnlyOnAtomOutOfRange, 12: HydrogenErrorKind.InvalidAdditionPlan, 13: HydrogenErrorKind.InvalidRemovalCandidate, 14: HydrogenErrorKind.MissingSourceState, 15: HydrogenErrorKind.ValenceAssignmentLength, 16: HydrogenErrorKind.ExplicitHydrogenOverflow, 17: HydrogenErrorKind.InvalidStereoTransition, 18: HydrogenErrorKind.CoordinatePlacement, 19: HydrogenErrorKind.Valence, 20: HydrogenErrorKind.Sanitize})
class cosmolkit.InchiDiagnostic

One warning or error message produced by the InChI calculation.

Members (2)
level: InchiDiagnosticLevel

Severity of the InChI diagnostic.

message: str

Message emitted by the native InChI calculation.

class cosmolkit.InchiDiagnosticLevel(value)

Typed InchiDiagnosticLevel values corresponding to the Rust enum.

Members: Warning, Error, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Error = InchiDiagnosticLevel.Error
Warning = InchiDiagnosticLevel.Warning
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Warning': InchiDiagnosticLevel.Warning, 'Error': InchiDiagnosticLevel.Error})
values = mappingproxy({0: InchiDiagnosticLevel.Warning, 1: InchiDiagnosticLevel.Error})
exception cosmolkit.InchiError(*args, **kwargs)

InchiError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property detail: str

Native explanation of the InChI failure.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property operation: str

Native InChI operation reporting the failure.

property variant: InchiErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.InchiErrorKind(value)

Typed InchiErrorKind values corresponding to the Rust enum.

Members: AllocationFailed, UnsupportedState, InvalidInput, InvalidSourceOutput, SanitizeFailed, Toolkit, SourcePort, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (10)
AllocationFailed = InchiErrorKind.AllocationFailed
InvalidInput = InchiErrorKind.InvalidInput
InvalidSourceOutput = InchiErrorKind.InvalidSourceOutput
SanitizeFailed = InchiErrorKind.SanitizeFailed
SourcePort = InchiErrorKind.SourcePort
Toolkit = InchiErrorKind.Toolkit
UnsupportedState = InchiErrorKind.UnsupportedState
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'AllocationFailed': InchiErrorKind.AllocationFailed, 'UnsupportedState': InchiErrorKind.UnsupportedState, 'InvalidInput': InchiErrorKind.InvalidInput, 'InvalidSourceOutput': InchiErrorKind.InvalidSourceOutput, 'SanitizeFailed': InchiErrorKind.SanitizeFailed, 'Toolkit': InchiErrorKind.Toolkit, 'SourcePort': InchiErrorKind.SourcePort})
values = mappingproxy({0: InchiErrorKind.AllocationFailed, 1: InchiErrorKind.UnsupportedState, 2: InchiErrorKind.InvalidInput, 3: InchiErrorKind.InvalidSourceOutput, 4: InchiErrorKind.SanitizeFailed, 5: InchiErrorKind.Toolkit, 6: InchiErrorKind.SourcePort})
class cosmolkit.InchiReadParams(*, sanitize=Ellipsis, remove_hs=Ellipsis)

Controls the source-defined InChI post-processing stages.

Members (2)
remove_hs: bool

Remove removable explicit hydrogens from the decoded molecule.

sanitize: bool

Sanitize the molecule returned by InChI decoding.

class cosmolkit.InchiResult

InChI output with AuxInfo, native status, message, log and structured diagnostics.

Members (6)
aux_info: str

AuxInfo text accompanying the InChI result.

diagnostics: list[InchiDiagnostic]

Independent list of structured warning/error diagnostics.

inchi: str

Generated InChI identifier.

log: str

Native InChI diagnostic log.

message: str

Message emitted by the native InChI calculation.

return_code: int

Native InChI return status code.

class cosmolkit.InchiWriteParams(*, options=Ellipsis)

Official InChI option string; an empty string selects the engine defaults.

Members (1)
options: str

Official InChI option string; empty text uses engine defaults.

exception cosmolkit.IoError(*args, **kwargs)

IoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property kind: IoErrorKind

“error_payload”} Native IO error category.

Type:

{“role”

property raw_os_error: int | None

Original operating-system error number, or None for a non-OS error.

property source: IoError | Utf8Error | FromUtf8Error | ExternalError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.IoErrorKind

Native IO failure category; named constants compare by category rather than object identity.

Members (39)
AddrInUse = IoErrorKind.AddrInUse
AddrNotAvailable = IoErrorKind.AddrNotAvailable
AlreadyExists = IoErrorKind.AlreadyExists
ArgumentListTooLong = IoErrorKind.ArgumentListTooLong
BrokenPipe = IoErrorKind.BrokenPipe
ConnectionAborted = IoErrorKind.ConnectionAborted
ConnectionRefused = IoErrorKind.ConnectionRefused
ConnectionReset = IoErrorKind.ConnectionReset
CrossesDevices = IoErrorKind.CrossesDevices
Deadlock = IoErrorKind.Deadlock
DirectoryNotEmpty = IoErrorKind.DirectoryNotEmpty
ExecutableFileBusy = IoErrorKind.ExecutableFileBusy
FileTooLarge = IoErrorKind.FileTooLarge
HostUnreachable = IoErrorKind.HostUnreachable
Interrupted = IoErrorKind.Interrupted
InvalidData = IoErrorKind.InvalidData
InvalidFilename = IoErrorKind.InvalidFilename
InvalidInput = IoErrorKind.InvalidInput
IsADirectory = IoErrorKind.IsADirectory
NetworkDown = IoErrorKind.NetworkDown
NetworkUnreachable = IoErrorKind.NetworkUnreachable
NotADirectory = IoErrorKind.NotADirectory
NotConnected = IoErrorKind.NotConnected
NotFound = IoErrorKind.NotFound
NotSeekable = IoErrorKind.NotSeekable
Other = IoErrorKind.Other
OutOfMemory = IoErrorKind.OutOfMemory
PermissionDenied = IoErrorKind.PermissionDenied
QuotaExceeded = IoErrorKind.QuotaExceeded
ReadOnlyFilesystem = IoErrorKind.ReadOnlyFilesystem
ResourceBusy = IoErrorKind.ResourceBusy
StaleNetworkFileHandle = IoErrorKind.StaleNetworkFileHandle
StorageFull = IoErrorKind.StorageFull
TimedOut = IoErrorKind.TimedOut
UnexpectedEof = IoErrorKind.UnexpectedEof
Unsupported = IoErrorKind.Unsupported
WouldBlock = IoErrorKind.WouldBlock
WriteZero = IoErrorKind.WriteZero
exception cosmolkit.JsonError(*args, **kwargs)

JsonError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property argument: int | None

Optional numeric argument carried by this parser diagnostic.

property byte_offset: int

Byte offset of the JSON parsing failure.

property column: int

Column reported by the JSON parser.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property kind: JsonErrorKind

“error_payload”} Native JSON parser error category.

Type:

{“role”

property line: int

Line reported by the JSON parser.

class cosmolkit.JsonErrorKind(value)

Typed JsonErrorKind values corresponding to the Rust enum.

Members: NoError, OutOfMemory, UnexpectedEnd, MissingRootElement, BadRoot, ExpectedComma, MissingObjectKey, ExpectedColon, ExpectedEndOfInput, UnexpectedComma, ExpectedValue, ExpectedNull, ExpectedFalse, ExpectedTrue, InvalidNumber, MissingExponent, IllegalCodepoint, InvalidUnicodeEscape, UnexpectedEndOfUtf16, ExpectedU, InvalidUtf16TrailSurrogate, UnknownEscape, InvalidUtf8, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (26)
BadRoot = JsonErrorKind.BadRoot
ExpectedColon = JsonErrorKind.ExpectedColon
ExpectedComma = JsonErrorKind.ExpectedComma
ExpectedEndOfInput = JsonErrorKind.ExpectedEndOfInput
ExpectedFalse = JsonErrorKind.ExpectedFalse
ExpectedNull = JsonErrorKind.ExpectedNull
ExpectedTrue = JsonErrorKind.ExpectedTrue
ExpectedU = JsonErrorKind.ExpectedU
ExpectedValue = JsonErrorKind.ExpectedValue
IllegalCodepoint = JsonErrorKind.IllegalCodepoint
InvalidNumber = JsonErrorKind.InvalidNumber
InvalidUnicodeEscape = JsonErrorKind.InvalidUnicodeEscape
InvalidUtf16TrailSurrogate = JsonErrorKind.InvalidUtf16TrailSurrogate
InvalidUtf8 = JsonErrorKind.InvalidUtf8
MissingExponent = JsonErrorKind.MissingExponent
MissingObjectKey = JsonErrorKind.MissingObjectKey
MissingRootElement = JsonErrorKind.MissingRootElement
NoError = JsonErrorKind.NoError
OutOfMemory = JsonErrorKind.OutOfMemory
UnexpectedComma = JsonErrorKind.UnexpectedComma
UnexpectedEnd = JsonErrorKind.UnexpectedEnd
UnexpectedEndOfUtf16 = JsonErrorKind.UnexpectedEndOfUtf16
UnknownEscape = JsonErrorKind.UnknownEscape
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NoError': JsonErrorKind.NoError, 'OutOfMemory': JsonErrorKind.OutOfMemory, 'UnexpectedEnd': JsonErrorKind.UnexpectedEnd, 'MissingRootElement': JsonErrorKind.MissingRootElement, 'BadRoot': JsonErrorKind.BadRoot, 'ExpectedComma': JsonErrorKind.ExpectedComma, 'MissingObjectKey': JsonErrorKind.MissingObjectKey, 'ExpectedColon': JsonErrorKind.ExpectedColon, 'ExpectedEndOfInput': JsonErrorKind.ExpectedEndOfInput, 'UnexpectedComma': JsonErrorKind.UnexpectedComma, 'ExpectedValue': JsonErrorKind.ExpectedValue, 'ExpectedNull': JsonErrorKind.ExpectedNull, 'ExpectedFalse': JsonErrorKind.ExpectedFalse, 'ExpectedTrue': JsonErrorKind.ExpectedTrue, 'InvalidNumber': JsonErrorKind.InvalidNumber, 'MissingExponent': JsonErrorKind.MissingExponent, 'IllegalCodepoint': JsonErrorKind.IllegalCodepoint, 'InvalidUnicodeEscape': JsonErrorKind.InvalidUnicodeEscape, 'UnexpectedEndOfUtf16': JsonErrorKind.UnexpectedEndOfUtf16, 'ExpectedU': JsonErrorKind.ExpectedU, 'InvalidUtf16TrailSurrogate': JsonErrorKind.InvalidUtf16TrailSurrogate, 'UnknownEscape': JsonErrorKind.UnknownEscape, 'InvalidUtf8': JsonErrorKind.InvalidUtf8})
values = mappingproxy({0: JsonErrorKind.NoError, 1: JsonErrorKind.OutOfMemory, 2: JsonErrorKind.UnexpectedEnd, 3: JsonErrorKind.MissingRootElement, 4: JsonErrorKind.BadRoot, 5: JsonErrorKind.ExpectedComma, 6: JsonErrorKind.MissingObjectKey, 7: JsonErrorKind.ExpectedColon, 8: JsonErrorKind.ExpectedEndOfInput, 9: JsonErrorKind.UnexpectedComma, 10: JsonErrorKind.ExpectedValue, 11: JsonErrorKind.ExpectedNull, 12: JsonErrorKind.ExpectedFalse, 13: JsonErrorKind.ExpectedTrue, 14: JsonErrorKind.InvalidNumber, 15: JsonErrorKind.MissingExponent, 16: JsonErrorKind.IllegalCodepoint, 17: JsonErrorKind.InvalidUnicodeEscape, 18: JsonErrorKind.UnexpectedEndOfUtf16, 19: JsonErrorKind.ExpectedU, 20: JsonErrorKind.InvalidUtf16TrailSurrogate, 21: JsonErrorKind.UnknownEscape, 22: JsonErrorKind.InvalidUtf8})
exception cosmolkit.KekulizeError(*args, **kwargs)

Failure in the kekulize domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

KekulizeError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (23)
property actual: int | None

Observed value reported by the native check. Applies to KekulizeError.AtomSelectionLength, KekulizeError.BondSelectionLength, KekulizeError.MatchingStateLength. None when this payload is absent.

property after: int | None

Readonly after payload of the PostconditionValenceMismatch error variant; None for other variants.

property atom: int | None

Atom identifier implicated in the failure. Applies to KekulizeError.CandidateAtomOutOfRange, KekulizeError.DuplicateCandidateAtom, KekulizeError.DuplicateDoneAtom, KekulizeError.MissingBacktrackAnchor, KekulizeError.AromaticAtomOutsideRing, KekulizeError.PostconditionValenceMismatch, KekulizeError.IntegerOverflow. None when this payload is absent.

property atom_count: int | None

Readonly atom_count payload of the CandidateAtomOutOfRange error variant; None for other variants.

property before: int | None

Readonly before payload of the PostconditionValenceMismatch error variant; None for other variants.

property begin: int | None

Readonly begin payload of the MissingCandidateBond error variant; None for other variants.

property bit_width: int | None

Readonly bit_width payload of the QuestionSubsetOverflow error variant; None for other variants.

property bond: int | None

Readonly bond payload of the UnsupportedQueryState error variant; None for other variants.

property canonical_rank: CanonicalRankError | None

“error_payload”} Structured CanonicalRankError payload of KekulizeError.CanonicalRank; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property detail: str | None

Readonly detail payload of the UnsupportedQueryState error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the MissingCandidateBond error variant; None for other variants.

property expected: int | None

Required value reported by the native check. Applies to KekulizeError.AtomSelectionLength, KekulizeError.BondSelectionLength, KekulizeError.MatchingStateLength. None when this payload is absent.

property field: str | None

Field whose content or type caused the failure. Applies to KekulizeError.MatchingStateLength, KekulizeError.IntegerOverflow. None when this payload is absent.

property problem_atoms: list[int] | None

Readonly problem_atoms payload of the NotKekulizable error variant; None for other variants.

property query_state: QueryStateError | None

“error_payload”} Structured QueryStateError payload of KekulizeError.InvalidQueryState; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property questions: int | None

Readonly questions payload of the QuestionSubsetOverflow error variant; None for other variants.

property ring_finding: RingFindingError | None

“error_payload”} Structured RingFindingError payload of KekulizeError.RingFinding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: TopologyValidationError | MappingValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of KekulizeError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of KekulizeError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: KekulizeErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.KekulizeErrorKind(value)

Discriminants of KekulizeErrorKind.

Members: InvalidTopology, AtomSelectionLength, BondSelectionLength, CandidateAtomOutOfRange, DuplicateCandidateAtom, MatchingStateLength, DuplicateDoneAtom, MissingCandidateBond, MissingBacktrackAnchor, QuestionSubsetOverflow, AromaticAtomOutsideRing, NotKekulizable, PostconditionValenceMismatch, UnsupportedQueryState, InvalidQueryState, IntegerOverflow, RingFinding, Valence, CanonicalRank, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (22)
AromaticAtomOutsideRing = KekulizeErrorKind.AromaticAtomOutsideRing
AtomSelectionLength = KekulizeErrorKind.AtomSelectionLength
BondSelectionLength = KekulizeErrorKind.BondSelectionLength
CandidateAtomOutOfRange = KekulizeErrorKind.CandidateAtomOutOfRange
CanonicalRank = KekulizeErrorKind.CanonicalRank
DuplicateCandidateAtom = KekulizeErrorKind.DuplicateCandidateAtom
DuplicateDoneAtom = KekulizeErrorKind.DuplicateDoneAtom
IntegerOverflow = KekulizeErrorKind.IntegerOverflow
InvalidQueryState = KekulizeErrorKind.InvalidQueryState
InvalidTopology = KekulizeErrorKind.InvalidTopology
MatchingStateLength = KekulizeErrorKind.MatchingStateLength
MissingBacktrackAnchor = KekulizeErrorKind.MissingBacktrackAnchor
MissingCandidateBond = KekulizeErrorKind.MissingCandidateBond
NotKekulizable = KekulizeErrorKind.NotKekulizable
PostconditionValenceMismatch = KekulizeErrorKind.PostconditionValenceMismatch
QuestionSubsetOverflow = KekulizeErrorKind.QuestionSubsetOverflow
RingFinding = KekulizeErrorKind.RingFinding
UnsupportedQueryState = KekulizeErrorKind.UnsupportedQueryState
Valence = KekulizeErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': KekulizeErrorKind.InvalidTopology, 'AtomSelectionLength': KekulizeErrorKind.AtomSelectionLength, 'BondSelectionLength': KekulizeErrorKind.BondSelectionLength, 'CandidateAtomOutOfRange': KekulizeErrorKind.CandidateAtomOutOfRange, 'DuplicateCandidateAtom': KekulizeErrorKind.DuplicateCandidateAtom, 'MatchingStateLength': KekulizeErrorKind.MatchingStateLength, 'DuplicateDoneAtom': KekulizeErrorKind.DuplicateDoneAtom, 'MissingCandidateBond': KekulizeErrorKind.MissingCandidateBond, 'MissingBacktrackAnchor': KekulizeErrorKind.MissingBacktrackAnchor, 'QuestionSubsetOverflow': KekulizeErrorKind.QuestionSubsetOverflow, 'AromaticAtomOutsideRing': KekulizeErrorKind.AromaticAtomOutsideRing, 'NotKekulizable': KekulizeErrorKind.NotKekulizable, 'PostconditionValenceMismatch': KekulizeErrorKind.PostconditionValenceMismatch, 'UnsupportedQueryState': KekulizeErrorKind.UnsupportedQueryState, 'InvalidQueryState': KekulizeErrorKind.InvalidQueryState, 'IntegerOverflow': KekulizeErrorKind.IntegerOverflow, 'RingFinding': KekulizeErrorKind.RingFinding, 'Valence': KekulizeErrorKind.Valence, 'CanonicalRank': KekulizeErrorKind.CanonicalRank})
values = mappingproxy({0: KekulizeErrorKind.InvalidTopology, 1: KekulizeErrorKind.AtomSelectionLength, 2: KekulizeErrorKind.BondSelectionLength, 3: KekulizeErrorKind.CandidateAtomOutOfRange, 4: KekulizeErrorKind.DuplicateCandidateAtom, 5: KekulizeErrorKind.MatchingStateLength, 6: KekulizeErrorKind.DuplicateDoneAtom, 7: KekulizeErrorKind.MissingCandidateBond, 8: KekulizeErrorKind.MissingBacktrackAnchor, 9: KekulizeErrorKind.QuestionSubsetOverflow, 10: KekulizeErrorKind.AromaticAtomOutsideRing, 11: KekulizeErrorKind.NotKekulizable, 12: KekulizeErrorKind.PostconditionValenceMismatch, 13: KekulizeErrorKind.UnsupportedQueryState, 14: KekulizeErrorKind.InvalidQueryState, 15: KekulizeErrorKind.IntegerOverflow, 16: KekulizeErrorKind.RingFinding, 17: KekulizeErrorKind.Valence, 18: KekulizeErrorKind.CanonicalRank})
class cosmolkit.KekulizeParams(*, mark_atoms_bonds=Ellipsis, canonical=Ellipsis, max_backtracks=Ellipsis)

Kekule bond assignment and aromatic-flag handling options.

Members (3)
canonical: bool

Use canonical atom ordering when choosing the Kekule assignment.

mark_atoms_bonds: bool

Clear aromatic flags on atoms and bonds after Kekule assignment.

max_backtracks: int

Maximum number of backtracking attempts in Kekule assignment.

class cosmolkit.LabuteAsaContributions(asa, atom_contributions, hydrogen_contribution)

Labute approximate surface area with per-atom and aggregate hydrogen contributions.

Members (3)
asa: float

Total Labute approximate molecular surface area.

atom_contributions: list[float]

Independent list of Labute surface-area contributions in atom order.

hydrogen_contribution: float

Aggregate hydrogen contribution to the Labute surface-area result.

exception cosmolkit.LayeredFingerprintError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

LayeredFingerprintError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property reason: str | None

Readonly reason payload of the InvalidArguments error variant; None for other variants.

property source: TopologyValidationError | QueryGraphError | RingFindingError | PathError | FingerprintError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: LayeredFingerprintErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.LayeredFingerprintErrorKind(value)

Discriminants of LayeredFingerprintErrorKind.

Members: InvalidArguments, Topology, Query, Rings, Paths, Value, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
InvalidArguments = LayeredFingerprintErrorKind.InvalidArguments
Paths = LayeredFingerprintErrorKind.Paths
Query = LayeredFingerprintErrorKind.Query
Rings = LayeredFingerprintErrorKind.Rings
Topology = LayeredFingerprintErrorKind.Topology
Value = LayeredFingerprintErrorKind.Value
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidArguments': LayeredFingerprintErrorKind.InvalidArguments, 'Topology': LayeredFingerprintErrorKind.Topology, 'Query': LayeredFingerprintErrorKind.Query, 'Rings': LayeredFingerprintErrorKind.Rings, 'Paths': LayeredFingerprintErrorKind.Paths, 'Value': LayeredFingerprintErrorKind.Value})
values = mappingproxy({0: LayeredFingerprintErrorKind.InvalidArguments, 1: LayeredFingerprintErrorKind.Topology, 2: LayeredFingerprintErrorKind.Query, 3: LayeredFingerprintErrorKind.Rings, 4: LayeredFingerprintErrorKind.Paths, 5: LayeredFingerprintErrorKind.Value})
class cosmolkit.LayeredFingerprintLayers

LayeredFingerprintLayers native option bit mask. Combine named constants with the bitwise OR operator; bits exposes its integer representation.

Members (12)
ACTIVE = <cosmolkit.LayeredFingerprintLayers object>
ALL_SOURCE_BITS = <cosmolkit.LayeredFingerprintLayers object>
AROMATICITY = <cosmolkit.LayeredFingerprintLayers object>
ATOM_TYPE = <cosmolkit.LayeredFingerprintLayers object>
BOND_ORDER = <cosmolkit.LayeredFingerprintLayers object>
RING_PRESENCE = <cosmolkit.LayeredFingerprintLayers object>
RING_SIZE = <cosmolkit.LayeredFingerprintLayers object>
SUBSTRUCTURE = <cosmolkit.LayeredFingerprintLayers object>
TOPOLOGY = <cosmolkit.LayeredFingerprintLayers object>
bits: int

Integer representation of this option mask.

contains(other) → bool

Whether every bit in the supplied mask is present.

static from_bits_retain(bits) → LayeredFingerprintLayers

Construct a mask retaining all supplied bits, including unknown bits.

class cosmolkit.LayeredFingerprintParams(*, layers=Ellipsis, min_path=Ellipsis, max_path=Ellipsis, fp_size=Ellipsis, atom_counts=Ellipsis, set_only_bits=Ellipsis, branched_paths=Ellipsis, from_atoms=Ellipsis)

Parameters for the source-backed Layered fingerprint API.

The defaults reproduce the source wrapper: all source flag bits, bond-path lengths 1 through 7, 2,048 output bits, branched path enumeration, no atom counts, no output-bit mask, and no root selection. from_atoms: None selects the whole graph, while Some(Vec::new()) is a present but empty root selection and therefore enumerates no paths.

Members (8)
atom_counts: tuple[int, ...] | None

Optional seeded source atomCounts vector. Values are incremented and returned without clearing the caller-provided seed.

branched_paths: bool

Enumerate branched subgraphs when true and linear paths when false. Unrooted linear paths preserve the pinned source’s atom-index selection and subsequent bond-index interpretation; invalid accesses return an error.

fp_size: int

Explicit output width. Zero is rejected.

from_atoms: tuple[int, ...] | None

None is an absent source pointer; Some(Vec::new()) is a present empty selection and therefore enumerates no paths.

layers: int

Layer flags. Unknown high bits are retained and emit no components.

max_path: int

Maximum path length, in the same units as min_path. Values below min_path are rejected.

min_path: int

Minimum path length. The unrooted linear source branch counts atoms; branched and rooted paths count bonds. Zero is rejected as minPath==0.

set_only_bits: Fingerprint | None

Optional projection mask, which must have exactly fp_size bits.

class cosmolkit.LayeredFingerprintResult(fingerprint, atom_counts)

Layered fingerprint and optional atom contribution counts.

Members (2)
atom_counts: list[int] | None

Optional per-atom contribution counts requested during fingerprint generation.

fingerprint: Fingerprint

Generated bit fingerprint.

exception cosmolkit.LegacyStereoError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

LegacyStereoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (14)
property atom_property: AtomPropertyError | None

“error_payload”} Structured AtomPropertyError payload of LegacyStereoError.AtomProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property atropisomer: AtropisomerError | None

“error_payload”} Structured AtropisomerError payload of LegacyStereoError.Atropisomer; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property bond_value: BondValueError | None

“error_payload”} Structured BondValueError payload of LegacyStereoError.BondValue; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property cip_rank: CipRankError | None

“error_payload”} Structured CipRankError payload of LegacyStereoError.CipRank; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property double_bond: DoubleBondStereoError | None

“error_payload”} Structured DoubleBondStereoError payload of LegacyStereoError.DoubleBond; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property potential_stereo: PotentialStereoError | None

“error_payload”} Structured PotentialStereoError payload of LegacyStereoError.PotentialStereo; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property ring_finding: RingFindingError | None

“error_payload”} Structured RingFindingError payload of LegacyStereoError.RingFinding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | StereoOrderError | AtomPropertyError | PropertyIntReadError | TemplateAttachmentOrderError | MappingValidationError | PropertyUIntReadError | CanonicalRankError | DoubleBondStereoError | MoleculePropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stereo_order: StereoOrderError | None

“error_payload”} Structured StereoOrderError payload of LegacyStereoError.StereoOrder; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of LegacyStereoError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of LegacyStereoError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: LegacyStereoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.LegacyStereoErrorKind(value)

Discriminants of LegacyStereoErrorKind.

Members: StereoGroup, InvalidTopology, CipRank, DoubleBond, StereoOrder, Valence, AtomProperty, BondValue, PotentialStereo, RingFinding, Atropisomer, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (14)
AtomProperty = LegacyStereoErrorKind.AtomProperty
Atropisomer = LegacyStereoErrorKind.Atropisomer
BondValue = LegacyStereoErrorKind.BondValue
CipRank = LegacyStereoErrorKind.CipRank
DoubleBond = LegacyStereoErrorKind.DoubleBond
InvalidTopology = LegacyStereoErrorKind.InvalidTopology
PotentialStereo = LegacyStereoErrorKind.PotentialStereo
RingFinding = LegacyStereoErrorKind.RingFinding
StereoGroup = LegacyStereoErrorKind.StereoGroup
StereoOrder = LegacyStereoErrorKind.StereoOrder
Valence = LegacyStereoErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': LegacyStereoErrorKind.StereoGroup, 'InvalidTopology': LegacyStereoErrorKind.InvalidTopology, 'CipRank': LegacyStereoErrorKind.CipRank, 'DoubleBond': LegacyStereoErrorKind.DoubleBond, 'StereoOrder': LegacyStereoErrorKind.StereoOrder, 'Valence': LegacyStereoErrorKind.Valence, 'AtomProperty': LegacyStereoErrorKind.AtomProperty, 'BondValue': LegacyStereoErrorKind.BondValue, 'PotentialStereo': LegacyStereoErrorKind.PotentialStereo, 'RingFinding': LegacyStereoErrorKind.RingFinding, 'Atropisomer': LegacyStereoErrorKind.Atropisomer})
values = mappingproxy({0: LegacyStereoErrorKind.StereoGroup, 1: LegacyStereoErrorKind.InvalidTopology, 2: LegacyStereoErrorKind.CipRank, 3: LegacyStereoErrorKind.DoubleBond, 4: LegacyStereoErrorKind.StereoOrder, 5: LegacyStereoErrorKind.Valence, 6: LegacyStereoErrorKind.AtomProperty, 7: LegacyStereoErrorKind.BondValue, 8: LegacyStereoErrorKind.PotentialStereo, 9: LegacyStereoErrorKind.RingFinding, 10: LegacyStereoErrorKind.Atropisomer})
class cosmolkit.LegacyTopologicalTorsionParams(*, torsion_atom_count=Ellipsis, include_chirality=Ellipsis, fp_size=Ellipsis, bits_per_entry=Ellipsis, from_atoms=Ellipsis, ignore_atoms=Ellipsis, custom_atom_invariants=Ellipsis)

Immutable call configuration preserving source optional-vector semantics.

Members (8)
bits_per_entry: int

Number of bits used for count simulation per torsion.

custom_atom_invariants: tuple[int, ...] | None

Optional per-atom invariant values replacing generated invariants.

fp_size: int

Number of bins in hashed fingerprints.

from_atoms: tuple[int, ...] | None

Optional atom indices restricting torsion endpoints.

ignore_atoms: tuple[int, ...] | None

Optional atom indices excluded from torsion paths.

include_chirality: bool

Include atom chirality in torsion codes.

static new(torsion_atom_count=Ellipsis, include_chirality=Ellipsis, fp_size=Ellipsis, bits_per_entry=Ellipsis, from_atoms=Ellipsis, ignore_atoms=Ellipsis, custom_atom_invariants=Ellipsis) → LegacyTopologicalTorsionParams

Create an independent configuration through the native constructor using the supplied field values.

torsion_atom_count: int

Number of atoms in each torsion path.

class cosmolkit.LigandRef(atom=None)

Tetrahedral ligand represented by an atom, implicit hydrogen or lone pair.

Members (4)
static Atom(value) → LigandRef

Represent a tetrahedral ligand using a zero-based atom identifier.

ImplicitHydrogen = <cosmolkit.LigandRef object>
LonePair = <cosmolkit.LigandRef object>
atom_id: int | None

Ligand atom identifier, or None for a hydrogen or lone-pair position.

exception cosmolkit.MaccsFingerprintError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MaccsFingerprintError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property bit: int | None

Readonly bit payload of the MissingPattern error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property option: str | None

Readonly option payload of the UnsupportedOption error variant; None for other variants.

property reason: str | None

Readonly reason payload of the UnsupportedOption error variant; None for other variants.

property source: TopologyValidationError | RingFindingError | ValenceError | PathError | SmartsParseError | QueryCompileError | QueryMatchContextError | SubstructMatchError | FingerprintError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MaccsFingerprintErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MaccsFingerprintErrorKind(value)

Discriminants of MaccsFingerprintErrorKind.

Members: UnsupportedOption, MissingPattern, Topology, Rings, Valence, Paths, Smarts, QueryCompile, QueryContext, Match, Value, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (14)
Match = MaccsFingerprintErrorKind.Match
MissingPattern = MaccsFingerprintErrorKind.MissingPattern
Paths = MaccsFingerprintErrorKind.Paths
QueryCompile = MaccsFingerprintErrorKind.QueryCompile
QueryContext = MaccsFingerprintErrorKind.QueryContext
Rings = MaccsFingerprintErrorKind.Rings
Smarts = MaccsFingerprintErrorKind.Smarts
Topology = MaccsFingerprintErrorKind.Topology
UnsupportedOption = MaccsFingerprintErrorKind.UnsupportedOption
Valence = MaccsFingerprintErrorKind.Valence
Value = MaccsFingerprintErrorKind.Value
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnsupportedOption': MaccsFingerprintErrorKind.UnsupportedOption, 'MissingPattern': MaccsFingerprintErrorKind.MissingPattern, 'Topology': MaccsFingerprintErrorKind.Topology, 'Rings': MaccsFingerprintErrorKind.Rings, 'Valence': MaccsFingerprintErrorKind.Valence, 'Paths': MaccsFingerprintErrorKind.Paths, 'Smarts': MaccsFingerprintErrorKind.Smarts, 'QueryCompile': MaccsFingerprintErrorKind.QueryCompile, 'QueryContext': MaccsFingerprintErrorKind.QueryContext, 'Match': MaccsFingerprintErrorKind.Match, 'Value': MaccsFingerprintErrorKind.Value})
values = mappingproxy({0: MaccsFingerprintErrorKind.UnsupportedOption, 1: MaccsFingerprintErrorKind.MissingPattern, 2: MaccsFingerprintErrorKind.Topology, 3: MaccsFingerprintErrorKind.Rings, 4: MaccsFingerprintErrorKind.Valence, 5: MaccsFingerprintErrorKind.Paths, 6: MaccsFingerprintErrorKind.Smarts, 7: MaccsFingerprintErrorKind.QueryCompile, 8: MaccsFingerprintErrorKind.QueryContext, 9: MaccsFingerprintErrorKind.Match, 10: MaccsFingerprintErrorKind.Value})
class cosmolkit.MaccsFingerprintParams(*, n_bits=Ellipsis)

Exact source fixed-width public projection. Other widths remain source-defined rejected options.

Members (1)
n_bits: int

MACCS public fingerprint width; the supported fixed width is 166 bits.

exception cosmolkit.MappingValidationError(*args, **kwargs)

Failure in the model domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MappingValidationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property actual: int | None

Readonly actual payload of the Length error variant; None for other variants.

property direction: str

Direction of the atom or bond mapping that failed validation.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property entity: str

Structural entity involved in the failure. Applies to MappingValidationError.Length, MappingValidationError.OutOfRange, MappingValidationError.InverseMismatch.

property expected: int | None

Readonly expected payload of the Length error variant; None for other variants.

property mapped: int | None

Mapped identifier rejected during validation. Present for MappingValidationError.OutOfRange, MappingValidationError.InverseMismatch; None when unavailable.

property row: int | None

Row reported by the native failure. Applies to MappingValidationError.OutOfRange, MappingValidationError.InverseMismatch. None when this payload is absent.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property target_count: int | None

Readonly target_count payload of the OutOfRange error variant; None for other variants.

property variant: MappingValidationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MappingValidationErrorKind(value)

Discriminants of MappingValidationErrorKind.

Members: Length, OutOfRange, InverseMismatch, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
InverseMismatch = MappingValidationErrorKind.InverseMismatch
Length = MappingValidationErrorKind.Length
OutOfRange = MappingValidationErrorKind.OutOfRange
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Length': MappingValidationErrorKind.Length, 'OutOfRange': MappingValidationErrorKind.OutOfRange, 'InverseMismatch': MappingValidationErrorKind.InverseMismatch})
values = mappingproxy({0: MappingValidationErrorKind.Length, 1: MappingValidationErrorKind.OutOfRange, 2: MappingValidationErrorKind.InverseMismatch})
exception cosmolkit.MatchError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MatchError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (9)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property invalid_query: str | None

Explanation of an invalid query, or None for another failure.

property invalid_target: str | None

Explanation of an invalid target, or None for another failure.

property source: PropertyUIntReadError | AtomPropertyError | PropertyIntReadError | TopologyValidationError | RingFindingError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property substruct: SubstructMatchError | None

“error_payload”} Structured SubstructMatchError payload of MatchError.Substruct; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property unsupported_atom_predicate: str | None

Unsupported atom predicate name; None for other failures.

property unsupported_bond_predicate: str | None

Unsupported bond predicate name; None for other failures.

property variant: MatchErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MatchErrorKind(value)

Discriminants of MatchErrorKind.

Members: InvalidQuery, InvalidTarget, UnsupportedAtomPredicate, UnsupportedBondPredicate, Substruct, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
InvalidQuery = MatchErrorKind.InvalidQuery
InvalidTarget = MatchErrorKind.InvalidTarget
Substruct = MatchErrorKind.Substruct
UnsupportedAtomPredicate = MatchErrorKind.UnsupportedAtomPredicate
UnsupportedBondPredicate = MatchErrorKind.UnsupportedBondPredicate
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidQuery': MatchErrorKind.InvalidQuery, 'InvalidTarget': MatchErrorKind.InvalidTarget, 'UnsupportedAtomPredicate': MatchErrorKind.UnsupportedAtomPredicate, 'UnsupportedBondPredicate': MatchErrorKind.UnsupportedBondPredicate, 'Substruct': MatchErrorKind.Substruct})
values = mappingproxy({0: MatchErrorKind.InvalidQuery, 1: MatchErrorKind.InvalidTarget, 2: MatchErrorKind.UnsupportedAtomPredicate, 3: MatchErrorKind.UnsupportedBondPredicate, 4: MatchErrorKind.Substruct})
class cosmolkit.MatchResult(atom_mapping, bond_mapping)

Atom and bond correspondences returned by native substructure matching.

Members (3)
atom_mapping: list[int]

Target atom indices in query-atom order.

atom_pairs() → list[tuple[int, int]]

Query-to-target atom pairs represented by this match.

bond_mapping: list[int]

Target bond indices in query-bond order.

class cosmolkit.MatrixAxis(value)

Typed MatrixAxis values corresponding to the Rust enum.

Members: Row, Column, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Column = MatrixAxis.Column
Row = MatrixAxis.Row
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Row': MatrixAxis.Row, 'Column': MatrixAxis.Column})
values = mappingproxy({0: MatrixAxis.Row, 1: MatrixAxis.Column})
exception cosmolkit.MatrixError(*args, **kwargs)

Failure in the matrix domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MatrixError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (17)
property atom: int | None

Atom identifier implicated in the failure. Applies to MatrixError.ActiveAtomOutOfRange, MatrixError.DuplicateActiveAtom, MatrixError.ActiveBondEndpointMissing. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to MatrixError.ActiveAtomOutOfRange. None when this payload is absent.

property bond: int | None

Bond identifier implicated in the failure. Applies to MatrixError.ActiveBondOutOfRange, MatrixError.DuplicateActiveBond, MatrixError.ActiveBondEndpointMissing, MatrixError.UnsupportedBondOrder. None when this payload is absent.

property bond_count: int | None

Bond count used when validating the reported bond reference. Applies to MatrixError.ActiveBondOutOfRange. None when this payload is absent.

property conformer_id: int | None

Readonly conformer_id payload of the ConformerNotFound error variant; None for other variants.

property coordinates: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of MatrixError.InvalidCoordinates; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property dimension: int | None

Readonly dimension payload of the MatrixDimensionOverflow error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property endpoint: str | None

Readonly endpoint payload of the ActiveBondEndpointMissing error variant; None for other variants.

property first_position: int | None

First position involved in the reported conflict. Applies to MatrixError.DuplicateActiveAtom, MatrixError.DuplicateActiveBond. None when this payload is absent.

property order: BondOrder | None

Readonly order payload of the UnsupportedBondOrder error variant; None for other variants.

property position: int | None

Position reported by the native failure. Applies to MatrixError.ActiveAtomOutOfRange, MatrixError.ActiveBondOutOfRange. None when this payload is absent.

property second_position: int | None

Second position involved in the reported conflict. Applies to MatrixError.DuplicateActiveAtom, MatrixError.DuplicateActiveBond. None when this payload is absent.

property source: StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of MatrixError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: MatrixErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MatrixErrorKind(value)

Discriminants of MatrixErrorKind.

Members: InvalidTopology, InvalidCoordinates, ActiveBondsWithoutAtoms, ActiveAtomOutOfRange, DuplicateActiveAtom, ActiveBondOutOfRange, DuplicateActiveBond, ActiveBondEndpointMissing, UnsupportedBondOrder, No3dConformer, ConformerNotFound, MatrixDimensionOverflow, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (15)
ActiveAtomOutOfRange = MatrixErrorKind.ActiveAtomOutOfRange
ActiveBondEndpointMissing = MatrixErrorKind.ActiveBondEndpointMissing
ActiveBondOutOfRange = MatrixErrorKind.ActiveBondOutOfRange
ActiveBondsWithoutAtoms = MatrixErrorKind.ActiveBondsWithoutAtoms
ConformerNotFound = MatrixErrorKind.ConformerNotFound
DuplicateActiveAtom = MatrixErrorKind.DuplicateActiveAtom
DuplicateActiveBond = MatrixErrorKind.DuplicateActiveBond
InvalidCoordinates = MatrixErrorKind.InvalidCoordinates
InvalidTopology = MatrixErrorKind.InvalidTopology
MatrixDimensionOverflow = MatrixErrorKind.MatrixDimensionOverflow
No3dConformer = MatrixErrorKind.No3dConformer
UnsupportedBondOrder = MatrixErrorKind.UnsupportedBondOrder
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': MatrixErrorKind.InvalidTopology, 'InvalidCoordinates': MatrixErrorKind.InvalidCoordinates, 'ActiveBondsWithoutAtoms': MatrixErrorKind.ActiveBondsWithoutAtoms, 'ActiveAtomOutOfRange': MatrixErrorKind.ActiveAtomOutOfRange, 'DuplicateActiveAtom': MatrixErrorKind.DuplicateActiveAtom, 'ActiveBondOutOfRange': MatrixErrorKind.ActiveBondOutOfRange, 'DuplicateActiveBond': MatrixErrorKind.DuplicateActiveBond, 'ActiveBondEndpointMissing': MatrixErrorKind.ActiveBondEndpointMissing, 'UnsupportedBondOrder': MatrixErrorKind.UnsupportedBondOrder, 'No3dConformer': MatrixErrorKind.No3dConformer, 'ConformerNotFound': MatrixErrorKind.ConformerNotFound, 'MatrixDimensionOverflow': MatrixErrorKind.MatrixDimensionOverflow})
values = mappingproxy({0: MatrixErrorKind.InvalidTopology, 1: MatrixErrorKind.InvalidCoordinates, 2: MatrixErrorKind.ActiveBondsWithoutAtoms, 3: MatrixErrorKind.ActiveAtomOutOfRange, 4: MatrixErrorKind.DuplicateActiveAtom, 5: MatrixErrorKind.ActiveBondOutOfRange, 6: MatrixErrorKind.DuplicateActiveBond, 7: MatrixErrorKind.ActiveBondEndpointMissing, 8: MatrixErrorKind.UnsupportedBondOrder, 9: MatrixErrorKind.No3dConformer, 10: MatrixErrorKind.ConformerNotFound, 11: MatrixErrorKind.MatrixDimensionOverflow})
class cosmolkit.McsAtomComparator(value)

Typed McsAtomComparator values corresponding to the Rust enum.

Members: Any, Elements, Isotopes, AnyHeavyAtom, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
Any = McsAtomComparator.Any
AnyHeavyAtom = McsAtomComparator.AnyHeavyAtom
Elements = McsAtomComparator.Elements
Isotopes = McsAtomComparator.Isotopes
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Any': McsAtomComparator.Any, 'Elements': McsAtomComparator.Elements, 'Isotopes': McsAtomComparator.Isotopes, 'AnyHeavyAtom': McsAtomComparator.AnyHeavyAtom})
values = mappingproxy({0: McsAtomComparator.Any, 1: McsAtomComparator.Elements, 2: McsAtomComparator.Isotopes, 3: McsAtomComparator.AnyHeavyAtom})
class cosmolkit.McsAtomCompareParameters(*, match_valences=Ellipsis, match_chiral_tag=Ellipsis, match_formal_charge=Ellipsis, ring_matches_ring_only=Ellipsis, complete_rings_only=Ellipsis, match_isotope=Ellipsis, max_distance=Ellipsis)

Atom-side FMCS comparison options.

Members (7)
complete_rings_only: bool

Permit only complete rings in the common substructure.

match_chiral_tag: bool

Require compatible atom chirality.

match_formal_charge: bool

Require equal formal charges.

match_isotope: bool

Require matching isotope labels.

match_valences: bool

Require matching atom valences.

max_distance: float

Maximum distance between matching atoms in angstroms; a negative value disables this check.

ring_matches_ring_only: bool

Match ring atoms only to ring atoms.

class cosmolkit.McsBondComparator(value)

Typed McsBondComparator values corresponding to the Rust enum.

Members: Any, Order, OrderExact, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
Any = McsBondComparator.Any
Order = McsBondComparator.Order
OrderExact = McsBondComparator.OrderExact
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Any': McsBondComparator.Any, 'Order': McsBondComparator.Order, 'OrderExact': McsBondComparator.OrderExact})
values = mappingproxy({0: McsBondComparator.Any, 1: McsBondComparator.Order, 2: McsBondComparator.OrderExact})
class cosmolkit.McsBondCompareParameters(*, ring_matches_ring_only=Ellipsis, complete_rings_only=Ellipsis, match_fused_rings=Ellipsis, match_fused_rings_strict=Ellipsis, match_stereo=Ellipsis)

Bond-side FMCS comparison options.

Members (5)
complete_rings_only: bool

Permit only complete rings in the common substructure.

match_fused_rings: bool

Require compatible fused-ring membership.

match_fused_rings_strict: bool

Require strict matching of fused-ring topology.

match_stereo: bool

Require compatible bond stereochemistry.

ring_matches_ring_only: bool

Match ring bonds only to ring bonds.

exception cosmolkit.McsError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

McsError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (21)
property begin: int | None

Beginning endpoint reported by the native check. Applies to McsError.MappedBondMissing, McsError.SeedReconstructionBondMissing. None when this payload is absent.

property bond: int | None

Bond identifier implicated in the failure. Applies to McsError.RingMembershipMissing, McsError.InitialSeedBondMissing. None when this payload is absent.

property column: int | None

Readonly column payload of the MatchTableOutOfRange error variant; None for other variants.

property count: int | None

Readonly count payload of the TooManyNewBonds error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Ending endpoint reported by the native check. Applies to McsError.MappedBondMissing, McsError.SeedReconstructionBondMissing. None when this payload is absent.

property kind: str | None

Native failure-specific category or value kind. Applies to McsError.MatchTableOutOfRange, McsError.ResultValueOutOfRange. None when this payload is absent.

property message: str | None

Detailed native diagnostic message. Applies to McsError.InitialSeedParse, McsError.InitialSeedMatch, McsError.ResultQueryGraph, McsError.ResultSmarts. None when this payload is absent.

property progress: McsProgressError | None

“error_payload”} Structured McsProgressError payload of McsError.Progress; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property ring: int | None

Readonly ring payload of the RingOutOfRange error variant; None for other variants.

property row: int | None

Readonly row payload of the MatchTableOutOfRange error variant; None for other variants.

property side: str | None

Readonly side payload of the MappedBondMissing error variant; None for other variants.

property source: PropertyUIntReadError | AtomPropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property state: SearchMcsError | None

“error_payload”} Structured SearchMcsError payload of McsError.State; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property stereo_order: StereoOrderError | None

“error_payload”} Structured StereoOrderError payload of McsError.StereoOrder; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property tables: int | None

Readonly tables payload of the TargetTableCount error variant; None for other variants.

property targets: int | None

Number of targets associated with the failed count check, or None when not applicable.

property threshold: int | None

Readonly threshold payload of the ThresholdCountOutOfRange error variant; None for other variants.

property value: int | None

Readonly value payload of the ResultValueOutOfRange error variant; None for other variants.

property variant: McsErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.McsErrorKind(value)

Discriminants of McsErrorKind.

Members: TargetTableCount, ThresholdCountOutOfRange, MatchTableOutOfRange, RingMembershipMissing, RingOutOfRange, MappedBondMissing, StereoOrder, TooManyNewBonds, InitialSeedParse, InitialSeedMatch, InitialSeedBondMissing, ResultValueOutOfRange, ResultQueryGraph, ResultSmarts, SeedReconstructionBondMissing, ResultContextMissing, Progress, State, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (21)
InitialSeedBondMissing = McsErrorKind.InitialSeedBondMissing
InitialSeedMatch = McsErrorKind.InitialSeedMatch
InitialSeedParse = McsErrorKind.InitialSeedParse
MappedBondMissing = McsErrorKind.MappedBondMissing
MatchTableOutOfRange = McsErrorKind.MatchTableOutOfRange
Progress = McsErrorKind.Progress
ResultContextMissing = McsErrorKind.ResultContextMissing
ResultQueryGraph = McsErrorKind.ResultQueryGraph
ResultSmarts = McsErrorKind.ResultSmarts
ResultValueOutOfRange = McsErrorKind.ResultValueOutOfRange
RingMembershipMissing = McsErrorKind.RingMembershipMissing
RingOutOfRange = McsErrorKind.RingOutOfRange
SeedReconstructionBondMissing = McsErrorKind.SeedReconstructionBondMissing
State = McsErrorKind.State
StereoOrder = McsErrorKind.StereoOrder
TargetTableCount = McsErrorKind.TargetTableCount
ThresholdCountOutOfRange = McsErrorKind.ThresholdCountOutOfRange
TooManyNewBonds = McsErrorKind.TooManyNewBonds
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TargetTableCount': McsErrorKind.TargetTableCount, 'ThresholdCountOutOfRange': McsErrorKind.ThresholdCountOutOfRange, 'MatchTableOutOfRange': McsErrorKind.MatchTableOutOfRange, 'RingMembershipMissing': McsErrorKind.RingMembershipMissing, 'RingOutOfRange': McsErrorKind.RingOutOfRange, 'MappedBondMissing': McsErrorKind.MappedBondMissing, 'StereoOrder': McsErrorKind.StereoOrder, 'TooManyNewBonds': McsErrorKind.TooManyNewBonds, 'InitialSeedParse': McsErrorKind.InitialSeedParse, 'InitialSeedMatch': McsErrorKind.InitialSeedMatch, 'InitialSeedBondMissing': McsErrorKind.InitialSeedBondMissing, 'ResultValueOutOfRange': McsErrorKind.ResultValueOutOfRange, 'ResultQueryGraph': McsErrorKind.ResultQueryGraph, 'ResultSmarts': McsErrorKind.ResultSmarts, 'SeedReconstructionBondMissing': McsErrorKind.SeedReconstructionBondMissing, 'ResultContextMissing': McsErrorKind.ResultContextMissing, 'Progress': McsErrorKind.Progress, 'State': McsErrorKind.State})
values = mappingproxy({0: McsErrorKind.TargetTableCount, 1: McsErrorKind.ThresholdCountOutOfRange, 2: McsErrorKind.MatchTableOutOfRange, 3: McsErrorKind.RingMembershipMissing, 4: McsErrorKind.RingOutOfRange, 5: McsErrorKind.MappedBondMissing, 6: McsErrorKind.StereoOrder, 7: McsErrorKind.TooManyNewBonds, 8: McsErrorKind.InitialSeedParse, 9: McsErrorKind.InitialSeedMatch, 10: McsErrorKind.InitialSeedBondMissing, 11: McsErrorKind.ResultValueOutOfRange, 12: McsErrorKind.ResultQueryGraph, 13: McsErrorKind.ResultSmarts, 14: McsErrorKind.SeedReconstructionBondMissing, 15: McsErrorKind.ResultContextMissing, 16: McsErrorKind.Progress, 17: McsErrorKind.State})
class cosmolkit.McsParameters(*, store_all=Ellipsis, maximize_bonds=Ellipsis, threshold=Ellipsis, timeout=Ellipsis, verbose=Ellipsis, atom_compare_parameters=Ellipsis, bond_compare_parameters=Ellipsis, atom_comparator=Ellipsis, bond_comparator=Ellipsis, initial_seed=Ellipsis)

Detached FMCS parameter value.

Members (10)
atom_comparator: McsAtomComparator

Policy used to compare candidate atoms.

atom_compare_parameters: McsAtomCompareParameters

Atom matching constraints applied in addition to the selected atom comparator.

bond_comparator: McsBondComparator

Policy used to compare candidate bonds.

bond_compare_parameters: McsBondCompareParameters

Bond matching constraints applied in addition to the selected bond comparator.

initial_seed: str

Initial query seed as SMARTS; an empty string supplies no explicit seed.

maximize_bonds: bool

Maximize the number of matched bonds rather than matched atoms.

store_all: bool

Retain all degenerate maximum-common-substructure solutions.

threshold: float

Minimum fraction of input molecules that must contain the common substructure.

timeout: int

Search timeout in seconds.

verbose: bool

Enable native search diagnostics.

exception cosmolkit.McsProgressError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

McsProgressError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property message: str | None

Readonly message payload of the Callback error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: McsProgressErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.McsProgressErrorKind(value)

Discriminants of McsProgressErrorKind.

Members: Callback, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
Callback = McsProgressErrorKind.Callback
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Callback': McsProgressErrorKind.Callback})
values = mappingproxy({0: McsProgressErrorKind.Callback})
class cosmolkit.McsResult

Native maximum-common-substructure result, completion state and retained query graphs.

Members (6)
atom_count: int

Number of atoms in the reported common substructure.

bond_count: int

Number of bonds in the reported common substructure.

completed: bool

Whether the native search completed rather than stopping early.

degenerate: dict[str, QueryGraph]

Alternative maximum-common-substructure query graphs keyed by their SMARTS.

query: QueryGraph | None

Maximum-common-substructure query graph, or None if no query was produced.

smarts: str

SMARTS representation of the reported common substructure.

exception cosmolkit.MissingAtomSiteIdentityField(*args, **kwargs)

MissingAtomSiteIdentityField is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property field: AtomSiteIdentityField

“error_payload”} Required atom-site identity field absent from the mmCIF table.

Type:

{“role”

exception cosmolkit.MissingExplicitHydrogensError(*args, **kwargs)

MissingExplicitHydrogensError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: UffBuilderError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.MissingPropertyError(*args, **kwargs)

MissingPropertyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property key: str

Name of the required property that was not present.

exception cosmolkit.MmcifAssemblyError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifAssemblyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: CifReadError | MmcifCrystalInfoError | MmcifOperationExprError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmcifAssemblyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifAssemblyErrorKind(value)

Discriminants of MmcifAssemblyErrorKind.

Members: Cif, Transform, OperationExpr, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Cif = MmcifAssemblyErrorKind.Cif
OperationExpr = MmcifAssemblyErrorKind.OperationExpr
Transform = MmcifAssemblyErrorKind.Transform
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifAssemblyErrorKind.Cif, 'Transform': MmcifAssemblyErrorKind.Transform, 'OperationExpr': MmcifAssemblyErrorKind.OperationExpr})
values = mappingproxy({0: MmcifAssemblyErrorKind.Cif, 1: MmcifAssemblyErrorKind.Transform, 2: MmcifAssemblyErrorKind.OperationExpr})
exception cosmolkit.MmcifAtomSiteGroupingError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifAtomSiteGroupingError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Readonly index payload of the UndefinedGroupPdbIndex error variant; None for other variants.

property length: int | None

Readonly length payload of the UndefinedGroupPdbIndex error variant; None for other variants.

property row_index: int | None

Readonly row_index payload of the MissingActiveModel error variant; None for other variants.

property source: MissingAtomSiteIdentityField | MmcifSequenceIdError | MmcifAtomSiteScalarError | CifReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to MmcifAtomSiteGroupingError.AtomNameNotRepresentable, MmcifAtomSiteGroupingError.AuthorChainIdNotRepresentable, MmcifAtomSiteGroupingError.ResidueNameNotRepresentable, MmcifAtomSiteGroupingError.ResidueAddressNotRepresentable, MmcifAtomSiteGroupingError.UndefinedGroupPdbIndex. None when this payload is absent.

property variant: MmcifAtomSiteGroupingErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifAtomSiteGroupingErrorKind(value)

Discriminants of MmcifAtomSiteGroupingErrorKind.

Members: IdentityField, SequenceId, AtomNameNotRepresentable, AtomScalar, ModelNumber, LabelSequenceNumber, AuthorChainIdNotRepresentable, ResidueNameNotRepresentable, ResidueAddressNotRepresentable, ResidueSourceIdsNotRepresentable, UndefinedGroupPdbIndex, MissingActiveModel, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (15)
AtomNameNotRepresentable = MmcifAtomSiteGroupingErrorKind.AtomNameNotRepresentable
AtomScalar = MmcifAtomSiteGroupingErrorKind.AtomScalar
AuthorChainIdNotRepresentable = MmcifAtomSiteGroupingErrorKind.AuthorChainIdNotRepresentable
IdentityField = MmcifAtomSiteGroupingErrorKind.IdentityField
LabelSequenceNumber = MmcifAtomSiteGroupingErrorKind.LabelSequenceNumber
MissingActiveModel = MmcifAtomSiteGroupingErrorKind.MissingActiveModel
ModelNumber = MmcifAtomSiteGroupingErrorKind.ModelNumber
ResidueAddressNotRepresentable = MmcifAtomSiteGroupingErrorKind.ResidueAddressNotRepresentable
ResidueNameNotRepresentable = MmcifAtomSiteGroupingErrorKind.ResidueNameNotRepresentable
ResidueSourceIdsNotRepresentable = MmcifAtomSiteGroupingErrorKind.ResidueSourceIdsNotRepresentable
SequenceId = MmcifAtomSiteGroupingErrorKind.SequenceId
UndefinedGroupPdbIndex = MmcifAtomSiteGroupingErrorKind.UndefinedGroupPdbIndex
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'IdentityField': MmcifAtomSiteGroupingErrorKind.IdentityField, 'SequenceId': MmcifAtomSiteGroupingErrorKind.SequenceId, 'AtomNameNotRepresentable': MmcifAtomSiteGroupingErrorKind.AtomNameNotRepresentable, 'AtomScalar': MmcifAtomSiteGroupingErrorKind.AtomScalar, 'ModelNumber': MmcifAtomSiteGroupingErrorKind.ModelNumber, 'LabelSequenceNumber': MmcifAtomSiteGroupingErrorKind.LabelSequenceNumber, 'AuthorChainIdNotRepresentable': MmcifAtomSiteGroupingErrorKind.AuthorChainIdNotRepresentable, 'ResidueNameNotRepresentable': MmcifAtomSiteGroupingErrorKind.ResidueNameNotRepresentable, 'ResidueAddressNotRepresentable': MmcifAtomSiteGroupingErrorKind.ResidueAddressNotRepresentable, 'ResidueSourceIdsNotRepresentable': MmcifAtomSiteGroupingErrorKind.ResidueSourceIdsNotRepresentable, 'UndefinedGroupPdbIndex': MmcifAtomSiteGroupingErrorKind.UndefinedGroupPdbIndex, 'MissingActiveModel': MmcifAtomSiteGroupingErrorKind.MissingActiveModel})
values = mappingproxy({0: MmcifAtomSiteGroupingErrorKind.IdentityField, 1: MmcifAtomSiteGroupingErrorKind.SequenceId, 2: MmcifAtomSiteGroupingErrorKind.AtomNameNotRepresentable, 3: MmcifAtomSiteGroupingErrorKind.AtomScalar, 4: MmcifAtomSiteGroupingErrorKind.ModelNumber, 5: MmcifAtomSiteGroupingErrorKind.LabelSequenceNumber, 6: MmcifAtomSiteGroupingErrorKind.AuthorChainIdNotRepresentable, 7: MmcifAtomSiteGroupingErrorKind.ResidueNameNotRepresentable, 8: MmcifAtomSiteGroupingErrorKind.ResidueAddressNotRepresentable, 9: MmcifAtomSiteGroupingErrorKind.ResidueSourceIdsNotRepresentable, 10: MmcifAtomSiteGroupingErrorKind.UndefinedGroupPdbIndex, 11: MmcifAtomSiteGroupingErrorKind.MissingActiveModel})
exception cosmolkit.MmcifAtomSiteRowOutOfBounds(*args, **kwargs)

MmcifAtomSiteRowOutOfBounds is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property parsed_count: int

Number of atom-site rows successfully parsed.

property row_index: int

Requested atom-site row index.

exception cosmolkit.MmcifAtomSiteScalarError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifAtomSiteScalarError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: CifReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to MmcifAtomSiteScalarError.SerialOutsideSourceDefinedRange, MmcifAtomSiteScalarError.TlsOutsideSourceDefinedRange. None when this payload is absent.

property variant: MmcifAtomSiteScalarErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifAtomSiteScalarErrorKind(value)

Discriminants of MmcifAtomSiteScalarErrorKind.

Members: SerialOutsideSourceDefinedRange, TlsOutsideSourceDefinedRange, CifCharacter, CifInteger, CifNumber, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
CifCharacter = MmcifAtomSiteScalarErrorKind.CifCharacter
CifInteger = MmcifAtomSiteScalarErrorKind.CifInteger
CifNumber = MmcifAtomSiteScalarErrorKind.CifNumber
SerialOutsideSourceDefinedRange = MmcifAtomSiteScalarErrorKind.SerialOutsideSourceDefinedRange
TlsOutsideSourceDefinedRange = MmcifAtomSiteScalarErrorKind.TlsOutsideSourceDefinedRange
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SerialOutsideSourceDefinedRange': MmcifAtomSiteScalarErrorKind.SerialOutsideSourceDefinedRange, 'TlsOutsideSourceDefinedRange': MmcifAtomSiteScalarErrorKind.TlsOutsideSourceDefinedRange, 'CifCharacter': MmcifAtomSiteScalarErrorKind.CifCharacter, 'CifInteger': MmcifAtomSiteScalarErrorKind.CifInteger, 'CifNumber': MmcifAtomSiteScalarErrorKind.CifNumber})
values = mappingproxy({0: MmcifAtomSiteScalarErrorKind.SerialOutsideSourceDefinedRange, 1: MmcifAtomSiteScalarErrorKind.TlsOutsideSourceDefinedRange, 2: MmcifAtomSiteScalarErrorKind.CifCharacter, 3: MmcifAtomSiteScalarErrorKind.CifInteger, 4: MmcifAtomSiteScalarErrorKind.CifNumber})
exception cosmolkit.MmcifCcdRestoreError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifCcdRestoreError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: PdbResidueKeyError | FromUtf8Error | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmcifCcdRestoreErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifCcdRestoreErrorKind(value)

Discriminants of MmcifCcdRestoreErrorKind.

Members: Residue, SequenceUtf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Residue = MmcifCcdRestoreErrorKind.Residue
SequenceUtf8 = MmcifCcdRestoreErrorKind.SequenceUtf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Residue': MmcifCcdRestoreErrorKind.Residue, 'SequenceUtf8': MmcifCcdRestoreErrorKind.SequenceUtf8})
values = mappingproxy({0: MmcifCcdRestoreErrorKind.Residue, 1: MmcifCcdRestoreErrorKind.SequenceUtf8})
exception cosmolkit.MmcifCisPepError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifCisPepError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property error: MmcifSequenceIdError | None

“error_payload”} Structured native error payload. Present for MmcifCisPepError.SequenceId; None when unavailable.

Type:

{“role”

property partner: str | None

Partner atom or endpoint involved in the native check. Applies to MmcifCisPepError.ChainNameNotRepresentable, MmcifCisPepError.ResidueNameNotRepresentable, MmcifCisPepError.ResidueAddressNotRepresentable, MmcifCisPepError.SequenceId. None when this payload is absent.

property source: CifReadError | MmcifSequenceIdError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to MmcifCisPepError.ChainNameNotRepresentable, MmcifCisPepError.ResidueNameNotRepresentable. None when this payload is absent.

property variant: MmcifCisPepErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifCisPepErrorKind(value)

Discriminants of MmcifCisPepErrorKind.

Members: Cif, ChainNameNotRepresentable, ResidueNameNotRepresentable, ResidueAddressNotRepresentable, SequenceId, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
ChainNameNotRepresentable = MmcifCisPepErrorKind.ChainNameNotRepresentable
Cif = MmcifCisPepErrorKind.Cif
ResidueAddressNotRepresentable = MmcifCisPepErrorKind.ResidueAddressNotRepresentable
ResidueNameNotRepresentable = MmcifCisPepErrorKind.ResidueNameNotRepresentable
SequenceId = MmcifCisPepErrorKind.SequenceId
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifCisPepErrorKind.Cif, 'ChainNameNotRepresentable': MmcifCisPepErrorKind.ChainNameNotRepresentable, 'ResidueNameNotRepresentable': MmcifCisPepErrorKind.ResidueNameNotRepresentable, 'ResidueAddressNotRepresentable': MmcifCisPepErrorKind.ResidueAddressNotRepresentable, 'SequenceId': MmcifCisPepErrorKind.SequenceId})
values = mappingproxy({0: MmcifCisPepErrorKind.Cif, 1: MmcifCisPepErrorKind.ChainNameNotRepresentable, 2: MmcifCisPepErrorKind.ResidueNameNotRepresentable, 3: MmcifCisPepErrorKind.ResidueAddressNotRepresentable, 4: MmcifCisPepErrorKind.SequenceId})
exception cosmolkit.MmcifConnectionError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifConnectionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property partner: int | None

Partner atom or endpoint involved in the native check. Applies to MmcifConnectionError.MissingAddressIdentifiers, MmcifConnectionError.ChainNameNotRepresentable, MmcifConnectionError.ResidueNameNotRepresentable, MmcifConnectionError.ResidueAddressNotRepresentable. None when this payload is absent.

property source: CifReadError | MmcifSequenceIdError | MmcifLabelAddressError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | int | None

Value rejected or reported by the native operation. Applies to MmcifConnectionError.ChainNameNotRepresentable, MmcifConnectionError.ResidueNameNotRepresentable, MmcifConnectionError.ResidueAddressNotRepresentable, MmcifConnectionError.SymmetryOperatorOutsideSourceDefinedRange, MmcifConnectionError.SymmetryOperatorNotRepresentable. None when this payload is absent.

property variant: MmcifConnectionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifConnectionErrorKind(value)

Discriminants of MmcifConnectionErrorKind.

Members: Cif, SequenceId, LabelAddress, MissingAddressIdentifiers, NoStructuralModels, ChainNameNotRepresentable, ResidueNameNotRepresentable, ResidueAddressNotRepresentable, SymmetryOperatorOutsideSourceDefinedRange, SymmetryOperatorNotRepresentable, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (13)
ChainNameNotRepresentable = MmcifConnectionErrorKind.ChainNameNotRepresentable
Cif = MmcifConnectionErrorKind.Cif
LabelAddress = MmcifConnectionErrorKind.LabelAddress
MissingAddressIdentifiers = MmcifConnectionErrorKind.MissingAddressIdentifiers
NoStructuralModels = MmcifConnectionErrorKind.NoStructuralModels
ResidueAddressNotRepresentable = MmcifConnectionErrorKind.ResidueAddressNotRepresentable
ResidueNameNotRepresentable = MmcifConnectionErrorKind.ResidueNameNotRepresentable
SequenceId = MmcifConnectionErrorKind.SequenceId
SymmetryOperatorNotRepresentable = MmcifConnectionErrorKind.SymmetryOperatorNotRepresentable
SymmetryOperatorOutsideSourceDefinedRange = MmcifConnectionErrorKind.SymmetryOperatorOutsideSourceDefinedRange
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifConnectionErrorKind.Cif, 'SequenceId': MmcifConnectionErrorKind.SequenceId, 'LabelAddress': MmcifConnectionErrorKind.LabelAddress, 'MissingAddressIdentifiers': MmcifConnectionErrorKind.MissingAddressIdentifiers, 'NoStructuralModels': MmcifConnectionErrorKind.NoStructuralModels, 'ChainNameNotRepresentable': MmcifConnectionErrorKind.ChainNameNotRepresentable, 'ResidueNameNotRepresentable': MmcifConnectionErrorKind.ResidueNameNotRepresentable, 'ResidueAddressNotRepresentable': MmcifConnectionErrorKind.ResidueAddressNotRepresentable, 'SymmetryOperatorOutsideSourceDefinedRange': MmcifConnectionErrorKind.SymmetryOperatorOutsideSourceDefinedRange, 'SymmetryOperatorNotRepresentable': MmcifConnectionErrorKind.SymmetryOperatorNotRepresentable})
values = mappingproxy({0: MmcifConnectionErrorKind.Cif, 1: MmcifConnectionErrorKind.SequenceId, 2: MmcifConnectionErrorKind.LabelAddress, 3: MmcifConnectionErrorKind.MissingAddressIdentifiers, 4: MmcifConnectionErrorKind.NoStructuralModels, 5: MmcifConnectionErrorKind.ChainNameNotRepresentable, 6: MmcifConnectionErrorKind.ResidueNameNotRepresentable, 7: MmcifConnectionErrorKind.ResidueAddressNotRepresentable, 8: MmcifConnectionErrorKind.SymmetryOperatorOutsideSourceDefinedRange, 9: MmcifConnectionErrorKind.SymmetryOperatorNotRepresentable})
exception cosmolkit.MmcifCrystalInfoError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifCrystalInfoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: CifReadError | BioStructureError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stage: str | None

Readonly stage payload of the StagingInvariant error variant; None for other variants.

property variant: MmcifCrystalInfoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifCrystalInfoErrorKind(value)

Discriminants of MmcifCrystalInfoErrorKind.

Members: Cif, Bio, StagingInvariant, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Bio = MmcifCrystalInfoErrorKind.Bio
Cif = MmcifCrystalInfoErrorKind.Cif
StagingInvariant = MmcifCrystalInfoErrorKind.StagingInvariant
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifCrystalInfoErrorKind.Cif, 'Bio': MmcifCrystalInfoErrorKind.Bio, 'StagingInvariant': MmcifCrystalInfoErrorKind.StagingInvariant})
values = mappingproxy({0: MmcifCrystalInfoErrorKind.Cif, 1: MmcifCrystalInfoErrorKind.Bio, 2: MmcifCrystalInfoErrorKind.StagingInvariant})
exception cosmolkit.MmcifEntityInfoError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifEntityInfoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: CifReadError | MmcifSequenceIdError | MmcifSiftsUnpError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmcifEntityInfoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifEntityInfoErrorKind(value)

Discriminants of MmcifEntityInfoErrorKind.

Members: Cif, SequenceId, Sifts, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Cif = MmcifEntityInfoErrorKind.Cif
SequenceId = MmcifEntityInfoErrorKind.SequenceId
Sifts = MmcifEntityInfoErrorKind.Sifts
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifEntityInfoErrorKind.Cif, 'SequenceId': MmcifEntityInfoErrorKind.SequenceId, 'Sifts': MmcifEntityInfoErrorKind.Sifts})
values = mappingproxy({0: MmcifEntityInfoErrorKind.Cif, 1: MmcifEntityInfoErrorKind.SequenceId, 2: MmcifEntityInfoErrorKind.Sifts})
exception cosmolkit.MmcifHelixError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifHelixError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property endpoint: str | None

Bond endpoint associated with the stereo failure. Present for MmcifHelixError.ChainNameNotRepresentable, MmcifHelixError.ResidueNameNotRepresentable, MmcifHelixError.ResidueAddressNotRepresentable, MmcifHelixError.SequenceId; None when unavailable.

property error: MmcifSequenceIdError | None

“error_payload”} Structured native error payload. Present for MmcifHelixError.SequenceId; None when unavailable.

Type:

{“role”

property source: CifReadError | MmcifSequenceIdError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to MmcifHelixError.ChainNameNotRepresentable, MmcifHelixError.ResidueNameNotRepresentable. None when this payload is absent.

property variant: MmcifHelixErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifHelixErrorKind(value)

Discriminants of MmcifHelixErrorKind.

Members: Cif, ChainNameNotRepresentable, ResidueNameNotRepresentable, ResidueAddressNotRepresentable, SequenceId, HelixClass, HelixLength, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (10)
ChainNameNotRepresentable = MmcifHelixErrorKind.ChainNameNotRepresentable
Cif = MmcifHelixErrorKind.Cif
HelixClass = MmcifHelixErrorKind.HelixClass
HelixLength = MmcifHelixErrorKind.HelixLength
ResidueAddressNotRepresentable = MmcifHelixErrorKind.ResidueAddressNotRepresentable
ResidueNameNotRepresentable = MmcifHelixErrorKind.ResidueNameNotRepresentable
SequenceId = MmcifHelixErrorKind.SequenceId
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifHelixErrorKind.Cif, 'ChainNameNotRepresentable': MmcifHelixErrorKind.ChainNameNotRepresentable, 'ResidueNameNotRepresentable': MmcifHelixErrorKind.ResidueNameNotRepresentable, 'ResidueAddressNotRepresentable': MmcifHelixErrorKind.ResidueAddressNotRepresentable, 'SequenceId': MmcifHelixErrorKind.SequenceId, 'HelixClass': MmcifHelixErrorKind.HelixClass, 'HelixLength': MmcifHelixErrorKind.HelixLength})
values = mappingproxy({0: MmcifHelixErrorKind.Cif, 1: MmcifHelixErrorKind.ChainNameNotRepresentable, 2: MmcifHelixErrorKind.ResidueNameNotRepresentable, 3: MmcifHelixErrorKind.ResidueAddressNotRepresentable, 4: MmcifHelixErrorKind.SequenceId, 5: MmcifHelixErrorKind.HelixClass, 6: MmcifHelixErrorKind.HelixLength})
exception cosmolkit.MmcifLabelAddressError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifLabelAddressError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: CifReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Readonly value payload of the ChainNameNotRepresentable error variant; None for other variants.

property variant: MmcifLabelAddressErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifLabelAddressErrorKind(value)

Discriminants of MmcifLabelAddressErrorKind.

Members: LabelSequenceId, ChainNameNotRepresentable, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
ChainNameNotRepresentable = MmcifLabelAddressErrorKind.ChainNameNotRepresentable
LabelSequenceId = MmcifLabelAddressErrorKind.LabelSequenceId
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'LabelSequenceId': MmcifLabelAddressErrorKind.LabelSequenceId, 'ChainNameNotRepresentable': MmcifLabelAddressErrorKind.ChainNameNotRepresentable})
values = mappingproxy({0: MmcifLabelAddressErrorKind.LabelSequenceId, 1: MmcifLabelAddressErrorKind.ChainNameNotRepresentable})
exception cosmolkit.MmcifModResError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifModResError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: CifReadError | MmcifSequenceIdError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to MmcifModResError.ChainNameNotRepresentable, MmcifModResError.ResidueNameNotRepresentable. None when this payload is absent.

property variant: MmcifModResErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifModResErrorKind(value)

Discriminants of MmcifModResErrorKind.

Members: Cif, ChainNameNotRepresentable, ResidueNameNotRepresentable, ResidueAddressNotRepresentable, SequenceId, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
ChainNameNotRepresentable = MmcifModResErrorKind.ChainNameNotRepresentable
Cif = MmcifModResErrorKind.Cif
ResidueAddressNotRepresentable = MmcifModResErrorKind.ResidueAddressNotRepresentable
ResidueNameNotRepresentable = MmcifModResErrorKind.ResidueNameNotRepresentable
SequenceId = MmcifModResErrorKind.SequenceId
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifModResErrorKind.Cif, 'ChainNameNotRepresentable': MmcifModResErrorKind.ChainNameNotRepresentable, 'ResidueNameNotRepresentable': MmcifModResErrorKind.ResidueNameNotRepresentable, 'ResidueAddressNotRepresentable': MmcifModResErrorKind.ResidueAddressNotRepresentable, 'SequenceId': MmcifModResErrorKind.SequenceId})
values = mappingproxy({0: MmcifModResErrorKind.Cif, 1: MmcifModResErrorKind.ChainNameNotRepresentable, 2: MmcifModResErrorKind.ResidueNameNotRepresentable, 3: MmcifModResErrorKind.ResidueAddressNotRepresentable, 4: MmcifModResErrorKind.SequenceId})
exception cosmolkit.MmcifOperationExprError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifOperationExprError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmcifOperationExprErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifOperationExprErrorKind(value)

Discriminants of MmcifOperationExprErrorKind.

Members: SourceUndefinedIntegerOverflow, SourceUndefinedRangeIncrement, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
SourceUndefinedIntegerOverflow = MmcifOperationExprErrorKind.SourceUndefinedIntegerOverflow
SourceUndefinedRangeIncrement = MmcifOperationExprErrorKind.SourceUndefinedRangeIncrement
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SourceUndefinedIntegerOverflow': MmcifOperationExprErrorKind.SourceUndefinedIntegerOverflow, 'SourceUndefinedRangeIncrement': MmcifOperationExprErrorKind.SourceUndefinedRangeIncrement})
values = mappingproxy({0: MmcifOperationExprErrorKind.SourceUndefinedIntegerOverflow, 1: MmcifOperationExprErrorKind.SourceUndefinedRangeIncrement})
exception cosmolkit.MmcifSequenceIdError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifSequenceIdError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property sequence_id: str | None

Readonly sequence_id payload of the InconsistentInsertionCode error variant; None for other variants.

property source: CifReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmcifSequenceIdErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifSequenceIdErrorKind(value)

Discriminants of MmcifSequenceIdErrorKind.

Members: InconsistentInsertionCode, InvalidInsertionCode, InvalidSequenceNumber, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
InconsistentInsertionCode = MmcifSequenceIdErrorKind.InconsistentInsertionCode
InvalidInsertionCode = MmcifSequenceIdErrorKind.InvalidInsertionCode
InvalidSequenceNumber = MmcifSequenceIdErrorKind.InvalidSequenceNumber
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InconsistentInsertionCode': MmcifSequenceIdErrorKind.InconsistentInsertionCode, 'InvalidInsertionCode': MmcifSequenceIdErrorKind.InvalidInsertionCode, 'InvalidSequenceNumber': MmcifSequenceIdErrorKind.InvalidSequenceNumber})
values = mappingproxy({0: MmcifSequenceIdErrorKind.InconsistentInsertionCode, 1: MmcifSequenceIdErrorKind.InvalidInsertionCode, 2: MmcifSequenceIdErrorKind.InvalidSequenceNumber})
exception cosmolkit.MmcifSheetError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifSheetError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property address: str | None

Structural address implicated in the failed lookup. Applies to MmcifSheetError.ChainNameNotRepresentable, MmcifSheetError.ResidueNameNotRepresentable, MmcifSheetError.ResidueAddressNotRepresentable, MmcifSheetError.SequenceId. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property error: MmcifSequenceIdError | None

“error_payload”} Structured native error payload. Present for MmcifSheetError.SequenceId; None when unavailable.

Type:

{“role”

property source: CifReadError | MmcifSequenceIdError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to MmcifSheetError.ChainNameNotRepresentable, MmcifSheetError.ResidueNameNotRepresentable. None when this payload is absent.

property variant: MmcifSheetErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifSheetErrorKind(value)

Discriminants of MmcifSheetErrorKind.

Members: Cif, ChainNameNotRepresentable, ResidueNameNotRepresentable, ResidueAddressNotRepresentable, SequenceId, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
ChainNameNotRepresentable = MmcifSheetErrorKind.ChainNameNotRepresentable
Cif = MmcifSheetErrorKind.Cif
ResidueAddressNotRepresentable = MmcifSheetErrorKind.ResidueAddressNotRepresentable
ResidueNameNotRepresentable = MmcifSheetErrorKind.ResidueNameNotRepresentable
SequenceId = MmcifSheetErrorKind.SequenceId
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifSheetErrorKind.Cif, 'ChainNameNotRepresentable': MmcifSheetErrorKind.ChainNameNotRepresentable, 'ResidueNameNotRepresentable': MmcifSheetErrorKind.ResidueNameNotRepresentable, 'ResidueAddressNotRepresentable': MmcifSheetErrorKind.ResidueAddressNotRepresentable, 'SequenceId': MmcifSheetErrorKind.SequenceId})
values = mappingproxy({0: MmcifSheetErrorKind.Cif, 1: MmcifSheetErrorKind.ChainNameNotRepresentable, 2: MmcifSheetErrorKind.ResidueNameNotRepresentable, 3: MmcifSheetErrorKind.ResidueAddressNotRepresentable, 4: MmcifSheetErrorKind.SequenceId})
exception cosmolkit.MmcifSiftsUnpError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifSiftsUnpError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (9)
property asym_id: str | None

Readonly asym_id payload of the SubchainNotFound error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property entity_id: str | None

Readonly entity_id payload of the EntityNotFound error variant; None for other variants.

property seq_id: str | None

Readonly seq_id payload of the SequenceNotFound error variant; None for other variants.

property source: CifReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stage: str | None

Readonly stage payload of the StagingInvariant error variant; None for other variants.

property value: str | None

Readonly value payload of the NumberOutsideU16 error variant; None for other variants.

property variant: MmcifSiftsUnpErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifSiftsUnpErrorKind(value)

Discriminants of MmcifSiftsUnpErrorKind.

Members: Cif, EntityNotFound, SubchainNotFound, SequenceNotFound, NumberOutsideU16, StagingInvariant, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
Cif = MmcifSiftsUnpErrorKind.Cif
EntityNotFound = MmcifSiftsUnpErrorKind.EntityNotFound
NumberOutsideU16 = MmcifSiftsUnpErrorKind.NumberOutsideU16
SequenceNotFound = MmcifSiftsUnpErrorKind.SequenceNotFound
StagingInvariant = MmcifSiftsUnpErrorKind.StagingInvariant
SubchainNotFound = MmcifSiftsUnpErrorKind.SubchainNotFound
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifSiftsUnpErrorKind.Cif, 'EntityNotFound': MmcifSiftsUnpErrorKind.EntityNotFound, 'SubchainNotFound': MmcifSiftsUnpErrorKind.SubchainNotFound, 'SequenceNotFound': MmcifSiftsUnpErrorKind.SequenceNotFound, 'NumberOutsideU16': MmcifSiftsUnpErrorKind.NumberOutsideU16, 'StagingInvariant': MmcifSiftsUnpErrorKind.StagingInvariant})
values = mappingproxy({0: MmcifSiftsUnpErrorKind.Cif, 1: MmcifSiftsUnpErrorKind.EntityNotFound, 2: MmcifSiftsUnpErrorKind.SubchainNotFound, 3: MmcifSiftsUnpErrorKind.SequenceNotFound, 4: MmcifSiftsUnpErrorKind.NumberOutsideU16, 5: MmcifSiftsUnpErrorKind.StagingInvariant})
exception cosmolkit.MmcifTlsInfoError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmcifTlsInfoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property chain: str | None

Readonly chain payload of the SelectionChainNotRepresentable error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property id: str | None

Readonly id payload of the NumericIdOutsideSourceDefinedRange error variant; None for other variants.

property source: CifReadError | MmcifSequenceIdError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmcifTlsInfoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmcifTlsInfoErrorKind(value)

Discriminants of MmcifTlsInfoErrorKind.

Members: Cif, SequenceId, NumericIdOutsideSourceDefinedRange, SelectionChainNotRepresentable, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
Cif = MmcifTlsInfoErrorKind.Cif
NumericIdOutsideSourceDefinedRange = MmcifTlsInfoErrorKind.NumericIdOutsideSourceDefinedRange
SelectionChainNotRepresentable = MmcifTlsInfoErrorKind.SelectionChainNotRepresentable
SequenceId = MmcifTlsInfoErrorKind.SequenceId
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': MmcifTlsInfoErrorKind.Cif, 'SequenceId': MmcifTlsInfoErrorKind.SequenceId, 'NumericIdOutsideSourceDefinedRange': MmcifTlsInfoErrorKind.NumericIdOutsideSourceDefinedRange, 'SelectionChainNotRepresentable': MmcifTlsInfoErrorKind.SelectionChainNotRepresentable})
values = mappingproxy({0: MmcifTlsInfoErrorKind.Cif, 1: MmcifTlsInfoErrorKind.SequenceId, 2: MmcifTlsInfoErrorKind.NumericIdOutsideSourceDefinedRange, 3: MmcifTlsInfoErrorKind.SelectionChainNotRepresentable})
exception cosmolkit.MmffAngleLookupError(*args, **kwargs)

Failure in the mmff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmffAngleLookupError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property atom_type: int | None

Readonly atom_type payload of the MissingDefinition error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmffAngleLookupErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmffAngleLookupErrorKind(value)

Discriminants of MmffAngleLookupErrorKind.

Members: MissingDefinition, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
MissingDefinition = MmffAngleLookupErrorKind.MissingDefinition
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingDefinition': MmffAngleLookupErrorKind.MissingDefinition})
values = mappingproxy({0: MmffAngleLookupErrorKind.MissingDefinition})
class cosmolkit.MmffAtomProperties(atom_type, formal_charge, partial_charge)

MMFF atom type and force-field formal/partial charge values.

Members (3)
atom_type: int

MMFF atom type code.

formal_charge: float

MMFF force-field formal charge, which may be fractional.

partial_charge: float

MMFF partial charge assigned to this atom.

exception cosmolkit.MmffBuilderError(*args, **kwargs)

Failure in the mmff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmffBuilderError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (12)
property components: PathError | None

“error_payload”} Structured PathError payload of MmffBuilderError.Components; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property conf_id: int | None

Conformer identifier implicated in the failure. Applies to MmffBuilderError.Missing3dConformer, MmffBuilderError.InvalidConformerId. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property force_field_kernel: ForceFieldKernelError | None

“error_payload”} Structured ForceFieldKernelError payload of MmffBuilderError.ForceFieldKernel; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property fragment: NonbondedFragmentMappingError | None

“error_payload”} Structured NonbondedFragmentMappingError payload of MmffBuilderError.Fragment; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property mol_properties: MmffMolPropertiesError | None

“error_payload”} Structured MmffMolPropertiesError payload of MmffBuilderError.MolProperties; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property rings: RingFindingError | None

“error_payload”} Structured RingFindingError payload of MmffBuilderError.Rings; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: TopologyValidationError | MappingValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | MmffParamParseError | UffDefaultTorsionQueryError | SmartsParseError | QueryCompileError | MatchError | MoleculeFragmentsError | FragmentCoordinateViewError | BondValueError | AtomPropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property torsion_bond_query: UffTorsionBondQueryError | None

“error_payload”} Structured UffTorsionBondQueryError payload of MmffBuilderError.TorsionBondQuery; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of MmffBuilderError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: MmffBuilderErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmffBuilderErrorKind(value)

Discriminants of MmffBuilderErrorKind.

Members: MolProperties, ForceFieldKernel, TorsionBondQuery, Fragment, Components, Valence, Rings, Missing3dConformer, InvalidConformerId, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
Components = MmffBuilderErrorKind.Components
ForceFieldKernel = MmffBuilderErrorKind.ForceFieldKernel
Fragment = MmffBuilderErrorKind.Fragment
InvalidConformerId = MmffBuilderErrorKind.InvalidConformerId
Missing3dConformer = MmffBuilderErrorKind.Missing3dConformer
MolProperties = MmffBuilderErrorKind.MolProperties
Rings = MmffBuilderErrorKind.Rings
TorsionBondQuery = MmffBuilderErrorKind.TorsionBondQuery
Valence = MmffBuilderErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MolProperties': MmffBuilderErrorKind.MolProperties, 'ForceFieldKernel': MmffBuilderErrorKind.ForceFieldKernel, 'TorsionBondQuery': MmffBuilderErrorKind.TorsionBondQuery, 'Fragment': MmffBuilderErrorKind.Fragment, 'Components': MmffBuilderErrorKind.Components, 'Valence': MmffBuilderErrorKind.Valence, 'Rings': MmffBuilderErrorKind.Rings, 'Missing3dConformer': MmffBuilderErrorKind.Missing3dConformer, 'InvalidConformerId': MmffBuilderErrorKind.InvalidConformerId})
values = mappingproxy({0: MmffBuilderErrorKind.MolProperties, 1: MmffBuilderErrorKind.ForceFieldKernel, 2: MmffBuilderErrorKind.TorsionBondQuery, 3: MmffBuilderErrorKind.Fragment, 4: MmffBuilderErrorKind.Components, 5: MmffBuilderErrorKind.Valence, 6: MmffBuilderErrorKind.Rings, 7: MmffBuilderErrorKind.Missing3dConformer, 8: MmffBuilderErrorKind.InvalidConformerId})
class cosmolkit.MmffConformerOptimizationParams(*, num_threads=Ellipsis, max_iterations=Ellipsis, mmff_variant=Ellipsis, non_bonded_threshold=Ellipsis, ignore_interfragment_interactions=Ellipsis)

MMFF parameterization, minimizer limits and threading for all stored conformers.

Members (5)
ignore_interfragment_interactions: bool

Omit non-bonded interactions between disconnected molecular fragments.

max_iterations: int

Maximum number of minimizer iterations.

mmff_variant: MmffVariant

MMFF94 or MMFF94s parameterization.

non_bonded_threshold: float

Distance cutoff for inclusion of MMFF non-bonded interactions, in angstroms.

num_threads: int

Native worker count for conformer optimization; zero requests the available hardware thread count.

class cosmolkit.MmffEnergyGradient(energy, gradient)

Force-field energy and Cartesian gradient at the evaluated coordinates.

Members (2)
energy: float

Evaluated force-field energy; optimization outcomes without parameters return None.

gradient: list[float]

Flat Cartesian energy-gradient components in atom order (x, y, z per atom).

class cosmolkit.MmffEvaluationParams(*, mmff_variant=Ellipsis, non_bonded_threshold=Ellipsis, conformer_id=Ellipsis, ignore_interfragment_interactions=Ellipsis)

Non-mutating MMFF field evaluation over one stored 3D conformer.

Members (4)
conformer_id: int | None

Stored 3D conformer identifier, or None for the native default selection.

ignore_interfragment_interactions: bool

Omit non-bonded interactions between disconnected molecular fragments.

mmff_variant: MmffVariant

MMFF94 or MMFF94s parameterization.

non_bonded_threshold: float

Distance cutoff for inclusion of MMFF non-bonded interactions, in angstroms.

exception cosmolkit.MmffForceFieldError(*args, **kwargs)

MmffForceFieldError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property actual: int | None

Observed size or index reported by the native failure, or None when inapplicable.

property atom_index: int | None

Atom index implicated in the failure, or None for failures without an atom.

property component: int | None

Coordinate component implicated in the failure, or None when inapplicable.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property expected: int | None

Required size reported by the native failure, or None when inapplicable.

property kind: MolecularForceFieldErrorKind

Typed native persistent-force-field failure category.

property requested: int | None

Requested conformer identifier when relevant, otherwise None.

property source: ForceFieldError

“error_source”} Actual underlying exception, identical to __cause__.

Type:

{“role”

class cosmolkit.MmffForceFieldParams(*, conformer_id=Ellipsis, mmff_variant=Ellipsis, non_bonded_threshold=Ellipsis, ignore_interfragment_interactions=Ellipsis)

Configuration for constructing a persistent MMFF force field over a selected conformer.

Members (4)
conformer_id: int | None

Stored 3D conformer identifier, or None for the native default selection.

ignore_interfragment_interactions: bool

Omit non-bonded interactions between disconnected molecular fragments.

mmff_variant: MmffVariant

MMFF94 or MMFF94s parameterization.

non_bonded_threshold: float

Distance cutoff for inclusion of MMFF non-bonded interactions, in angstroms.

exception cosmolkit.MmffMolPropertiesError(*args, **kwargs)

Failure in the mmff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmffMolPropertiesError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (12)
property aromaticity: AromaticityError | None

“error_payload”} Structured AromaticityError payload of MmffMolPropertiesError.Aromaticity; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property atom_index: int | None

Readonly atom_index payload of the AtomIndexOutOfRange error variant; None for other variants.

property atom_type: int | None

Force-field atom type involved in the failure. Applies to MmffMolPropertiesError.AtomTypePropertiesMissing, MmffMolPropertiesError.AtomTypePbciMissing. None when this payload is absent.

property atoms: int | None

Readonly atoms payload of the AtomIndexOutOfRange error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property kekulize: KekulizeError | None

“error_payload”} Structured KekulizeError payload of MmffMolPropertiesError.Kekulize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property params: MmffParamError | None

“error_payload”} Structured MmffParamError payload of MmffMolPropertiesError.Params; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property ring_finding: RingFindingError | None

“error_payload”} Structured RingFindingError payload of MmffMolPropertiesError.RingFinding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: TopologyValidationError | MappingValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | MmffParamParseError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of MmffMolPropertiesError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: MmffMolPropertiesErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmffMolPropertiesErrorKind(value)

Discriminants of MmffMolPropertiesErrorKind.

Members: Params, Kekulize, Aromaticity, RingFinding, Valence, AtomIndexOutOfRange, AtomTypePropertiesMissing, AtomTypePbciMissing, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
Aromaticity = MmffMolPropertiesErrorKind.Aromaticity
AtomIndexOutOfRange = MmffMolPropertiesErrorKind.AtomIndexOutOfRange
AtomTypePbciMissing = MmffMolPropertiesErrorKind.AtomTypePbciMissing
AtomTypePropertiesMissing = MmffMolPropertiesErrorKind.AtomTypePropertiesMissing
Kekulize = MmffMolPropertiesErrorKind.Kekulize
Params = MmffMolPropertiesErrorKind.Params
RingFinding = MmffMolPropertiesErrorKind.RingFinding
Valence = MmffMolPropertiesErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Params': MmffMolPropertiesErrorKind.Params, 'Kekulize': MmffMolPropertiesErrorKind.Kekulize, 'Aromaticity': MmffMolPropertiesErrorKind.Aromaticity, 'RingFinding': MmffMolPropertiesErrorKind.RingFinding, 'Valence': MmffMolPropertiesErrorKind.Valence, 'AtomIndexOutOfRange': MmffMolPropertiesErrorKind.AtomIndexOutOfRange, 'AtomTypePropertiesMissing': MmffMolPropertiesErrorKind.AtomTypePropertiesMissing, 'AtomTypePbciMissing': MmffMolPropertiesErrorKind.AtomTypePbciMissing})
values = mappingproxy({0: MmffMolPropertiesErrorKind.Params, 1: MmffMolPropertiesErrorKind.Kekulize, 2: MmffMolPropertiesErrorKind.Aromaticity, 3: MmffMolPropertiesErrorKind.RingFinding, 4: MmffMolPropertiesErrorKind.Valence, 5: MmffMolPropertiesErrorKind.AtomIndexOutOfRange, 6: MmffMolPropertiesErrorKind.AtomTypePropertiesMissing, 7: MmffMolPropertiesErrorKind.AtomTypePbciMissing})
exception cosmolkit.MmffOopLookupError(*args, **kwargs)

Failure in the mmff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmffOopLookupError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property atom_type: int | None

Readonly atom_type payload of the MissingDefinition error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmffOopLookupErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmffOopLookupErrorKind(value)

Discriminants of MmffOopLookupErrorKind.

Members: MissingDefinition, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
MissingDefinition = MmffOopLookupErrorKind.MissingDefinition
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingDefinition': MmffOopLookupErrorKind.MissingDefinition})
values = mappingproxy({0: MmffOopLookupErrorKind.MissingDefinition})
exception cosmolkit.MmffOptimizationError(*args, **kwargs)

MmffOptimizationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: MmffOptimizationSourceError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.MmffOptimizationFailure(*args, **kwargs)

Failure in the mmff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmffOptimizationFailure is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property builder: MmffBuilderError | None

“error_payload”} Structured MmffBuilderError payload of MmffOptimizationFailure.Builder; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property kernel: ForceFieldKernelError | None

“error_payload”} Structured ForceFieldKernelError payload of MmffOptimizationFailure.Kernel; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property properties: MmffMolPropertiesError | None

“error_payload”} Structured MmffMolPropertiesError payload of MmffOptimizationFailure.Properties; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property serial: SerialConformerOptimizationError | None

“error_payload”} Structured SerialConformerOptimizationError payload of MmffOptimizationFailure.Serial; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: TopologyValidationError | MappingValidationError | MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | MmffParamParseError | UffDefaultTorsionQueryError | SmartsParseError | QueryCompileError | MatchError | MoleculeFragmentsError | FragmentCoordinateViewError | BondValueError | AtomPropertyError | ForceFieldKernelError | SerialResultCapacityError | SerialCoordinateCountError | OptimizationStageError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stage: OptimizationStageError | None

“error_payload”} Structured OptimizationStageError payload of MmffOptimizationFailure.Stage; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property threads: UffThreadCountError | None

“error_payload”} Structured UffThreadCountError payload of MmffOptimizationFailure.Threads; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: MmffOptimizationFailureKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmffOptimizationFailureKind(value)

Discriminants of MmffOptimizationFailureKind.

Members: Properties, Builder, Kernel, Stage, Serial, Threads, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
Builder = MmffOptimizationFailureKind.Builder
Kernel = MmffOptimizationFailureKind.Kernel
Properties = MmffOptimizationFailureKind.Properties
Serial = MmffOptimizationFailureKind.Serial
Stage = MmffOptimizationFailureKind.Stage
Threads = MmffOptimizationFailureKind.Threads
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Properties': MmffOptimizationFailureKind.Properties, 'Builder': MmffOptimizationFailureKind.Builder, 'Kernel': MmffOptimizationFailureKind.Kernel, 'Stage': MmffOptimizationFailureKind.Stage, 'Serial': MmffOptimizationFailureKind.Serial, 'Threads': MmffOptimizationFailureKind.Threads})
values = mappingproxy({0: MmffOptimizationFailureKind.Properties, 1: MmffOptimizationFailureKind.Builder, 2: MmffOptimizationFailureKind.Kernel, 3: MmffOptimizationFailureKind.Stage, 4: MmffOptimizationFailureKind.Serial, 5: MmffOptimizationFailureKind.Threads})
class cosmolkit.MmffOptimizationParams(*, mmff_variant=Ellipsis, max_iterations=Ellipsis, non_bonded_threshold=Ellipsis, conformer_id=Ellipsis, ignore_interfragment_interactions=Ellipsis)

MMFF parameterization and minimization settings for one stored conformer.

Members (5)
conformer_id: int | None

Stored 3D conformer identifier, or None for the native default selection.

ignore_interfragment_interactions: bool

Omit non-bonded interactions between disconnected molecular fragments.

max_iterations: int

Maximum number of minimizer iterations.

mmff_variant: MmffVariant

MMFF94 or MMFF94s parameterization.

non_bonded_threshold: float

Distance cutoff for inclusion of MMFF non-bonded interactions, in angstroms.

exception cosmolkit.MmffOptimizationSourceError(*args, **kwargs)

MmffOptimizationSourceError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: MmffOptimizationFailure

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.MmffOptimizeMoleculeConfResult(outcome)

MMFF outcome for one conformer optimization.

Members (4)
energy: float | None

Evaluated force-field energy; optimization outcomes without parameters return None.

needs_more: bool

Whether the native outcome reports nonconvergence requiring further optimization.

outcome: OptimizationOutcome

Typed optimization outcome retaining both convergence status and optional energy.

status_code: int

Native optimization status code corresponding to the typed outcome.

class cosmolkit.MmffOptimizeMoleculeConfsResult(molecule, conformer_results)

MMFF multi-conformer optimization result with the output molecule and ordered per-conformer outcomes.

Members (2)
conformer_results: list[MmffOptimizeMoleculeConfResult]

Independent list of per-conformer outcomes in native result order.

molecule: Molecule

Output molecule as a copy-on-write value; editing this value does not alter the result.

class cosmolkit.MmffOptimizeMoleculeResult(molecule, outcome)

MMFF optimization result containing the output molecule and optimization outcome.

Members (5)
energy: float | None

Evaluated force-field energy; optimization outcomes without parameters return None.

molecule: Molecule

Output molecule as a copy-on-write value; editing this value does not alter the result.

needs_more: bool

Whether the native outcome reports nonconvergence requiring further optimization.

outcome: OptimizationOutcome

Typed optimization outcome retaining both convergence status and optional energy.

status_code: int

Native optimization status code corresponding to the typed outcome.

exception cosmolkit.MmffParamError(*args, **kwargs)

Failure in the mmff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmffParamError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property angle: MmffAngleLookupError | None

“error_payload”} Structured MmffAngleLookupError payload of MmffParamError.Angle; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property oop: MmffOopLookupError | None

“error_payload”} Structured MmffOopLookupError payload of MmffParamError.Oop; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: MmffParamParseError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property symbol: str | None

Readonly symbol payload of the MissingDefaultData error variant; None for other variants.

property table: MmffParamParseError | None

“error_payload”} Structured MmffParamParseError payload of MmffParamError.Table; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property torsion: MmffTorLookupError | None

“error_payload”} Structured MmffTorLookupError payload of MmffParamError.Torsion; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: MmffParamErrorKind

Exact Rust error variant, independent of the human-readable message.

property vdw: MmffVdwParseError | None

“error_payload”} Structured MmffVdwParseError payload of MmffParamError.Vdw; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

class cosmolkit.MmffParamErrorKind(value)

Discriminants of MmffParamErrorKind.

Members: Table, Vdw, Angle, Torsion, Oop, MissingDefaultData, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
Angle = MmffParamErrorKind.Angle
MissingDefaultData = MmffParamErrorKind.MissingDefaultData
Oop = MmffParamErrorKind.Oop
Table = MmffParamErrorKind.Table
Torsion = MmffParamErrorKind.Torsion
Vdw = MmffParamErrorKind.Vdw
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Table': MmffParamErrorKind.Table, 'Vdw': MmffParamErrorKind.Vdw, 'Angle': MmffParamErrorKind.Angle, 'Torsion': MmffParamErrorKind.Torsion, 'Oop': MmffParamErrorKind.Oop, 'MissingDefaultData': MmffParamErrorKind.MissingDefaultData})
values = mappingproxy({0: MmffParamErrorKind.Table, 1: MmffParamErrorKind.Vdw, 2: MmffParamErrorKind.Angle, 3: MmffParamErrorKind.Torsion, 4: MmffParamErrorKind.Oop, 5: MmffParamErrorKind.MissingDefaultData})
class cosmolkit.MmffParamParseCause

Reason an MMFF parameter-table cell or line could not be parsed.

Members (2)
cell: str | None

Original numeric table cell for invalid numbers; None for missing tokens or empty lines.

variant: MmffParamParseCauseKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.MmffParamParseCauseKind(value)

Discriminants of MmffParamParseCauseKind.

Members: InvalidUnsigned, InvalidFloat, MissingToken, EmptyProcessedLine, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
EmptyProcessedLine = MmffParamParseCauseKind.EmptyProcessedLine
InvalidFloat = MmffParamParseCauseKind.InvalidFloat
InvalidUnsigned = MmffParamParseCauseKind.InvalidUnsigned
MissingToken = MmffParamParseCauseKind.MissingToken
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidUnsigned': MmffParamParseCauseKind.InvalidUnsigned, 'InvalidFloat': MmffParamParseCauseKind.InvalidFloat, 'MissingToken': MmffParamParseCauseKind.MissingToken, 'EmptyProcessedLine': MmffParamParseCauseKind.EmptyProcessedLine})
values = mappingproxy({0: MmffParamParseCauseKind.InvalidUnsigned, 1: MmffParamParseCauseKind.InvalidFloat, 2: MmffParamParseCauseKind.MissingToken, 3: MmffParamParseCauseKind.EmptyProcessedLine})
exception cosmolkit.MmffParamParseError(*args, **kwargs)

MmffParamParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property cause: MmffParamParseCause

“error_payload”} Structured reason the parameter entry could not be read.

Type:

{“role”

property column: int

Column of the malformed parameter entry.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property line: int

Line of the malformed parameter entry.

property table: MmffParamTable

“error_payload”} MMFF parameter table that could not be parsed.

Type:

{“role”

class cosmolkit.MmffParamTable(value)

Typed MmffParamTable values corresponding to the Rust enum.

Members: Def, Prop, Pbci, Chg, Bond, Bndk, Stbn, Dfsb, Angle, Oop, Tor, Vdw, HerschbachLaurie, CovRadPauEle, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (17)
Angle = MmffParamTable.Angle
Bndk = MmffParamTable.Bndk
Bond = MmffParamTable.Bond
Chg = MmffParamTable.Chg
CovRadPauEle = MmffParamTable.CovRadPauEle
Def = MmffParamTable.Def
Dfsb = MmffParamTable.Dfsb
HerschbachLaurie = MmffParamTable.HerschbachLaurie
Oop = MmffParamTable.Oop
Pbci = MmffParamTable.Pbci
Prop = MmffParamTable.Prop
Stbn = MmffParamTable.Stbn
Tor = MmffParamTable.Tor
Vdw = MmffParamTable.Vdw
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Def': MmffParamTable.Def, 'Prop': MmffParamTable.Prop, 'Pbci': MmffParamTable.Pbci, 'Chg': MmffParamTable.Chg, 'Bond': MmffParamTable.Bond, 'Bndk': MmffParamTable.Bndk, 'Stbn': MmffParamTable.Stbn, 'Dfsb': MmffParamTable.Dfsb, 'Angle': MmffParamTable.Angle, 'Oop': MmffParamTable.Oop, 'Tor': MmffParamTable.Tor, 'Vdw': MmffParamTable.Vdw, 'HerschbachLaurie': MmffParamTable.HerschbachLaurie, 'CovRadPauEle': MmffParamTable.CovRadPauEle})
values = mappingproxy({0: MmffParamTable.Def, 1: MmffParamTable.Prop, 2: MmffParamTable.Pbci, 3: MmffParamTable.Chg, 4: MmffParamTable.Bond, 5: MmffParamTable.Bndk, 6: MmffParamTable.Stbn, 7: MmffParamTable.Dfsb, 8: MmffParamTable.Angle, 9: MmffParamTable.Oop, 10: MmffParamTable.Tor, 11: MmffParamTable.Vdw, 12: MmffParamTable.HerschbachLaurie, 13: MmffParamTable.CovRadPauEle})
class cosmolkit.MmffProperties

MMFF atom typing and charges in molecule atom order, with parameter availability.

Members (6)
atom_type(atom_index) → int

Return the MMFF atom type at a zero-based atom index.

atoms: list[MmffAtomProperties]

Per-atom MMFF types and charges in molecule atom order.

formal_charge(atom_index) → float

Return the MMFF formal charge at a zero-based atom index.

is_valid: bool

Whether MMFF parameters are available for the entire molecule.

partial_charge(atom_index) → float

Return the MMFF partial charge at a zero-based atom index.

variant: MmffVariant

MMFF parameterization used to compute these properties.

class cosmolkit.MmffPropertiesParams(*, mmff_variant=Ellipsis)

Options for MMFF atom typing and charge assignment.

Members (1)
mmff_variant: MmffVariant

MMFF parameterization to use for atom typing and charges.

exception cosmolkit.MmffTorLookupError(*args, **kwargs)

Failure in the mmff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmffTorLookupError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property atom_type: int | None

Readonly atom_type payload of the MissingDefinition error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property level: int | None

Readonly level payload of the InvalidEquivalentLevel error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmffTorLookupErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmffTorLookupErrorKind(value)

Discriminants of MmffTorLookupErrorKind.

Members: MissingDefinition, InvalidEquivalentLevel, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
InvalidEquivalentLevel = MmffTorLookupErrorKind.InvalidEquivalentLevel
MissingDefinition = MmffTorLookupErrorKind.MissingDefinition
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingDefinition': MmffTorLookupErrorKind.MissingDefinition, 'InvalidEquivalentLevel': MmffTorLookupErrorKind.InvalidEquivalentLevel})
values = mappingproxy({0: MmffTorLookupErrorKind.MissingDefinition, 1: MmffTorLookupErrorKind.InvalidEquivalentLevel})
class cosmolkit.MmffVariant(value)

Typed MmffVariant values corresponding to the Rust enum.

Members: Mmff94, Mmff94s, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Mmff94 = MmffVariant.Mmff94
Mmff94s = MmffVariant.Mmff94s
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Mmff94': MmffVariant.Mmff94, 'Mmff94s': MmffVariant.Mmff94s})
values = mappingproxy({0: MmffVariant.Mmff94, 1: MmffVariant.Mmff94s})
exception cosmolkit.MmffVdwParseError(*args, **kwargs)

Failure in the mmff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmffVdwParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: MmffParamParseError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmffVdwParseErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmffVdwParseErrorKind(value)

Discriminants of MmffVdwParseErrorKind.

Members: Table, MissingHeader, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
MissingHeader = MmffVdwParseErrorKind.MissingHeader
Table = MmffVdwParseErrorKind.Table
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Table': MmffVdwParseErrorKind.Table, 'MissingHeader': MmffVdwParseErrorKind.MissingHeader})
values = mappingproxy({0: MmffVdwParseErrorKind.Table, 1: MmffVdwParseErrorKind.MissingHeader})
exception cosmolkit.MmjsonReadError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmjsonReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property error: JsonError | MmjsonStructureError

“error_payload”} Concrete JSON or structure error, identical to this exception’s __cause__.

Type:

{“role”

property source: JsonError | MmjsonStructureError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property source_name: str

Source label attached to the parsing failure. Applies to MmjsonReadError.Parse, MmjsonReadError.Structure.

property variant: MmjsonReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmjsonReadErrorKind(value)

Discriminants of MmjsonReadErrorKind.

Members: Parse, Structure, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Parse = MmjsonReadErrorKind.Parse
Structure = MmjsonReadErrorKind.Structure
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Parse': MmjsonReadErrorKind.Parse, 'Structure': MmjsonReadErrorKind.Structure})
values = mappingproxy({0: MmjsonReadErrorKind.Parse, 1: MmjsonReadErrorKind.Structure})
exception cosmolkit.MmjsonStructureError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmjsonStructureError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property actual: int | None

Readonly actual payload of the ArrayLength error variant; None for other variants.

property block: int | None

Input or structural block involved in the failure. Applies to MmjsonStructureError.BlockKeyPrefix, MmjsonStructureError.BlockNotObject, MmjsonStructureError.InvalidCategory. None when this payload is absent.

property category: int | None

Readonly category payload of the InvalidCategory error variant; None for other variants.

property column: int | None

Input column involved in the failure. Applies to MmjsonStructureError.ExpectedArray, MmjsonStructureError.ArrayLength. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the ArrayLength error variant; None for other variants.

property kind: str | None

Readonly kind payload of the ExpectedArray error variant; None for other variants.

property source: MmjsonValueError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MmjsonStructureErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmjsonStructureErrorKind(value)

Discriminants of MmjsonStructureErrorKind.

Members: RootNotObject, BlockKeyPrefix, BlockNotObject, InvalidCategory, ExpectedArray, ArrayLength, RowCountOverflow, MissingArenaValue, Text, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
ArrayLength = MmjsonStructureErrorKind.ArrayLength
BlockKeyPrefix = MmjsonStructureErrorKind.BlockKeyPrefix
BlockNotObject = MmjsonStructureErrorKind.BlockNotObject
ExpectedArray = MmjsonStructureErrorKind.ExpectedArray
InvalidCategory = MmjsonStructureErrorKind.InvalidCategory
MissingArenaValue = MmjsonStructureErrorKind.MissingArenaValue
RootNotObject = MmjsonStructureErrorKind.RootNotObject
RowCountOverflow = MmjsonStructureErrorKind.RowCountOverflow
Text = MmjsonStructureErrorKind.Text
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'RootNotObject': MmjsonStructureErrorKind.RootNotObject, 'BlockKeyPrefix': MmjsonStructureErrorKind.BlockKeyPrefix, 'BlockNotObject': MmjsonStructureErrorKind.BlockNotObject, 'InvalidCategory': MmjsonStructureErrorKind.InvalidCategory, 'ExpectedArray': MmjsonStructureErrorKind.ExpectedArray, 'ArrayLength': MmjsonStructureErrorKind.ArrayLength, 'RowCountOverflow': MmjsonStructureErrorKind.RowCountOverflow, 'MissingArenaValue': MmjsonStructureErrorKind.MissingArenaValue, 'Text': MmjsonStructureErrorKind.Text})
values = mappingproxy({0: MmjsonStructureErrorKind.RootNotObject, 1: MmjsonStructureErrorKind.BlockKeyPrefix, 2: MmjsonStructureErrorKind.BlockNotObject, 3: MmjsonStructureErrorKind.InvalidCategory, 4: MmjsonStructureErrorKind.ExpectedArray, 5: MmjsonStructureErrorKind.ArrayLength, 6: MmjsonStructureErrorKind.RowCountOverflow, 7: MmjsonStructureErrorKind.MissingArenaValue, 8: MmjsonStructureErrorKind.Text})
class cosmolkit.MmjsonUnexpectedType(value)

Typed MmjsonUnexpectedType values corresponding to the Rust enum.

Members: Null, False_, True_, Array, Object, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (8)
Array = MmjsonUnexpectedType.Array
False_ = MmjsonUnexpectedType.False_
Null = MmjsonUnexpectedType.Null
Object = MmjsonUnexpectedType.Object
True_ = MmjsonUnexpectedType.True_
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Null': MmjsonUnexpectedType.Null, 'False_': MmjsonUnexpectedType.False_, 'True_': MmjsonUnexpectedType.True_, 'Array': MmjsonUnexpectedType.Array, 'Object': MmjsonUnexpectedType.Object})
values = mappingproxy({0: MmjsonUnexpectedType.Null, 1: MmjsonUnexpectedType.False_, 2: MmjsonUnexpectedType.True_, 3: MmjsonUnexpectedType.Array, 4: MmjsonUnexpectedType.Object})
exception cosmolkit.MmjsonValueError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MmjsonValueError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the InvalidSpan error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property start: int | None

Readonly start payload of the InvalidSpan error variant; None for other variants.

property valid_up_to: int | None

Readonly valid_up_to payload of the InvalidUtf8 error variant; None for other variants.

property value: MmjsonUnexpectedType | None

“error_payload”} Value rejected or reported by the native operation. Applies to MmjsonValueError.UnexpectedType, MmjsonValueError.InvalidArrayElement. None when this payload is absent.

Type:

{“role”

property variant: MmjsonValueErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MmjsonValueErrorKind(value)

Discriminants of MmjsonValueErrorKind.

Members: UnexpectedType, InvalidArrayElement, MissingArrayFirstElement, InvalidSpan, InvalidUtf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
InvalidArrayElement = MmjsonValueErrorKind.InvalidArrayElement
InvalidSpan = MmjsonValueErrorKind.InvalidSpan
InvalidUtf8 = MmjsonValueErrorKind.InvalidUtf8
MissingArrayFirstElement = MmjsonValueErrorKind.MissingArrayFirstElement
UnexpectedType = MmjsonValueErrorKind.UnexpectedType
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnexpectedType': MmjsonValueErrorKind.UnexpectedType, 'InvalidArrayElement': MmjsonValueErrorKind.InvalidArrayElement, 'MissingArrayFirstElement': MmjsonValueErrorKind.MissingArrayFirstElement, 'InvalidSpan': MmjsonValueErrorKind.InvalidSpan, 'InvalidUtf8': MmjsonValueErrorKind.InvalidUtf8})
values = mappingproxy({0: MmjsonValueErrorKind.UnexpectedType, 1: MmjsonValueErrorKind.InvalidArrayElement, 2: MmjsonValueErrorKind.MissingArrayFirstElement, 3: MmjsonValueErrorKind.InvalidSpan, 4: MmjsonValueErrorKind.InvalidUtf8})
exception cosmolkit.Mol2PostError(*args, **kwargs)

Mol2PostError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: ValenceError | StereoError | SanitizeError | MolPostError | HydrogenError | RingFindingError | CoordinateValidationError | LegacyStereoError | MoleculePropertyError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property stage: str

MOL2 post-processing stage that failed.

exception cosmolkit.Mol2ReadError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

Mol2ReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property feature: str | None

Readonly feature payload of the Unsupported error variant; None for other variants.

property message: str | None

Detailed native diagnostic message. Applies to Mol2ReadError.Parse. None when this payload is absent.

property property_error: PropertyStringError | None

“error_payload”} Structured PropertyStringError payload of Mol2ReadError.PropertyString; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: TopologyValidationError | CoordinateValidationError | AtomPropertyError | MoleculePropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: Mol2ReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.Mol2ReadErrorKind(value)

Discriminants of Mol2ReadErrorKind.

Members: Parse, Unsupported, Topology, Coordinates, PropertyString, AtomProperty, MoleculeProperty, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (10)
AtomProperty = Mol2ReadErrorKind.AtomProperty
Coordinates = Mol2ReadErrorKind.Coordinates
MoleculeProperty = Mol2ReadErrorKind.MoleculeProperty
Parse = Mol2ReadErrorKind.Parse
PropertyString = Mol2ReadErrorKind.PropertyString
Topology = Mol2ReadErrorKind.Topology
Unsupported = Mol2ReadErrorKind.Unsupported
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Parse': Mol2ReadErrorKind.Parse, 'Unsupported': Mol2ReadErrorKind.Unsupported, 'Topology': Mol2ReadErrorKind.Topology, 'Coordinates': Mol2ReadErrorKind.Coordinates, 'PropertyString': Mol2ReadErrorKind.PropertyString, 'AtomProperty': Mol2ReadErrorKind.AtomProperty, 'MoleculeProperty': Mol2ReadErrorKind.MoleculeProperty})
values = mappingproxy({0: Mol2ReadErrorKind.Parse, 1: Mol2ReadErrorKind.Unsupported, 2: Mol2ReadErrorKind.Topology, 3: Mol2ReadErrorKind.Coordinates, 4: Mol2ReadErrorKind.PropertyString, 5: Mol2ReadErrorKind.AtomProperty, 6: Mol2ReadErrorKind.MoleculeProperty})
class cosmolkit.Mol2ReadParams(*, sanitize=Ellipsis, remove_hs=Ellipsis, variant=Ellipsis, cleanup_substructures=Ellipsis)

MOL2 parser variant and native post-processing options.

Members (4)
cleanup_substructures: bool

Apply the native MOL2 substructure cleanup rules.

remove_hs: bool

Remove removable explicit hydrogens during native post-processing.

sanitize: bool

Sanitize the parsed molecule.

variant: Mol2Type

MOL2 atom-typing convention used by the parser.

class cosmolkit.Mol2Type(value)

Typed Mol2Type values corresponding to the Rust enum.

Members: Corina, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (4)
Corina = Mol2Type.Corina
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Corina': Mol2Type.Corina})
values = mappingproxy({0: Mol2Type.Corina})
class cosmolkit.MolBlockWriteParams(*, format=Ellipsis, force_2d=Ellipsis, include_stereo=Ellipsis, kekulize=Ellipsis, precision=Ellipsis, coordinate_selection=Ellipsis, include_coordinates=Ellipsis)

MolBlock format, stereochemistry and coordinate-output options.

Members (7)
coordinate_selection: MolCoordinateSelection

Select automatic, explicit 2D or explicit 3D coordinates.

force_2d: bool

Request two-dimensional coordinate output.

format: SdfFormat

V2000 or V3000 MolBlock encoding.

include_coordinates: bool

Include coordinates; when false no stored conformer is selected.

include_stereo: bool

Include stereochemical information in the output.

kekulize: bool

Kekulize aromatic bonds for MolBlock output.

precision: int

Decimal precision used by coordinate output formats that support it.

class cosmolkit.MolCoordinateSelection

Select a stored coordinate set: Auto uses the unique available set; TwoD and ThreeD select by ID.

Members (4)
Auto = <cosmolkit.MolCoordinateSelection object>
static ThreeD(id) → MolCoordinateSelection

Select a stored three-dimensional conformer by its dimension-scoped identifier.

static TwoD(id) → MolCoordinateSelection

Select a stored two-dimensional layout by its dimension-scoped identifier.

id: int | None

Dimension-scoped coordinate identifier, or None for Auto selection.

class cosmolkit.MolecularForceField

Persistent native force-field evaluator owning positions, constraints and minimization state. Position edits and minimization affect this evaluator, not the molecule used to construct it.

Members (15)
add_angle_constraint_(atom1: SupportsIndex, atom2: SupportsIndex, atom3: SupportsIndex, *, relative: bool, min_angle_deg: SupportsFloat | SupportsIndex, max_angle_deg: SupportsFloat | SupportsIndex, force_constant: SupportsFloat | SupportsIndex) → None
add_angle_constraint_(atom1: SupportsIndex, atom2: SupportsIndex, atom3: SupportsIndex, params: ForceFieldAngleConstraintParams) → None

Add the constraint specified by ForceFieldAngleConstraintParams to this force-field evaluator in place. Atom arguments are zero-based indices. Supply the parameter object or the required keyword fields, not both; the source molecule is unchanged.

add_distance_constraint_(atom1: SupportsIndex, atom2: SupportsIndex, *, relative: bool, min_distance: SupportsFloat | SupportsIndex, max_distance: SupportsFloat | SupportsIndex, force_constant: SupportsFloat | SupportsIndex) → None
add_distance_constraint_(atom1: SupportsIndex, atom2: SupportsIndex, params: ForceFieldDistanceConstraintParams) → None

Add the constraint specified by ForceFieldDistanceConstraintParams to this force-field evaluator in place. Atom arguments are zero-based indices. Supply the parameter object or the required keyword fields, not both; the source molecule is unchanged.

add_position_constraint_(atom: SupportsIndex, *, max_displacement: SupportsFloat | SupportsIndex, force_constant: SupportsFloat | SupportsIndex) → None
add_position_constraint_(atom: SupportsIndex, params: ForceFieldPositionConstraintParams) → None

Add the constraint specified by ForceFieldPositionConstraintParams to this force-field evaluator in place. Atom arguments are zero-based indices. Supply the parameter object or the required keyword fields, not both; the source molecule is unchanged.

add_torsion_constraint_(atom1: SupportsIndex, atom2: SupportsIndex, atom3: SupportsIndex, atom4: SupportsIndex, *, relative: bool, min_dihedral_deg: SupportsFloat | SupportsIndex, max_dihedral_deg: SupportsFloat | SupportsIndex, force_constant: SupportsFloat | SupportsIndex) → None
add_torsion_constraint_(atom1: SupportsIndex, atom2: SupportsIndex, atom3: SupportsIndex, atom4: SupportsIndex, params: ForceFieldTorsionConstraintParams) → None

Add the constraint specified by ForceFieldTorsionConstraintParams to this force-field evaluator in place. Atom arguments are zero-based indices. Supply the parameter object or the required keyword fields, not both; the source molecule is unchanged.

energy() → float

Evaluate the native force-field energy at the evaluator’s current positions.

energy_gradient() → ForceFieldEnergyGradient

Evaluate energy and per-atom Cartesian gradients together.

fixed_atoms: list[int]

Atom indices currently held fixed during minimization.

gradient() → list[list[float]]

Evaluate the Cartesian gradient with the native fixed-atom treatment.

gradient_unconstrained() → list[list[float]]

Evaluate the Cartesian gradient without fixing gradient components for fixed atoms.

minimize_(*, max_iterations: SupportsIndex | None = None, force_tolerance: SupportsFloat | SupportsIndex | None = None, energy_tolerance: SupportsFloat | SupportsIndex | None = None) → ForceFieldMinimizeOutcome
minimize_(params: ForceFieldMinimizeParams | None = None) → ForceFieldMinimizeOutcome

Minimize the evaluator’s positions in place and return convergence, iteration and energy information.

position(atom_id) → list[float]

Return the force field’s current Cartesian position for the specified atom.

positions: list[list[float]]

Independent list of the evaluator’s current Cartesian position triples.

set_fixed_atoms_(atom_ids) → None

Replace the set of atoms held fixed during minimization.

set_position_(atom_id, position) → None

Update one atom’s position in this force-field evaluator, not in the source molecule.

set_positions_(positions) → None

Replace the evaluator’s positions from one triple per atom; native shape and value errors propagate.

class cosmolkit.MolecularForceFieldErrorKind(value)

Typed MolecularForceFieldErrorKind values corresponding to the Rust enum.

Members: MissingConformer, Parameterization, InvalidParameterization, InvalidAtomIndex, InvalidFixedAtom, CoordinateCount, CoordinateShape, NonFiniteCoordinate, InvalidTolerance, InvalidConstraintBounds, InvalidConstraintRange, Preparation, Construction, Initialization, Rings, Kernel, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (19)
Construction = MolecularForceFieldErrorKind.Construction
CoordinateCount = MolecularForceFieldErrorKind.CoordinateCount
CoordinateShape = MolecularForceFieldErrorKind.CoordinateShape
Initialization = MolecularForceFieldErrorKind.Initialization
InvalidAtomIndex = MolecularForceFieldErrorKind.InvalidAtomIndex
InvalidConstraintBounds = MolecularForceFieldErrorKind.InvalidConstraintBounds
InvalidConstraintRange = MolecularForceFieldErrorKind.InvalidConstraintRange
InvalidFixedAtom = MolecularForceFieldErrorKind.InvalidFixedAtom
InvalidParameterization = MolecularForceFieldErrorKind.InvalidParameterization
InvalidTolerance = MolecularForceFieldErrorKind.InvalidTolerance
Kernel = MolecularForceFieldErrorKind.Kernel
MissingConformer = MolecularForceFieldErrorKind.MissingConformer
NonFiniteCoordinate = MolecularForceFieldErrorKind.NonFiniteCoordinate
Parameterization = MolecularForceFieldErrorKind.Parameterization
Preparation = MolecularForceFieldErrorKind.Preparation
Rings = MolecularForceFieldErrorKind.Rings
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingConformer': MolecularForceFieldErrorKind.MissingConformer, 'Parameterization': MolecularForceFieldErrorKind.Parameterization, 'InvalidParameterization': MolecularForceFieldErrorKind.InvalidParameterization, 'InvalidAtomIndex': MolecularForceFieldErrorKind.InvalidAtomIndex, 'InvalidFixedAtom': MolecularForceFieldErrorKind.InvalidFixedAtom, 'CoordinateCount': MolecularForceFieldErrorKind.CoordinateCount, 'CoordinateShape': MolecularForceFieldErrorKind.CoordinateShape, 'NonFiniteCoordinate': MolecularForceFieldErrorKind.NonFiniteCoordinate, 'InvalidTolerance': MolecularForceFieldErrorKind.InvalidTolerance, 'InvalidConstraintBounds': MolecularForceFieldErrorKind.InvalidConstraintBounds, 'InvalidConstraintRange': MolecularForceFieldErrorKind.InvalidConstraintRange, 'Preparation': MolecularForceFieldErrorKind.Preparation, 'Construction': MolecularForceFieldErrorKind.Construction, 'Initialization': MolecularForceFieldErrorKind.Initialization, 'Rings': MolecularForceFieldErrorKind.Rings, 'Kernel': MolecularForceFieldErrorKind.Kernel})
values = mappingproxy({0: MolecularForceFieldErrorKind.MissingConformer, 1: MolecularForceFieldErrorKind.Parameterization, 2: MolecularForceFieldErrorKind.InvalidParameterization, 3: MolecularForceFieldErrorKind.InvalidAtomIndex, 4: MolecularForceFieldErrorKind.InvalidFixedAtom, 5: MolecularForceFieldErrorKind.CoordinateCount, 6: MolecularForceFieldErrorKind.CoordinateShape, 7: MolecularForceFieldErrorKind.NonFiniteCoordinate, 8: MolecularForceFieldErrorKind.InvalidTolerance, 9: MolecularForceFieldErrorKind.InvalidConstraintBounds, 10: MolecularForceFieldErrorKind.InvalidConstraintRange, 11: MolecularForceFieldErrorKind.Preparation, 12: MolecularForceFieldErrorKind.Construction, 13: MolecularForceFieldErrorKind.Initialization, 14: MolecularForceFieldErrorKind.Rings, 15: MolecularForceFieldErrorKind.Kernel})
exception cosmolkit.MolecularIoError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MolecularIoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property detail: str | None

Readonly detail payload of the Parameter error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property format: str | None

Format involved in the failed conversion. Applies to MolecularIoError.NoRecord, MolecularIoError.OutputUtf8. None when this payload is absent.

property name: str | None

Readonly name payload of the Parameter error variant; None for other variants.

property path: pathlib.Path | None

Filesystem path involved in the operation. Applies to MolecularIoError.Io. None when this payload is absent.

property source: IoError | XyzReadError | XyzWriteError | OperationError | Mol2ReadError | Mol2PostError | MolWriteError | PdbWriteError | BioPdbReadError | BioMmcifReadError | BioMoleculeError | SdfError | FromUtf8Error | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MolecularIoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MolecularIoErrorKind(value)

Discriminants of MolecularIoErrorKind.

Members: Io, XyzRead, XyzWrite, Construction, Mol2Read, Mol2Post, MolWrite, PdbWrite, PdbRead, MmcifRead, BioMolecule, Sdf, NoRecord, OutputUtf8, Parameter, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (18)
BioMolecule = MolecularIoErrorKind.BioMolecule
Construction = MolecularIoErrorKind.Construction
Io = MolecularIoErrorKind.Io
MmcifRead = MolecularIoErrorKind.MmcifRead
Mol2Post = MolecularIoErrorKind.Mol2Post
Mol2Read = MolecularIoErrorKind.Mol2Read
MolWrite = MolecularIoErrorKind.MolWrite
NoRecord = MolecularIoErrorKind.NoRecord
OutputUtf8 = MolecularIoErrorKind.OutputUtf8
Parameter = MolecularIoErrorKind.Parameter
PdbRead = MolecularIoErrorKind.PdbRead
PdbWrite = MolecularIoErrorKind.PdbWrite
Sdf = MolecularIoErrorKind.Sdf
XyzRead = MolecularIoErrorKind.XyzRead
XyzWrite = MolecularIoErrorKind.XyzWrite
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Io': MolecularIoErrorKind.Io, 'XyzRead': MolecularIoErrorKind.XyzRead, 'XyzWrite': MolecularIoErrorKind.XyzWrite, 'Construction': MolecularIoErrorKind.Construction, 'Mol2Read': MolecularIoErrorKind.Mol2Read, 'Mol2Post': MolecularIoErrorKind.Mol2Post, 'MolWrite': MolecularIoErrorKind.MolWrite, 'PdbWrite': MolecularIoErrorKind.PdbWrite, 'PdbRead': MolecularIoErrorKind.PdbRead, 'MmcifRead': MolecularIoErrorKind.MmcifRead, 'BioMolecule': MolecularIoErrorKind.BioMolecule, 'Sdf': MolecularIoErrorKind.Sdf, 'NoRecord': MolecularIoErrorKind.NoRecord, 'OutputUtf8': MolecularIoErrorKind.OutputUtf8, 'Parameter': MolecularIoErrorKind.Parameter})
values = mappingproxy({0: MolecularIoErrorKind.Io, 1: MolecularIoErrorKind.XyzRead, 2: MolecularIoErrorKind.XyzWrite, 3: MolecularIoErrorKind.Construction, 4: MolecularIoErrorKind.Mol2Read, 5: MolecularIoErrorKind.Mol2Post, 6: MolecularIoErrorKind.MolWrite, 7: MolecularIoErrorKind.PdbWrite, 8: MolecularIoErrorKind.PdbRead, 9: MolecularIoErrorKind.MmcifRead, 10: MolecularIoErrorKind.BioMolecule, 11: MolecularIoErrorKind.Sdf, 12: MolecularIoErrorKind.NoRecord, 13: MolecularIoErrorKind.OutputUtf8, 14: MolecularIoErrorKind.Parameter})
class cosmolkit.MoleculeAtom

Readonly atom view retaining its molecule’s topology version for degree, valence and hydrogen queries. Subsequent copy-on-write edits of another molecule value do not alter this view.

Members (24)
atom_map: int | None

Atom-mapping number, or None when no map is assigned.

atomic_number: int

Atomic number of the atom’s element.

chiral_tag: ChiralTag

Stored atom stereochemical tag; reading does not assign stereochemistry.

chiral_tag_code: int

Integer code of the stored chiral tag.

chiral_tag_name: str

Canonical name of the stored chiral tag.

cip_descriptor: CipDescriptor | None

Stored CIP descriptor, or None if absent; invalid stored values raise CipDescriptorError.

cip_neighbor_order: list[int] | None

Stored CIP neighbor ordering as atom indices, or None if absent; invalid encodings raise CipDescriptorError.

cip_rank: int | None

Stored CIP rank, or None when absent; an incorrectly typed property raises PropertyValueError.

degree: int

Number of neighboring atoms in the retained molecular topology.

element: Element

Chemical element stored on this atom.

explicit_hydrogens: int

Explicit hydrogen count stored on the atom, distinct from neighboring hydrogen atom rows.

explicit_valence: int

Explicit valence computed from this atom’s retained molecular context.

formal_charge: int

Stored signed formal charge, not a partial charge.

hybridization: Hybridization

Stored hybridization assignment; reading does not recompute it.

id: int

Zero-based identifier within the originating topology.

implicit_hydrogens: int

Implicit hydrogen count computed from this atom’s retained molecular context.

is_aromatic: bool

Stored aromaticity flag; reading does not perform aromaticity perception.

isotope: int | None

Explicit isotope mass number, or None when no isotope is specified.

no_implicit: bool

Whether implicit hydrogens are disabled for this atom.

radical_electrons: int

Stored number of radical electrons.

template_attachment_order: TemplateAttachmentOrder | None

Template attachment ordering metadata, or None when absent.

total_hydrogens: int

Native total hydrogen count using this atom’s retained molecular context.

total_valence: int

Sum of explicit and implicit valence in the retained molecular context.

value() → Atom

Return detached atom data without retaining the molecular context.

class cosmolkit.MoleculeBatch

Ordered molecule/error records with native batch execution and copy-on-write transforms. Integer indexing returns a molecule or None for an error record; slices and index selections return another batch. Use records or get to inspect errors.

Members (71)
dg_bounds_matrix(params=None, *, n_jobs=None, progress_bar=None) → list[list[list[float]] | None]

Return per-record distance-geometry bounds matrices using native preparation and execution options.

dg_bounds_matrix_with_params(params) → list[list[list[float]] | None]

Return per-record distance-geometry bounds matrices with explicit preparation and execution parameters.

error_mode: BatchErrorMode

Error-handling mode retained by this batch.

errors: list[BatchError]

Structured errors retained by the batch, preserving their native record indices and causes.

fingerprint_atom_pair(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → FingerprintBatch
fingerprint_atom_pair(params: AtomPairFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → FingerprintBatch

Batch form of Molecule.fingerprint_atom_pair.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_atom_pair_count(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → list[SparseCountFingerprint32 | None]
fingerprint_atom_pair_count(params: AtomPairFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → list[SparseCountFingerprint32 | None]

Batch form of Molecule.fingerprint_atom_pair_count.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_atom_pair_count_with_params(options, execution) → list[SparseCountFingerprint32 | None]

Batch form of Molecule.fingerprint_atom_pair_count with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_atom_pair_sparse(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → list[SparseBitFingerprint | None]
fingerprint_atom_pair_sparse(params: AtomPairFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → list[SparseBitFingerprint | None]

Batch form of Molecule.fingerprint_atom_pair_sparse.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_atom_pair_sparse_count(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → list[SparseCountFingerprint | None]
fingerprint_atom_pair_sparse_count(params: AtomPairFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → list[SparseCountFingerprint | None]

Batch form of Molecule.fingerprint_atom_pair_sparse_count.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_atom_pair_sparse_count_with_params(options, execution) → list[SparseCountFingerprint | None]

Batch form of Molecule.fingerprint_atom_pair_sparse_count with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_atom_pair_sparse_with_params(options, execution) → list[SparseBitFingerprint | None]

Batch form of Molecule.fingerprint_atom_pair_sparse with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_atom_pair_with_output(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, collect_additional_output: bool = ..., min_distance: SupportsIndex | None = ..., max_distance: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_2d: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., conformer_id: SupportsIndex | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → list[BatchFingerprintOutput | None]
fingerprint_atom_pair_with_output(params: AtomPairFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, collect_additional_output: bool = ...) → list[BatchFingerprintOutput | None]

Batch form of Molecule.fingerprint_atom_pair_with_output.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_atom_pair_with_output_with_params(options, collect_additional_output, execution) → list[BatchFingerprintOutput | None]

Batch form of Molecule.fingerprint_atom_pair_with_output with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_atom_pair_with_params(options, execution) → FingerprintBatch

Batch form of Molecule.fingerprint_atom_pair with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_layered(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, layers: SupportsIndex | None = ..., min_path: SupportsIndex | None = ..., max_path: SupportsIndex | None = ..., fp_size: SupportsIndex | None = ..., atom_counts: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., set_only_bits: Fingerprint | None = ..., branched_paths: bool | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ...) → FingerprintBatch
fingerprint_layered(params: LayeredFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → FingerprintBatch

Batch form of Molecule.fingerprint_layered.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_layered_with_output(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, layers: SupportsIndex | None = ..., min_path: SupportsIndex | None = ..., max_path: SupportsIndex | None = ..., fp_size: SupportsIndex | None = ..., atom_counts: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., set_only_bits: Fingerprint | None = ..., branched_paths: bool | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ...) → list[LayeredFingerprintResult | None]
fingerprint_layered_with_output(params: LayeredFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → list[LayeredFingerprintResult | None]

Batch form of Molecule.fingerprint_layered_with_output.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_layered_with_output_with_params(options, execution) → list[LayeredFingerprintResult | None]

Batch form of Molecule.fingerprint_layered_with_output with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_layered_with_params(options, execution) → FingerprintBatch

Batch form of Molecule.fingerprint_layered with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_morgan(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, radius: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_bond_types: bool | None = ..., include_ring_membership: bool | None = ..., only_nonzero_invariants: bool | None = ..., include_redundant_environments: bool | None = ..., fp_size: SupportsIndex | None = ..., count_simulation: bool | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., invariants: MorganInvariants | None = ...) → FingerprintBatch
fingerprint_morgan(params: MorganFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → FingerprintBatch

Batch form of Molecule.fingerprint_morgan.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_morgan_with_generator_params(options, atom_invariants, bond_invariants, call, *, execution=None) → FingerprintBatch

Compute folded Morgan fingerprints for batch records using explicit generator configuration.

fingerprint_morgan_with_output(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, collect_additional_output: bool = ..., radius: SupportsIndex | None = ..., include_chirality: bool | None = ..., use_bond_types: bool | None = ..., include_ring_membership: bool | None = ..., only_nonzero_invariants: bool | None = ..., include_redundant_environments: bool | None = ..., fp_size: SupportsIndex | None = ..., count_simulation: bool | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., invariants: MorganInvariants | None = ...) → list[BatchFingerprintOutput | None]
fingerprint_morgan_with_output(params: MorganFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, collect_additional_output: bool = ...) → list[BatchFingerprintOutput | None]

Batch form of Molecule.fingerprint_morgan_with_output.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_morgan_with_output_with_generator_params(options, atom_invariants, bond_invariants, call, collect_additional_output, *, execution=None) → list[BatchFingerprintOutput | None]

Compute Morgan fingerprints with per-record feature provenance using explicit generator configuration.

fingerprint_morgan_with_output_with_params(options, collect_additional_output, execution) → list[BatchFingerprintOutput | None]

Batch form of Molecule.fingerprint_morgan_with_output with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_morgan_with_params(options, execution) → FingerprintBatch

Batch form of Molecule.fingerprint_morgan with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_pattern(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, n_bits: SupportsIndex | None = ..., tautomeric: bool | None = ...) → FingerprintBatch
fingerprint_pattern(params: PatternFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → FingerprintBatch

Batch form of Molecule.fingerprint_pattern.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_pattern_with_params(options, execution) → FingerprintBatch

Batch form of Molecule.fingerprint_pattern with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

fingerprint_topological_torsion(*, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, torsion_atom_count: SupportsIndex | None = ..., only_shortest_paths: bool | None = ..., include_chirality: bool | None = ..., count_simulation: bool | None = ..., fp_size: SupportsIndex | None = ..., bits_per_feature: SupportsIndex | None = ..., count_bounds: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., from_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., ignore_atoms: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_atom_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., custom_bond_invariants: _typeshed.SupportsGetItem[int, SupportsIndex] | None = ..., atom_invariants_generator: AtomPairAtomInvariantsGenerator | None = ..., use_legacy_stereo_perception: bool | None = ...) → FingerprintBatch
fingerprint_topological_torsion(params: TopologicalTorsionFingerprintParams | None = None, *, execution: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → FingerprintBatch

Batch form of Molecule.fingerprint_topological_torsion.

Results retain input order. Retained input failures reject the query before computation; filter with with_valid_records() and retry. Supply a parameter object or chemical keyword options, not both. n_jobs and progress_bar are forwarded to native batch execution.

fingerprint_topological_torsion_with_params(options, execution) → FingerprintBatch

Batch form of Molecule.fingerprint_topological_torsion with explicit chemical and execution parameters. Filter retained input failures with with_valid_records() before querying.

static from_dataset_indices(dataset, indices, errors=None) → MoleculeBatch

Construct a batch from selected SDF dataset indices in the supplied order.

static from_records(records, errors=None) → MoleculeBatch

Construct a batch from Molecule and BatchError records using the selected error policy.

static from_sdf_records(text: str, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → MoleculeBatch
static from_sdf_records(text: str, read: SdfReadParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch

Construct a batch from SDF record values using native parsing and error handling.

static from_sdf_records_with_params(text, read, errors=None, n_jobs=None, progress_bar=None) → MoleculeBatch

Construct a batch from SDF record values with explicit parameters.

static from_smiles_list(smiles: _typeshed.SupportsGetItem[int, str], *, params: BatchParams | None = None, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, sanitize: bool | None = None, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None, parse_name: bool | None = None, remove_hs: bool | None = None, skip_cleanup: bool | None = None, debug_parse: bool | None = None, replacements: dict[str, str] | None = None) → MoleculeBatch
static from_smiles_list(smiles: _typeshed.SupportsGetItem[int, str], parse: SmilesParseParams | None = None, params: BatchParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch

Parse an ordered list of SMILES into a batch; error mode determines how failed records are retained or reported.

static from_smiles_list_with_params(smiles, parse, params) → MoleculeBatch

Parse an ordered list of SMILES with explicit parsing and batch parameters.

get(index) → Molecule | BatchError | None

Return a Molecule or BatchError record at a nonnegative index, or None when out of range.

invalid_count: int

Number of error records.

invalid_mask: list[bool]

true for error records.

Type:

Boolean mask in record order

is_empty: bool

Whether the batch contains no records.

len: int

Number of records, including failed records.

parallel_jobs: int | None

Stored parallel-job override, or None to use the native default.

progress_bar: bool | None

Stored progress-display override, or None to use the native default.

static read_sdf(path: str | os.PathLike[str], *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → MoleculeBatch
static read_sdf(path: str | os.PathLike[str], read: SdfReadParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch

Read an SDF path into an ordered molecule batch.

static read_sdf_with_params(path, read, errors=None, n_jobs=None, progress_bar=None) → MoleculeBatch

Read an SDF path into a batch using explicit read and batch parameters.

records: list[Molecule | BatchError]

Ordered record values, each a Molecule or a structured BatchError.

sanitize(options: SanitizeParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch
sanitize(options: SanitizeParams | None = None, params: BatchParams | None = None) → MoleculeBatch

Return a new batch after sanitizing each molecule. Original records are unchanged; failures follow the selected batch error policy.

sanitize_with_params(options, params) → MoleculeBatch

Return a new sanitized batch with explicit sanitization and execution parameters.

select(indices) → MoleculeBatch | None

Return a new batch containing the specified indices in order, including duplicates; return None if an index is invalid.

to_list() → list[Molecule | None]

Return molecule values in record order with None placeholders for failed records.

to_smiles(*, params: BatchQueryParams | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None, isomeric_smiles: bool | None = None, kekule: bool | None = None, canonical: bool | None = None, clean_stereo: bool | None = None, rooted_at_atom: SupportsIndex | None = None, all_bonds_explicit: bool | None = None, all_hydrogens_explicit: bool | None = None, include_dative_bonds: bool | None = None, ignore_atom_map_numbers: bool | None = None) → list[str | None]
to_smiles(options: SmilesWriteParams | None = None, params: BatchQueryParams | None = None, *, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → list[str | None]

Return SMILES results in record order. Supply SmilesWriteParams or individual chemical options, not both; n_jobs and progress_bar control native execution.

to_smiles_with_params(options, params) → list[str | None]

Return SMILES results in record order using explicit writer and execution parameters.

to_svg(width, height, params=None, *, n_jobs=None, progress_bar=None) → list[str | None]

Render each molecule to SVG with the requested canvas dimensions and native execution settings.

to_svg_with_params(width, height, params) → list[str | None]

Render each molecule to SVG with explicit drawing and execution parameters.

valid_count: int

Number of molecule records.

valid_mask: list[bool]

true for molecule records.

Type:

Boolean mask in record order

with_2d_coordinates(options: Coordinate2DParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch
with_2d_coordinates(options: Coordinate2DParams | None = None, params: BatchParams | None = None) → MoleculeBatch

Return a new batch with generated two-dimensional layouts; source records are unchanged.

with_2d_coordinates_with_params(options, params) → MoleculeBatch

Return a new batch with generated layouts using explicit layout and execution parameters.

with_hydrogens(options: AddHsParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch
with_hydrogens(options: AddHsParams | None = None, params: BatchParams | None = None) → MoleculeBatch

Return a new batch with explicit hydrogen atoms added; source records are unchanged.

with_hydrogens_with_params(options, params) → MoleculeBatch

Return a new batch with hydrogens added using explicit chemistry and execution parameters.

with_kekulized_bonds(options: KekulizeParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch
with_kekulized_bonds(options: KekulizeParams | None = None, params: BatchParams | None = None) → MoleculeBatch

Return a new batch with Kekule bond assignments; source records are unchanged.

with_kekulized_bonds_with_params(options, params) → MoleculeBatch

Return a new Kekulized batch using explicit chemistry and execution parameters.

with_parallel_jobs(n_jobs=None) → MoleculeBatch

Return a new batch with the requested parallel-job setting; native validation errors propagate.

with_progress_bar(progress_bar=None) → MoleculeBatch

Return a new batch with the requested progress-display setting.

with_valid_records() → MoleculeBatch

Return a new batch containing only valid molecule records in their original order.

without_hydrogens(options: RemoveHsParams | None = None, *, errors: BatchErrorMode | str | None = None, n_jobs: SupportsIndex | None = None, progress_bar: bool | None = None) → MoleculeBatch
without_hydrogens(options: RemoveHsParams | None = None, params: BatchParams | None = None) → MoleculeBatch

Return a new batch with source-eligible hydrogen atoms removed; source records are unchanged.

without_hydrogens_with_params(options, params) → MoleculeBatch

Return a new batch with hydrogens removed using explicit chemistry and execution parameters.

write_images(directory, options=Ellipsis, *, format=Ellipsis, width=Ellipsis, height=Ellipsis, errors=Ellipsis, n_jobs=Ellipsis, progress_bar=Ellipsis, execution=Ellipsis, filenames=Ellipsis, report_path=Ellipsis) → BatchExportReport

Render batch molecules to image files using native drawing and batch-write options.

write_images_with_params(directory, options) → BatchExportReport

Render batch molecules to image files with explicit drawing and batch-write parameters.

write_sdf(path, params=None, *, format=None, errors=None, n_jobs=None, progress_bar=None, report_path=None) → BatchExportReport

Write batch records to one SDF file using native format, error and parallel options.

write_sdf_files(directory, params=None, *, format=None, errors=None, n_jobs=None, progress_bar=None, filenames=None, report_path=None) → BatchExportReport

Write separate SDF files using the native batch file-writing policy and return its write result.

write_sdf_files_with_params(directory, params, filenames, report_path) → BatchExportReport

Write separate SDF files with explicit batch-write parameters.

write_sdf_with_params(path, params, report_path) → BatchExportReport

Write batch records to one SDF file with explicit batch-write parameters.

class cosmolkit.MoleculeBuilder

Mutable construction state for assembling atoms, bonds, coordinates and metadata. build() produces a validated Molecule without consuming this Python builder.

Members (26)
add_2d_conformer(coordinates) → int

Append a two-dimensional conformer and return its identifier.

add_3d_conformer(coordinates) → int

Append a three-dimensional conformer and return its identifier.

add_atom(atom) → int

Append an atom specification and return its zero-based atom index.

add_bond(bond) → int

Append a bond specification and return its zero-based bond index; invalid endpoints raise OperationError.

add_stereo_group(group) → int

Append an enhanced stereochemistry group and return its index.

add_substance_group(group) → int

Append a substance group and return its index; native structural validation errors propagate.

atoms: list[Atom]

Independent list of detached atom values in builder order.

bond_between_atoms(begin_atom, end_atom) → int | None

Return the connecting bond index, or None when no bond connects the specified atoms.

bonds: list[Bond]

Independent list of detached bond values in builder order.

build() → Molecule

Validate and construct a Molecule while keeping this Python builder reusable.

coordinates: CoordinateBlock

Detached coordinate-block value from the builder.

degree(atom_id) → int

Return the number of neighbors of the specified atom in the current builder topology.

static from_parts(topology, coordinates, properties) → MoleculeBuilder

Initialize a builder from detached topology, coordinate and property values.

neighbor_bonds(atom_id) → list[int]

Return bond indices incident to the specified atom.

static new() → MoleculeBuilder

Create an empty molecular builder.

properties: MoleculeProperties

Detached molecule-property value from the builder.

remove_bond_between_atoms(begin_atom, end_atom) → bool

Remove a bond between the two atom indices; return whether a bond was removed.

set_2d_coordinates(coordinates) → None

Set the builder’s two-dimensional coordinates from one (x, y) pair per atom.

set_atom_formal_charge(atom_id, formal_charge) → None

Update the specified atom’s formal charge in this builder.

set_bond_order(bond_id, order) → None

Update the specified bond’s order in this builder.

stereo_groups: list[StereoGroup]

Independent list of enhanced stereochemistry-group values.

substance_groups: list[SubstanceGroup]

Independent list of substance-group values.

with_name(name) → MoleculeBuilder

Return an independent builder value with a new molecule name.

with_properties(properties) → MoleculeBuilder

Return an independent builder value with the supplied molecule properties.

with_property(key, value) → MoleculeBuilder

Return an independent builder value with the specified string property.

with_sdf_data_field(key, value) → MoleculeBuilder

Return an independent builder value with an SDF data field.

exception cosmolkit.MoleculeFragmentsError(*args, **kwargs)

MoleculeFragmentsError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property component_index: int | None

Connected-component index that failed, or None for a whole-operation failure.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property failure: MoleculeFragmentsFailure

“error_payload”} Concrete fragment failure, identical to the exception’s __cause__.

Type:

{“role”

property source: MoleculeFragmentsFailure

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.MoleculeFragmentsFailure(*args, **kwargs)

Failure in the fragments domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MoleculeFragmentsFailure is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property build: OrderedFragmentBuildError | None

“error_payload”} Structured OrderedFragmentBuildError payload of MoleculeFragmentsFailure.Build; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property component_index: int | None

Index of the disconnected component being processed. Present for MoleculeFragmentsFailure.FinalComputedProperties, MoleculeFragmentsFailure.FinalSanitize; None when unavailable. Connected-component index that failed, or None for a whole-operation failure.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: StereoGroupError | MoleculePropertyError | BondValueError | AtomPropertyError | TemplateAttachmentOrderError | AtomPathSubsetCopyError | FullCopyComponentError | SanitizeError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MoleculeFragmentsFailureKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MoleculeFragmentsFailureKind(value)

Discriminants of MoleculeFragmentsFailureKind.

Members: FinalComputedProperties, Build, FinalSanitize, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Build = MoleculeFragmentsFailureKind.Build
FinalComputedProperties = MoleculeFragmentsFailureKind.FinalComputedProperties
FinalSanitize = MoleculeFragmentsFailureKind.FinalSanitize
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'FinalComputedProperties': MoleculeFragmentsFailureKind.FinalComputedProperties, 'Build': MoleculeFragmentsFailureKind.Build, 'FinalSanitize': MoleculeFragmentsFailureKind.FinalSanitize})
values = mappingproxy({0: MoleculeFragmentsFailureKind.FinalComputedProperties, 1: MoleculeFragmentsFailureKind.Build, 2: MoleculeFragmentsFailureKind.FinalSanitize})
exception cosmolkit.MoleculeHashError(*args, **kwargs)

Failure in the hashing domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MoleculeHashError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property actual: int | None

Readonly actual payload of the RankCount error variant; None for other variants.

property atom_count: int | None

Readonly atom_count payload of the RankCount error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: CipRankError | TopologyValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MoleculeHashErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MoleculeHashErrorKind(value)

Discriminants of MoleculeHashErrorKind.

Members: EmptyMolecule, MissingPreparedValence, CipRanks, InvalidTopology, RankCount, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
CipRanks = MoleculeHashErrorKind.CipRanks
EmptyMolecule = MoleculeHashErrorKind.EmptyMolecule
InvalidTopology = MoleculeHashErrorKind.InvalidTopology
MissingPreparedValence = MoleculeHashErrorKind.MissingPreparedValence
RankCount = MoleculeHashErrorKind.RankCount
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyMolecule': MoleculeHashErrorKind.EmptyMolecule, 'MissingPreparedValence': MoleculeHashErrorKind.MissingPreparedValence, 'CipRanks': MoleculeHashErrorKind.CipRanks, 'InvalidTopology': MoleculeHashErrorKind.InvalidTopology, 'RankCount': MoleculeHashErrorKind.RankCount})
values = mappingproxy({0: MoleculeHashErrorKind.EmptyMolecule, 1: MoleculeHashErrorKind.MissingPreparedValence, 2: MoleculeHashErrorKind.CipRanks, 3: MoleculeHashErrorKind.InvalidTopology, 4: MoleculeHashErrorKind.RankCount})
class cosmolkit.MoleculeOpOutput(value)

Typed MoleculeOpOutput values corresponding to the Rust enum.

Members: Single, Multiple, LazyMultiple, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
LazyMultiple = MoleculeOpOutput.LazyMultiple
Multiple = MoleculeOpOutput.Multiple
Single = MoleculeOpOutput.Single
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Single': MoleculeOpOutput.Single, 'Multiple': MoleculeOpOutput.Multiple, 'LazyMultiple': MoleculeOpOutput.LazyMultiple})
values = mappingproxy({0: MoleculeOpOutput.Single, 1: MoleculeOpOutput.Multiple, 2: MoleculeOpOutput.LazyMultiple})
class cosmolkit.MoleculeOpSpec

Read-only operation specification generated by the canonical Rust declarations.

Members (6)
impl_fn: str

Native implementation function named by the operation declaration.

io_roundtrip: bool

Whether the operation declaration participates in IO round-trip checks.

method: str

Public Rust method name from the operation declaration.

parity: ParityPolicy

Declared comparison policy for this operation.

result_type: str

Declared operation result type.

status: FunctionStatus

Declared implementation status; this is metadata, not a report of tests run by this process.

class cosmolkit.MoleculeProperties

Detached molecular metadata, SDF fields and tagged properties. Returned containers are independent copies.

Members (7)
computed_prop_names: list[str] | None

Names recorded as computed properties, or None when no such metadata exists.

is_prop_computed(key) → bool

Whether the property is marked as computed; malformed computed-property metadata raises PropertyValueError.

name: str | None

Stored property-list name or molecular name; an absent molecular name is None.

prop(key) → PropertyValue | None

Look up a property by name; return None when absent without coercing its stored type.

props: dict[str, PropertyValue]

Independent mapping of property names to explicitly tagged values.

sdf_data_fields: list[tuple[str, str]]

Ordered SDF name/value pairs, preserving repeated names.

sdf_property_lists: list[SdfPropertyList]

Independent copies of SDF per-atom or per-bond property lists.

exception cosmolkit.MoleculePropertyError(*args, **kwargs)

Failure in the property domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MoleculePropertyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property computed_list_kind: PropertyValueError | None

“error_payload”} Structured PropertyValueError payload of MoleculePropertyError.ComputedListKind; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MoleculePropertyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MoleculePropertyErrorKind(value)

Discriminants of MoleculePropertyErrorKind.

Members: EmptyKey, ComputedListKind, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
ComputedListKind = MoleculePropertyErrorKind.ComputedListKind
EmptyKey = MoleculePropertyErrorKind.EmptyKey
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyKey': MoleculePropertyErrorKind.EmptyKey, 'ComputedListKind': MoleculePropertyErrorKind.ComputedListKind})
values = mappingproxy({0: MoleculePropertyErrorKind.EmptyKey, 1: MoleculePropertyErrorKind.ComputedListKind})
exception cosmolkit.MolPostError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MolPostError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (13)
property atom: int | None

Atom identifier implicated in the failure. Applies to MolPostError.UnsignedPropertyOverflow, MolPostError.InvalidPropertyKind, MolPostError.AttachmentValue. None when this payload is absent.

property capability: str | None

Capability required by the failing native operation. Applies to MolPostError.MissingCapability. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property field: str | None

Readonly field payload of the DataFieldNumber error variant; None for other variants.

property group: int | None

Readonly group payload of the SGroupPropertyKind error variant; None for other variants.

property kind: PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to MolPostError.InvalidPropertyKind, MolPostError.SGroupPropertyKind. None when this payload is absent.

Type:

{“role”

property property: str | None

Property name involved in the failure. Applies to MolPostError.UnsignedPropertyOverflow, MolPostError.InvalidPropertyKind, MolPostError.SGroupPropertyKind. None when this payload is absent.

property query_atom_conversion: QueryAtomConversionError | None

“error_payload”} Structured QueryAtomConversionError payload of MolPostError.QueryAtomConversion; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property representation: str | None

Representation the native operation could not support. Applies to MolPostError.Representation. None when this payload is absent.

property source: MolProcessingError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: int | str | None

Value rejected or reported by the native operation. Applies to MolPostError.UnsignedPropertyOverflow, MolPostError.AttachmentValue, MolPostError.DataFieldNumber. None when this payload is absent.

property variant: MolPostErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MolPostErrorKind(value)

Discriminants of MolPostErrorKind.

Members: MissingCapability, UnsignedPropertyOverflow, InvalidPropertyKind, AttachmentValue, SGroupPropertyKind, AttachmentExpansion, Representation, DataFieldNumber, QueryAtomConversion, Processing, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (13)
AttachmentExpansion = MolPostErrorKind.AttachmentExpansion
AttachmentValue = MolPostErrorKind.AttachmentValue
DataFieldNumber = MolPostErrorKind.DataFieldNumber
InvalidPropertyKind = MolPostErrorKind.InvalidPropertyKind
MissingCapability = MolPostErrorKind.MissingCapability
Processing = MolPostErrorKind.Processing
QueryAtomConversion = MolPostErrorKind.QueryAtomConversion
Representation = MolPostErrorKind.Representation
SGroupPropertyKind = MolPostErrorKind.SGroupPropertyKind
UnsignedPropertyOverflow = MolPostErrorKind.UnsignedPropertyOverflow
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingCapability': MolPostErrorKind.MissingCapability, 'UnsignedPropertyOverflow': MolPostErrorKind.UnsignedPropertyOverflow, 'InvalidPropertyKind': MolPostErrorKind.InvalidPropertyKind, 'AttachmentValue': MolPostErrorKind.AttachmentValue, 'SGroupPropertyKind': MolPostErrorKind.SGroupPropertyKind, 'AttachmentExpansion': MolPostErrorKind.AttachmentExpansion, 'Representation': MolPostErrorKind.Representation, 'DataFieldNumber': MolPostErrorKind.DataFieldNumber, 'QueryAtomConversion': MolPostErrorKind.QueryAtomConversion, 'Processing': MolPostErrorKind.Processing})
values = mappingproxy({0: MolPostErrorKind.MissingCapability, 1: MolPostErrorKind.UnsignedPropertyOverflow, 2: MolPostErrorKind.InvalidPropertyKind, 3: MolPostErrorKind.AttachmentValue, 4: MolPostErrorKind.SGroupPropertyKind, 5: MolPostErrorKind.AttachmentExpansion, 6: MolPostErrorKind.Representation, 7: MolPostErrorKind.DataFieldNumber, 8: MolPostErrorKind.QueryAtomConversion, 9: MolPostErrorKind.Processing})
exception cosmolkit.MolProcessingError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MolProcessingError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: PropertyIntReadError | PropertyStringError | PropertyValueError | AtomPropertyError | MoleculePropertyError | QueryAtomConversionError | QueryGraphError | QueryStateError | TopologyValidationError | TopologyEditError | BondValueError | CoordinateValidationError | StereoError | DoubleBondStereoError | BondDirectionStereoError | AtropisomerError | LegacyStereoError | ValenceError | RingFindingError | SanitizeError | HydrogenError | AttachmentExpansionError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MolProcessingErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MolProcessingErrorKind(value)

Discriminants of MolProcessingErrorKind.

Members: Valence, PropertyInt, PropertyString, Rings, Stereo, DoubleBondStereo, BondDirectionStereo, Atropisomer, Sanitize, Hydrogen, LegacyStereo, AttachmentExpansion, QueryAtom, QueryGraph, QueryState, Topology, TopologyEdit, PropertyValue, AtomProperty, BondValue, Coordinates, MoleculeProperty, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (25)
AtomProperty = MolProcessingErrorKind.AtomProperty
Atropisomer = MolProcessingErrorKind.Atropisomer
AttachmentExpansion = MolProcessingErrorKind.AttachmentExpansion
BondDirectionStereo = MolProcessingErrorKind.BondDirectionStereo
BondValue = MolProcessingErrorKind.BondValue
Coordinates = MolProcessingErrorKind.Coordinates
DoubleBondStereo = MolProcessingErrorKind.DoubleBondStereo
Hydrogen = MolProcessingErrorKind.Hydrogen
LegacyStereo = MolProcessingErrorKind.LegacyStereo
MoleculeProperty = MolProcessingErrorKind.MoleculeProperty
PropertyInt = MolProcessingErrorKind.PropertyInt
PropertyString = MolProcessingErrorKind.PropertyString
PropertyValue = MolProcessingErrorKind.PropertyValue
QueryAtom = MolProcessingErrorKind.QueryAtom
QueryGraph = MolProcessingErrorKind.QueryGraph
QueryState = MolProcessingErrorKind.QueryState
Rings = MolProcessingErrorKind.Rings
Sanitize = MolProcessingErrorKind.Sanitize
Stereo = MolProcessingErrorKind.Stereo
Topology = MolProcessingErrorKind.Topology
TopologyEdit = MolProcessingErrorKind.TopologyEdit
Valence = MolProcessingErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Valence': MolProcessingErrorKind.Valence, 'PropertyInt': MolProcessingErrorKind.PropertyInt, 'PropertyString': MolProcessingErrorKind.PropertyString, 'Rings': MolProcessingErrorKind.Rings, 'Stereo': MolProcessingErrorKind.Stereo, 'DoubleBondStereo': MolProcessingErrorKind.DoubleBondStereo, 'BondDirectionStereo': MolProcessingErrorKind.BondDirectionStereo, 'Atropisomer': MolProcessingErrorKind.Atropisomer, 'Sanitize': MolProcessingErrorKind.Sanitize, 'Hydrogen': MolProcessingErrorKind.Hydrogen, 'LegacyStereo': MolProcessingErrorKind.LegacyStereo, 'AttachmentExpansion': MolProcessingErrorKind.AttachmentExpansion, 'QueryAtom': MolProcessingErrorKind.QueryAtom, 'QueryGraph': MolProcessingErrorKind.QueryGraph, 'QueryState': MolProcessingErrorKind.QueryState, 'Topology': MolProcessingErrorKind.Topology, 'TopologyEdit': MolProcessingErrorKind.TopologyEdit, 'PropertyValue': MolProcessingErrorKind.PropertyValue, 'AtomProperty': MolProcessingErrorKind.AtomProperty, 'BondValue': MolProcessingErrorKind.BondValue, 'Coordinates': MolProcessingErrorKind.Coordinates, 'MoleculeProperty': MolProcessingErrorKind.MoleculeProperty})
values = mappingproxy({0: MolProcessingErrorKind.Valence, 1: MolProcessingErrorKind.PropertyInt, 2: MolProcessingErrorKind.PropertyString, 3: MolProcessingErrorKind.Rings, 4: MolProcessingErrorKind.Stereo, 5: MolProcessingErrorKind.DoubleBondStereo, 6: MolProcessingErrorKind.BondDirectionStereo, 7: MolProcessingErrorKind.Atropisomer, 8: MolProcessingErrorKind.Sanitize, 9: MolProcessingErrorKind.Hydrogen, 10: MolProcessingErrorKind.LegacyStereo, 11: MolProcessingErrorKind.AttachmentExpansion, 12: MolProcessingErrorKind.QueryAtom, 13: MolProcessingErrorKind.QueryGraph, 14: MolProcessingErrorKind.QueryState, 15: MolProcessingErrorKind.Topology, 16: MolProcessingErrorKind.TopologyEdit, 17: MolProcessingErrorKind.PropertyValue, 18: MolProcessingErrorKind.AtomProperty, 19: MolProcessingErrorKind.BondValue, 20: MolProcessingErrorKind.Coordinates, 21: MolProcessingErrorKind.MoleculeProperty})
exception cosmolkit.MolWriteError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MolWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (25)
property atropisomer: AtropisomerError | None

“error_payload”} Structured AtropisomerError payload of MolWriteError.Atropisomer; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property capability: str | None

Capability required by the failing native operation. Applies to MolWriteError.MissingCapability. None when this payload is absent.

property coordinates: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of MolWriteError.Coordinates; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property depict: Coordinate2DError | None

“error_payload”} Structured Coordinate2DError payload of MolWriteError.Depict; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property detached: SdfWriteError | None

“error_payload”} Structured SdfWriteError payload of MolWriteError.Detached; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property dimension: CoordinateDimension | None

Readonly dimension payload of the MissingCoordinate error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property id: int | None

Readonly id payload of the MissingCoordinate error variant; None for other variants.

property kekulize: KekulizeError | None

“error_payload”} Structured KekulizeError payload of MolWriteError.Kekulize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property property_error: PropertyValueError | None

“error_payload”} Structured PropertyValueError payload of MolWriteError.Property; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property query_atom: QueryAtomConversionError | None

“error_payload”} Structured QueryAtomConversionError payload of MolWriteError.QueryAtom; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property query_graph: QueryGraphError | None

“error_payload”} Structured QueryGraphError payload of MolWriteError.QueryGraph; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property query_smarts: SmartsWriteError | None

“error_payload”} Structured SmartsWriteError payload of MolWriteError.QuerySmarts; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property query_state: QueryStateError | None

“error_payload”} Structured QueryStateError payload of MolWriteError.QueryState; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: ValenceError | StereoGroupError | SmartsTraversalError | CoordinateValidationError | RingFindingError | WedgeError | SmilesParseError | PropertyUIntReadError | MoleculePropertyError | AtropisomerError | AtomPropertyError | PropertyIntReadError | PropertyValueError | RequiredPropertyStringError | QueryGraphError | PropertyStringError | TopologyValidationError | MappingValidationError | TemplateAttachmentOrderError | ConjugationError | HybridizationError | BondValueError | StereoOrderError | CanonicalRankError | DoubleBondStereoError | LegacyStereoError | Coordinate2DTemplateError | Coordinate2DLayoutError | UIntLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property three_d: int | None

Readonly three_d payload of the AmbiguousCoordinates error variant; None for other variants.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of MolWriteError.Topology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property two_d: int | None

Readonly two_d payload of the AmbiguousCoordinates error variant; None for other variants.

property unsigned_property: PropertyUIntReadError | None

“error_payload”} Structured PropertyUIntReadError payload of MolWriteError.UnsignedProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property unsupported_subset: str | None

Unsupported molecular output subset; None for other writer failures.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of MolWriteError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property value: str | None

Value rejected or reported by the native operation. Applies to MolWriteError.Value. None when this payload is absent.

property variant: MolWriteErrorKind

Exact Rust error variant, independent of the human-readable message.

property wedge: WedgeError | None

“error_payload”} Structured WedgeError payload of MolWriteError.Wedge; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

class cosmolkit.MolWriteErrorKind(value)

Discriminants of MolWriteErrorKind.

Members: MissingCapability, UnsupportedSubset, Value, AmbiguousCoordinates, MissingCoordinate, CoordinateDimensionMismatch, QueryGraph, QueryAtom, QueryState, QuerySmarts, Valence, Kekulize, Atropisomer, Wedge, Depict, Topology, Coordinates, Property, UnsignedProperty, Detached, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (23)
AmbiguousCoordinates = MolWriteErrorKind.AmbiguousCoordinates
Atropisomer = MolWriteErrorKind.Atropisomer
CoordinateDimensionMismatch = MolWriteErrorKind.CoordinateDimensionMismatch
Coordinates = MolWriteErrorKind.Coordinates
Depict = MolWriteErrorKind.Depict
Detached = MolWriteErrorKind.Detached
Kekulize = MolWriteErrorKind.Kekulize
MissingCapability = MolWriteErrorKind.MissingCapability
MissingCoordinate = MolWriteErrorKind.MissingCoordinate
Property = MolWriteErrorKind.Property
QueryAtom = MolWriteErrorKind.QueryAtom
QueryGraph = MolWriteErrorKind.QueryGraph
QuerySmarts = MolWriteErrorKind.QuerySmarts
QueryState = MolWriteErrorKind.QueryState
Topology = MolWriteErrorKind.Topology
UnsignedProperty = MolWriteErrorKind.UnsignedProperty
UnsupportedSubset = MolWriteErrorKind.UnsupportedSubset
Valence = MolWriteErrorKind.Valence
Value = MolWriteErrorKind.Value
Wedge = MolWriteErrorKind.Wedge
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingCapability': MolWriteErrorKind.MissingCapability, 'UnsupportedSubset': MolWriteErrorKind.UnsupportedSubset, 'Value': MolWriteErrorKind.Value, 'AmbiguousCoordinates': MolWriteErrorKind.AmbiguousCoordinates, 'MissingCoordinate': MolWriteErrorKind.MissingCoordinate, 'CoordinateDimensionMismatch': MolWriteErrorKind.CoordinateDimensionMismatch, 'QueryGraph': MolWriteErrorKind.QueryGraph, 'QueryAtom': MolWriteErrorKind.QueryAtom, 'QueryState': MolWriteErrorKind.QueryState, 'QuerySmarts': MolWriteErrorKind.QuerySmarts, 'Valence': MolWriteErrorKind.Valence, 'Kekulize': MolWriteErrorKind.Kekulize, 'Atropisomer': MolWriteErrorKind.Atropisomer, 'Wedge': MolWriteErrorKind.Wedge, 'Depict': MolWriteErrorKind.Depict, 'Topology': MolWriteErrorKind.Topology, 'Coordinates': MolWriteErrorKind.Coordinates, 'Property': MolWriteErrorKind.Property, 'UnsignedProperty': MolWriteErrorKind.UnsignedProperty, 'Detached': MolWriteErrorKind.Detached})
values = mappingproxy({0: MolWriteErrorKind.MissingCapability, 1: MolWriteErrorKind.UnsupportedSubset, 2: MolWriteErrorKind.Value, 3: MolWriteErrorKind.AmbiguousCoordinates, 4: MolWriteErrorKind.MissingCoordinate, 5: MolWriteErrorKind.CoordinateDimensionMismatch, 6: MolWriteErrorKind.QueryGraph, 7: MolWriteErrorKind.QueryAtom, 8: MolWriteErrorKind.QueryState, 9: MolWriteErrorKind.QuerySmarts, 10: MolWriteErrorKind.Valence, 11: MolWriteErrorKind.Kekulize, 12: MolWriteErrorKind.Atropisomer, 13: MolWriteErrorKind.Wedge, 14: MolWriteErrorKind.Depict, 15: MolWriteErrorKind.Topology, 16: MolWriteErrorKind.Coordinates, 17: MolWriteErrorKind.Property, 18: MolWriteErrorKind.UnsignedProperty, 19: MolWriteErrorKind.Detached})
class cosmolkit.MorganAtomInvariantsGenerator

Reusable atom-invariant provider for Morgan fingerprints.

Members (3)
static atom_pair(generator) → MorganAtomInvariantsGenerator

Create a Morgan atom provider from an independent copy of the atom-pair invariant configuration.

static connectivity(include_ring_membership=True) → MorganAtomInvariantsGenerator

Create a connectivity-invariant provider, optionally including ring membership.

static features(patterns=None) → MorganAtomInvariantsGenerator

Create a feature-invariant provider; None selects the native feature patterns.

class cosmolkit.MorganBondInvariantsGenerator(*, use_bond_types=Ellipsis, include_chirality=Ellipsis)

Explicit bond-provider inputs, captured independently of live settings.

Members (3)
include_chirality: bool

Include bond stereochemistry in bond invariants.

static new(use_bond_types=Ellipsis, include_chirality=Ellipsis) → MorganBondInvariantsGenerator

Create an independent configuration through the native constructor using the supplied field values.

use_bond_types: bool

Include bond-order information in bond invariants.

class cosmolkit.MorganCallParams(*, from_atoms=Ellipsis, ignore_atoms=Ellipsis, custom_atom_invariants=Ellipsis, custom_bond_invariants=Ellipsis)

Owned call selections. None and a present empty vector remain distinct.

Members (5)
custom_atom_invariants: tuple[int, ...] | None

Optional per-atom invariant values overriding the atom provider.

custom_bond_invariants: tuple[int, ...] | None

Optional per-bond invariant values overriding the bond provider.

from_atoms: tuple[int, ...] | None

Optional atom indices used as fingerprint centers; None uses all atoms.

ignore_atoms: tuple[int, ...] | None

Optional atom indices to exclude from fingerprint generation.

static new(from_atoms=Ellipsis, ignore_atoms=Ellipsis, custom_atom_invariants=Ellipsis, custom_bond_invariants=Ellipsis) → MorganCallParams

Create an independent configuration through the native constructor using the supplied field values.

exception cosmolkit.MorganError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MorganError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: FingerprintError | FingerprintJsonError | SmartsWriteError | AtomPairError | FingerprintWorkerError | MatrixError | ValenceError | PeriodicTableError | LegacyStereoError | MoleculePropertyError | PropertyStringError | SmartsParseError | QueryMatchContextError | SubstructMatchError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MorganErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MorganErrorKind(value)

Discriminants of MorganErrorKind.

Members: Fingerprint, Json, SmartsWrite, AtomPair, Worker, StatePoisoned, Matrix, Valence, PeriodicTable, LegacyStereo, MoleculeProperty, PropertyString, SmartsParse, QueryMatchContext, SubstructMatch, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (18)
AtomPair = MorganErrorKind.AtomPair
Fingerprint = MorganErrorKind.Fingerprint
Json = MorganErrorKind.Json
LegacyStereo = MorganErrorKind.LegacyStereo
Matrix = MorganErrorKind.Matrix
MoleculeProperty = MorganErrorKind.MoleculeProperty
PeriodicTable = MorganErrorKind.PeriodicTable
PropertyString = MorganErrorKind.PropertyString
QueryMatchContext = MorganErrorKind.QueryMatchContext
SmartsParse = MorganErrorKind.SmartsParse
SmartsWrite = MorganErrorKind.SmartsWrite
StatePoisoned = MorganErrorKind.StatePoisoned
SubstructMatch = MorganErrorKind.SubstructMatch
Valence = MorganErrorKind.Valence
Worker = MorganErrorKind.Worker
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Fingerprint': MorganErrorKind.Fingerprint, 'Json': MorganErrorKind.Json, 'SmartsWrite': MorganErrorKind.SmartsWrite, 'AtomPair': MorganErrorKind.AtomPair, 'Worker': MorganErrorKind.Worker, 'StatePoisoned': MorganErrorKind.StatePoisoned, 'Matrix': MorganErrorKind.Matrix, 'Valence': MorganErrorKind.Valence, 'PeriodicTable': MorganErrorKind.PeriodicTable, 'LegacyStereo': MorganErrorKind.LegacyStereo, 'MoleculeProperty': MorganErrorKind.MoleculeProperty, 'PropertyString': MorganErrorKind.PropertyString, 'SmartsParse': MorganErrorKind.SmartsParse, 'QueryMatchContext': MorganErrorKind.QueryMatchContext, 'SubstructMatch': MorganErrorKind.SubstructMatch})
values = mappingproxy({0: MorganErrorKind.Fingerprint, 1: MorganErrorKind.Json, 2: MorganErrorKind.SmartsWrite, 3: MorganErrorKind.AtomPair, 4: MorganErrorKind.Worker, 5: MorganErrorKind.StatePoisoned, 6: MorganErrorKind.Matrix, 7: MorganErrorKind.Valence, 8: MorganErrorKind.PeriodicTable, 9: MorganErrorKind.LegacyStereo, 10: MorganErrorKind.MoleculeProperty, 11: MorganErrorKind.PropertyString, 12: MorganErrorKind.SmartsParse, 13: MorganErrorKind.QueryMatchContext, 14: MorganErrorKind.SubstructMatch})
class cosmolkit.MorganFingerprintGenerator(params=None, atom_invariants=None, bond_invariants=None)

Reusable native Morgan fingerprint generator retaining its invariant providers and editable settings.

Members (9)
counts(molecules, num_threads=1) → list[SparseCountFingerprint32 | None]

Compute folded sparse count fingerprints in input order, retaining None entries.

fingerprints(molecules, num_threads=1) → FingerprintBatch

Compute fixed-size bit fingerprints in input order; retain None entries and use the requested native worker count.

static from_json(json) → MorganFingerprintGenerator

Restore generator configuration using the native JSON reader.

info_string() → str

Return the native summary of the generator and invariant-provider settings.

static new(params=None, atom_invariants=None, bond_invariants=None) → MorganFingerprintGenerator

Create a reusable Morgan fingerprint generator with native parameter defaults and optional invariant providers.

settings: MorganSettings

Live generator settings; edits affect subsequent calculations, not previously returned fingerprints.

sparse_counts(molecules, num_threads=1) → list[SparseCountFingerprint | None]

Compute unfolded sparse count fingerprints in input order, retaining None entries.

sparse_fingerprints(molecules, num_threads=1) → list[SparseBitFingerprint | None]

Compute sparse bit fingerprints in input order, retaining None entries.

to_json() → str

Serialize the generator configuration in its native JSON format.

class cosmolkit.MorganFingerprintParams(*, radius=Ellipsis, include_chirality=Ellipsis, use_bond_types=Ellipsis, include_ring_membership=Ellipsis, only_nonzero_invariants=Ellipsis, include_redundant_environments=Ellipsis, fp_size=Ellipsis, count_simulation=Ellipsis, count_bounds=Ellipsis, bits_per_feature=Ellipsis, from_atoms=Ellipsis, ignore_atoms=Ellipsis, custom_atom_invariants=Ellipsis, custom_bond_invariants=Ellipsis, invariants=Ellipsis)

Configuration shared by the four read-only Morgan fingerprint methods.

Optional vectors preserve None separately from Some(Vec::new()) and are borrowed when projected into the fingerprint owner’s call arguments.

Members (15)
bits_per_feature: int

Number of hash-derived positions generated for each environment.

count_bounds: tuple[int, ...]

Occurrence thresholds used when count simulation is enabled.

count_simulation: bool

Encode occurrence-count thresholds as separate bits in bit fingerprints.

custom_atom_invariants: tuple[int, ...] | None

Optional caller-supplied atom invariants.

custom_bond_invariants: tuple[int, ...] | None

Optional caller-supplied bond invariants.

fp_size: int

Number of positions in folded fingerprints; does not limit sparse identifiers.

from_atoms: tuple[int, ...] | None

Source atom indices at which to start fingerprint expansion.

ignore_atoms: tuple[int, ...] | None

Source atom indices to ignore.

include_chirality: bool

Include stereochemical information in environment identifiers.

include_redundant_environments: bool

Retain environments otherwise removed as redundant during expansion.

include_ring_membership: bool

Include ring membership in default connectivity atom invariants.

invariants: MorganInvariants

Atom invariant generation policy.

only_nonzero_invariants: bool

Generate environments only from atoms with nonzero initial invariants.

radius: int

Maximum number of bonds through which each atom environment is expanded.

use_bond_types: bool

Distinguish bond types when constructing environment identifiers.

class cosmolkit.MorganGeneratorParams(*, radius=Ellipsis, include_chirality=Ellipsis, use_bond_types=Ellipsis, include_ring_membership=Ellipsis, only_nonzero_invariants=Ellipsis, include_redundant_environments=Ellipsis, fp_size=Ellipsis, count_simulation=Ellipsis, count_bounds=Ellipsis, bits_per_feature=Ellipsis)

Morgan-specific and shared fingerprint generator options.

This type is defined inside the private morgan module. Public visibility here supports the frozen detached owner signature without exposing a new root, runtime, or binding API.

Members (13)
bits_per_feature: int

Number of hash-derived positions generated for each environment.

count_bounds: tuple[int, ...]

Occurrence thresholds used when count simulation is enabled.

count_simulation: bool

Encode occurrence-count thresholds as separate bits in bit fingerprints.

fp_size: int

Number of positions in folded fingerprints; does not limit sparse identifiers.

include_chirality: bool

Include stereochemical information in environment identifiers.

include_redundant_environments: bool

Retain environments otherwise removed as redundant during expansion.

include_ring_membership: bool

Include ring membership in default connectivity atom invariants.

info_string() → str

Return the native human-readable fingerprint generator settings summary.

only_nonzero_invariants: bool

Generate environments only from atoms with nonzero initial invariants.

radius: int

Maximum number of bonds through which each atom environment is expanded.

to_json() → str

Serialize generator parameters with the native JSON format.

use_bond_types: bool

Distinguish bond types when constructing environment identifiers.

with_json(json) → MorganGeneratorParams

Return an independent configuration updated by the native JSON parser.

class cosmolkit.MorganInvariants

Morgan atom-invariant selection: connectivity, standard features, or supplied feature query patterns.

Members (3)
Connectivity = <cosmolkit.MorganInvariants object>
static FeaturePatterns(patterns) → MorganInvariants

Use the supplied query patterns to define atom-feature invariants.

Features = <cosmolkit.MorganInvariants object>
exception cosmolkit.MorganReadError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

MorganReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: FingerprintPreparationError | MorganError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: MorganReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.MorganReadErrorKind(value)

Discriminants of MorganReadErrorKind.

Members: Preparation, Generator, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Generator = MorganReadErrorKind.Generator
Preparation = MorganReadErrorKind.Preparation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Preparation': MorganReadErrorKind.Preparation, 'Generator': MorganReadErrorKind.Generator})
values = mappingproxy({0: MorganReadErrorKind.Preparation, 1: MorganReadErrorKind.Generator})
class cosmolkit.MorganSettings

Live view of generator configuration. Property assignments update the owning generator.

Members (17)
bits_per_feature: int

Number of bits generated per feature.

count_bounds: list[int]

Occurrence thresholds used for count simulation.

count_simulation: bool

Encode feature occurrence thresholds as simulated count bits.

fp_size: int

Number of bits in folded bit fingerprints.

include_chirality: bool

Encode stereochemical information in the generated fingerprint.

include_redundant_environments: bool

Include otherwise redundant atom environments.

only_nonzero_invariants: bool

Restrict center atoms to those with nonzero invariants.

params: MorganGeneratorParams

Independent snapshot of the generator parameters; editing it does not change this generator.

radius: int

Maximum Morgan environment radius in bonds.

set_bits_per_feature(value) → None

Update the generator’s bits_per_feature setting; see the corresponding property for its meaning.

set_count_bounds(value) → None

Update the generator’s count_bounds setting; see the corresponding property for its meaning.

set_count_simulation(value) → None

Update the generator’s count_simulation setting; see the corresponding property for its meaning.

set_fp_size(value) → None

Update the generator’s fp_size setting; see the corresponding property for its meaning.

set_include_chirality(value) → None

Update the generator’s include_chirality setting; see the corresponding property for its meaning.

set_include_redundant_environments(value) → None

Update the generator’s include_redundant_environments setting; see the corresponding property for its meaning.

set_only_nonzero_invariants(value) → None

Update the generator’s only_nonzero_invariants setting; see the corresponding property for its meaning.

set_radius(value) → None

Update the generator’s radius setting; see the corresponding property for its meaning.

exception cosmolkit.NonbondedAssemblyError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

NonbondedAssemblyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: NonbondedFragmentMappingError | UffBuilderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: NonbondedAssemblyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.NonbondedAssemblyErrorKind(value)

Discriminants of NonbondedAssemblyErrorKind.

Members: FragmentMapping, PairBuilder, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
FragmentMapping = NonbondedAssemblyErrorKind.FragmentMapping
PairBuilder = NonbondedAssemblyErrorKind.PairBuilder
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'FragmentMapping': NonbondedAssemblyErrorKind.FragmentMapping, 'PairBuilder': NonbondedAssemblyErrorKind.PairBuilder})
values = mappingproxy({0: NonbondedAssemblyErrorKind.FragmentMapping, 1: NonbondedAssemblyErrorKind.PairBuilder})
exception cosmolkit.NonbondedFragmentMappingError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

NonbondedFragmentMappingError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (9)
property atom_count: int | None

Readonly atom_count payload of the AtomOutOfRange error variant; None for other variants.

property atom_index: int | None

Atom index involved in the native failure. Applies to NonbondedFragmentMappingError.AtomOutOfRange, NonbondedFragmentMappingError.DuplicateAtom, NonbondedFragmentMappingError.MissingAtom. None when this payload is absent.

property component_index: int | None

Readonly component_index payload of the AtomOutOfRange error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property first_component: int | None

Readonly first_component payload of the DuplicateAtom error variant; None for other variants.

property second_component: int | None

Readonly second_component payload of the DuplicateAtom error variant; None for other variants.

property source: MoleculeFragmentsError | FragmentCoordinateViewError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: NonbondedFragmentMappingErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.NonbondedFragmentMappingErrorKind(value)

Discriminants of NonbondedFragmentMappingErrorKind.

Members: FragmentCopy, CoordinateView, RequestedMappingMissing, AtomOutOfRange, DuplicateAtom, MissingAtom, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
AtomOutOfRange = NonbondedFragmentMappingErrorKind.AtomOutOfRange
CoordinateView = NonbondedFragmentMappingErrorKind.CoordinateView
DuplicateAtom = NonbondedFragmentMappingErrorKind.DuplicateAtom
FragmentCopy = NonbondedFragmentMappingErrorKind.FragmentCopy
MissingAtom = NonbondedFragmentMappingErrorKind.MissingAtom
RequestedMappingMissing = NonbondedFragmentMappingErrorKind.RequestedMappingMissing
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'FragmentCopy': NonbondedFragmentMappingErrorKind.FragmentCopy, 'CoordinateView': NonbondedFragmentMappingErrorKind.CoordinateView, 'RequestedMappingMissing': NonbondedFragmentMappingErrorKind.RequestedMappingMissing, 'AtomOutOfRange': NonbondedFragmentMappingErrorKind.AtomOutOfRange, 'DuplicateAtom': NonbondedFragmentMappingErrorKind.DuplicateAtom, 'MissingAtom': NonbondedFragmentMappingErrorKind.MissingAtom})
values = mappingproxy({0: NonbondedFragmentMappingErrorKind.FragmentCopy, 1: NonbondedFragmentMappingErrorKind.CoordinateView, 2: NonbondedFragmentMappingErrorKind.RequestedMappingMissing, 3: NonbondedFragmentMappingErrorKind.AtomOutOfRange, 4: NonbondedFragmentMappingErrorKind.DuplicateAtom, 5: NonbondedFragmentMappingErrorKind.MissingAtom})
class cosmolkit.OperationCipStatePolicy

Read-only CIP state policy from an operation contract failure.

Members (1)
discriminant: int

Integer discriminant of the declared CIP state policy.

class cosmolkit.OperationDerivedState

Read-only derived-state mask from an operation contract failure.

Members (1)
bits: int

Bit mask of derived molecular states involved in this contract failure.

exception cosmolkit.OperationError(*args, **kwargs)

Failure in the operation domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

OperationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (60)
property action: str | None

Readonly action payload of the DerivedEffectContract error variant; None for other variants.

property actual: int | str | MoleculeOpOutput | None

“error_payload”} Observed value reported by the native check. Applies to OperationError.InvalidDerivedCache, OperationError.InvalidAlgorithmResult, OperationError.OperationContract, OperationError.DerivedPreservationMismatch, OperationError.OutputMismatch. None when this payload is absent.

Type:

{“role”

property alignment: AlignmentError | None

“error_payload”} Structured native error payload. Present for OperationError.Alignment; None when unavailable.

Type:

{“role”

property aromaticity: AromaticityError | None

“error_payload”} Structured native error payload. Present for OperationError.Aromaticity; None when unavailable.

Type:

{“role”

property atom: int | None

Readonly atom payload of the AtomPropertyIndex error variant; None for other variants.

property atom_code: AtomCodeError | None

“error_payload”} Structured native error payload. Present for OperationError.AtomCode; None when unavailable.

Type:

{“role”

property atom_count: int | None

Readonly atom_count payload of the AtomPropertyIndex error variant; None for other variants.

property atom_property: AtomPropertyError | None

“error_payload”} Structured native error payload. Present for OperationError.AtomProperty; None when unavailable.

Type:

{“role”

property block: str | None

Input or structural block involved in the failure. Applies to OperationError.AccessDenied, OperationError.BlockCheckedOut, OperationError.BlockNotCheckedOut, OperationError.IncompleteCommit, OperationError.AutoRemapContract. None when this payload is absent.

property bond_property: BondValueError | None

“error_payload”} Structured native error payload. Present for OperationError.BondProperty; None when unavailable.

Type:

{“role”

property cause: MoleculeFragmentsError | ScaffoldError | ReactionRunError | ReactionApplyError | EnumerationRunError | AlignmentError | ConformerRunError | TautomerRunError | TopologyValidationError | TopologyEditError | CoordinateValidationError | MoleculePropertyError | AtomPropertyError | BondValueError | ValenceError | RadicalError | RingFindingError | PotentialStereoError | StereoError | CipLabelerError | AtomCodeError | TransformError | CoordinateInputError | Coordinate2DError | UffOptimizationError | MmffOptimizationError | KekulizeError | AromaticityError | SanitizeError | HydrogenError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property cip_labeler: CipLabelerError | None

“error_payload”} Structured native error payload. Present for OperationError.CipLabeler; None when unavailable.

Type:

{“role”

property conformer: ConformerRunError | None

“error_payload”} Structured native error payload. Present for OperationError.Conformer; None when unavailable.

Type:

{“role”

property coordinate2_d: Coordinate2DError | None

“error_payload”} Structured native error payload. Present for OperationError.Coordinate2D; None when unavailable.

Type:

{“role”

property coordinate_input: CoordinateInputError | None

“error_payload”} Structured native error payload. Present for OperationError.CoordinateInput; None when unavailable.

Type:

{“role”

property destination: int | None

Readonly destination payload of the InvalidReconstructionOrigin error variant; None for other variants.

property detail: str | None

Readonly detail payload of the Algorithm error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property entity: str | None

Readonly entity payload of the InvalidReconstructionOrigin error variant; None for other variants.

property enumeration: EnumerationRunError | None

“error_payload”} Structured native error payload. Present for OperationError.Enumeration; None when unavailable.

Type:

{“role”

property expected: int | str | MoleculeOpOutput | None

“error_payload”} Required value reported by the native check. Applies to OperationError.InvalidDerivedCache, OperationError.InvalidAlgorithmResult, OperationError.InvalidPropertyList, OperationError.OperationContract, OperationError.DerivedPreservationMismatch, OperationError.OutputMismatch. None when this payload is absent.

Type:

{“role”

property field: str | None

Field whose content or type caused the failure. Applies to OperationError.DerivedPreservationMismatch, OperationError.OperationContract, OperationError.InvalidDerivedCache, OperationError.InvalidAlgorithmResult. None when this payload is absent.

property fragments: MoleculeFragmentsError | None

“error_payload”} Structured native error payload. Present for OperationError.Fragments; None when unavailable.

Type:

{“role”

property hydrogen: HydrogenError | None

“error_payload”} Structured native error payload. Present for OperationError.Hydrogen; None when unavailable.

Type:

{“role”

property input: int | None

Readonly input payload of the InvalidReconstructionOrigin error variant; None for other variants.

property input_count: int | None

Readonly input_count payload of the InvalidReconstructionOrigin error variant; None for other variants.

property invalid_coordinates: CoordinateValidationError | None

“error_payload”} Structured native error payload. Present for OperationError.InvalidCoordinates; None when unavailable.

Type:

{“role”

property invalid_property: MoleculePropertyError | None

“error_payload”} Structured native error payload. Present for OperationError.InvalidProperty; None when unavailable.

Type:

{“role”

property invalid_topology: TopologyValidationError | None

“error_payload”} Structured native error payload. Present for OperationError.InvalidTopology; None when unavailable.

Type:

{“role”

property invalid_topology_edit: TopologyEditError | None

“error_payload”} Structured native error payload. Present for OperationError.InvalidTopologyEdit; None when unavailable.

Type:

{“role”

property issue: str | None

Description of the violated operation contract. Present for OperationError.MappingContract, OperationError.AutoRemapContract, OperationError.OperationContract, OperationError.SemanticPreconditionContract, OperationError.DerivedEffectContract, OperationError.CipStateContract; None when unavailable.

property kekulize: KekulizeError | None

“error_payload”} Structured native error payload. Present for OperationError.Kekulize; None when unavailable.

Type:

{“role”

property key: str | None

Readonly key payload of the ReservedAtomPropertyKey error variant; None for other variants.

property missing: OperationSemanticPreconditions | None

“error_payload”} Semantic preconditions missing for this operation. Present for OperationError.SemanticPreconditionContract; None when unavailable.

Type:

{“role”

property mmff_optimization: MmffOptimizationError | None

“error_payload”} Structured native error payload. Present for OperationError.MmffOptimization; None when unavailable.

Type:

{“role”

property name: str | None

Name associated with the rejected value or property list. Applies to OperationError.InvalidPropertyList. None when this payload is absent.

property operation: str | MoleculeOpSpec | None

“error_payload”} Operation name or registered operation descriptor reporting the failure. Present for OperationError.UnsupportedFeature, OperationError.Unsupported, OperationError.OutputMismatch, OperationError.AccessDenied, OperationError.BlockCheckedOut, OperationError.BlockNotCheckedOut, OperationError.IncompleteCommit, OperationError.MappingContract, OperationError.InvalidTopologyMapping, OperationError.AutoRemapContract, OperationError.OperationContract, OperationError.SemanticPreconditionContract, OperationError.CoordinateAppendRequiresValues, OperationError.DerivedEffectContract, OperationError.DerivedPreservationMismatch, OperationError.CipStateContract, OperationError.InvalidAlgorithmResult, OperationError.InvalidReconstructionOrigin, OperationError.Algorithm; None when unavailable.

Type:

{“role”

property policy: OperationCipStatePolicy | None

“error_payload”} CIP state policy governing this operation. Present for OperationError.CipStateContract; None when unavailable.

Type:

{“role”

property potential_stereo: PotentialStereoError | None

“error_payload”} Structured native error payload. Present for OperationError.PotentialStereo; None when unavailable.

Type:

{“role”

property radical: RadicalError | None

“error_payload”} Structured native error payload. Present for OperationError.Radical; None when unavailable.

Type:

{“role”

property reaction_apply: ReactionApplyError | None

“error_payload”} Structured native error payload. Present for OperationError.ReactionApply; None when unavailable.

Type:

{“role”

property reaction_run: ReactionRunError | None

“error_payload”} Structured native error payload. Present for OperationError.ReactionRun; None when unavailable.

Type:

{“role”

property requirement: OperationMappingRequirement | None

“error_payload”} Topology-mapping requirement declared for this operation. Present for OperationError.MappingContract; None when unavailable.

Type:

{“role”

property rings: RingFindingError | None

“error_payload”} Structured native error payload. Present for OperationError.Rings; None when unavailable.

Type:

{“role”

property row: int | None

Readonly row payload of the InvalidReconstructionOrigin error variant; None for other variants.

property row_count: int | None

Readonly row_count payload of the InvalidReconstructionOrigin error variant; None for other variants.

property sanitize: SanitizeError | None

“error_payload”} Structured native error payload. Present for OperationError.Sanitize; None when unavailable.

Type:

{“role”

property scaffold: ScaffoldError | None

“error_payload”} Structured native error payload. Present for OperationError.Scaffold; None when unavailable.

Type:

{“role”

property source: UnsupportedFeatureError | MappingValidationError | None

“error_payload”} Structured native error payload. Present for OperationError.UnsupportedFeature, OperationError.InvalidTopologyMapping; None when unavailable.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property state: str | None

Readonly state payload of the InvalidDerivedCache error variant; None for other variants.

property states: OperationDerivedState | None

“error_payload”} Expected and observed derived-state information. Present for OperationError.DerivedEffectContract, OperationError.DerivedPreservationMismatch; None when unavailable.

Type:

{“role”

property stereo: StereoError | None

“error_payload”} Structured native error payload. Present for OperationError.Stereo; None when unavailable.

Type:

{“role”

property target: str | None

Readonly target payload of the InvalidPropertyList error variant; None for other variants.

property tautomer: TautomerRunError | None

“error_payload”} Structured native error payload. Present for OperationError.Tautomer; None when unavailable.

Type:

{“role”

property transform: TransformError | None

“error_payload”} Structured native error payload. Present for OperationError.Transform; None when unavailable.

Type:

{“role”

property uff_optimization: UffOptimizationError | None

“error_payload”} Structured native error payload. Present for OperationError.UffOptimization; None when unavailable.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Valence value rejected by the native check. Applies to OperationError.Valence. None when this payload is absent.

Type:

{“role”

property values: int | None

Readonly values payload of the InvalidPropertyList error variant; None for other variants.

property variant: OperationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.OperationErrorKind(value)

Discriminants of OperationErrorKind.

Members: AtomPropertyIndex, ReservedAtomPropertyKey, Fragments, Scaffold, ReactionRun, ReactionApply, Enumeration, Alignment, Conformer, Tautomer, InvalidTopology, InvalidTopologyEdit, InvalidCoordinates, InvalidProperty, AtomProperty, BondProperty, Valence, Radical, Rings, PotentialStereo, Stereo, CipLabeler, AtomCode, Transform, CoordinateInput, Coordinate2D, UffOptimization, MmffOptimization, Kekulize, Aromaticity, Sanitize, Hydrogen, EmptyFragments, UnsupportedFeature, Unsupported, OutputMismatch, AccessDenied, BlockCheckedOut, BlockNotCheckedOut, IncompleteCommit, MappingContract, InvalidTopologyMapping, AutoRemapContract, OperationContract, SemanticPreconditionContract, CoordinateAppendRequiresValues, DerivedEffectContract, DerivedPreservationMismatch, CipStateContract, InvalidPropertyList, InvalidDerivedCache, InvalidAlgorithmResult, InvalidReconstructionOrigin, Algorithm, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (57)
AccessDenied = OperationErrorKind.AccessDenied
Algorithm = OperationErrorKind.Algorithm
Alignment = OperationErrorKind.Alignment
Aromaticity = OperationErrorKind.Aromaticity
AtomCode = OperationErrorKind.AtomCode
AtomProperty = OperationErrorKind.AtomProperty
AtomPropertyIndex = OperationErrorKind.AtomPropertyIndex
AutoRemapContract = OperationErrorKind.AutoRemapContract
BlockCheckedOut = OperationErrorKind.BlockCheckedOut
BlockNotCheckedOut = OperationErrorKind.BlockNotCheckedOut
BondProperty = OperationErrorKind.BondProperty
CipLabeler = OperationErrorKind.CipLabeler
CipStateContract = OperationErrorKind.CipStateContract
Conformer = OperationErrorKind.Conformer
Coordinate2D = OperationErrorKind.Coordinate2D
CoordinateAppendRequiresValues = OperationErrorKind.CoordinateAppendRequiresValues
CoordinateInput = OperationErrorKind.CoordinateInput
DerivedEffectContract = OperationErrorKind.DerivedEffectContract
DerivedPreservationMismatch = OperationErrorKind.DerivedPreservationMismatch
EmptyFragments = OperationErrorKind.EmptyFragments
Enumeration = OperationErrorKind.Enumeration
Fragments = OperationErrorKind.Fragments
Hydrogen = OperationErrorKind.Hydrogen
IncompleteCommit = OperationErrorKind.IncompleteCommit
InvalidAlgorithmResult = OperationErrorKind.InvalidAlgorithmResult
InvalidCoordinates = OperationErrorKind.InvalidCoordinates
InvalidDerivedCache = OperationErrorKind.InvalidDerivedCache
InvalidProperty = OperationErrorKind.InvalidProperty
InvalidPropertyList = OperationErrorKind.InvalidPropertyList
InvalidReconstructionOrigin = OperationErrorKind.InvalidReconstructionOrigin
InvalidTopology = OperationErrorKind.InvalidTopology
InvalidTopologyEdit = OperationErrorKind.InvalidTopologyEdit
InvalidTopologyMapping = OperationErrorKind.InvalidTopologyMapping
Kekulize = OperationErrorKind.Kekulize
MappingContract = OperationErrorKind.MappingContract
MmffOptimization = OperationErrorKind.MmffOptimization
OperationContract = OperationErrorKind.OperationContract
OutputMismatch = OperationErrorKind.OutputMismatch
PotentialStereo = OperationErrorKind.PotentialStereo
Radical = OperationErrorKind.Radical
ReactionApply = OperationErrorKind.ReactionApply
ReactionRun = OperationErrorKind.ReactionRun
ReservedAtomPropertyKey = OperationErrorKind.ReservedAtomPropertyKey
Rings = OperationErrorKind.Rings
Sanitize = OperationErrorKind.Sanitize
Scaffold = OperationErrorKind.Scaffold
SemanticPreconditionContract = OperationErrorKind.SemanticPreconditionContract
Stereo = OperationErrorKind.Stereo
Tautomer = OperationErrorKind.Tautomer
Transform = OperationErrorKind.Transform
UffOptimization = OperationErrorKind.UffOptimization
Unsupported = OperationErrorKind.Unsupported
UnsupportedFeature = OperationErrorKind.UnsupportedFeature
Valence = OperationErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'AtomPropertyIndex': OperationErrorKind.AtomPropertyIndex, 'ReservedAtomPropertyKey': OperationErrorKind.ReservedAtomPropertyKey, 'Fragments': OperationErrorKind.Fragments, 'Scaffold': OperationErrorKind.Scaffold, 'ReactionRun': OperationErrorKind.ReactionRun, 'ReactionApply': OperationErrorKind.ReactionApply, 'Enumeration': OperationErrorKind.Enumeration, 'Alignment': OperationErrorKind.Alignment, 'Conformer': OperationErrorKind.Conformer, 'Tautomer': OperationErrorKind.Tautomer, 'InvalidTopology': OperationErrorKind.InvalidTopology, 'InvalidTopologyEdit': OperationErrorKind.InvalidTopologyEdit, 'InvalidCoordinates': OperationErrorKind.InvalidCoordinates, 'InvalidProperty': OperationErrorKind.InvalidProperty, 'AtomProperty': OperationErrorKind.AtomProperty, 'BondProperty': OperationErrorKind.BondProperty, 'Valence': OperationErrorKind.Valence, 'Radical': OperationErrorKind.Radical, 'Rings': OperationErrorKind.Rings, 'PotentialStereo': OperationErrorKind.PotentialStereo, 'Stereo': OperationErrorKind.Stereo, 'CipLabeler': OperationErrorKind.CipLabeler, 'AtomCode': OperationErrorKind.AtomCode, 'Transform': OperationErrorKind.Transform, 'CoordinateInput': OperationErrorKind.CoordinateInput, 'Coordinate2D': OperationErrorKind.Coordinate2D, 'UffOptimization': OperationErrorKind.UffOptimization, 'MmffOptimization': OperationErrorKind.MmffOptimization, 'Kekulize': OperationErrorKind.Kekulize, 'Aromaticity': OperationErrorKind.Aromaticity, 'Sanitize': OperationErrorKind.Sanitize, 'Hydrogen': OperationErrorKind.Hydrogen, 'EmptyFragments': OperationErrorKind.EmptyFragments, 'UnsupportedFeature': OperationErrorKind.UnsupportedFeature, 'Unsupported': OperationErrorKind.Unsupported, 'OutputMismatch': OperationErrorKind.OutputMismatch, 'AccessDenied': OperationErrorKind.AccessDenied, 'BlockCheckedOut': OperationErrorKind.BlockCheckedOut, 'BlockNotCheckedOut': OperationErrorKind.BlockNotCheckedOut, 'IncompleteCommit': OperationErrorKind.IncompleteCommit, 'MappingContract': OperationErrorKind.MappingContract, 'InvalidTopologyMapping': OperationErrorKind.InvalidTopologyMapping, 'AutoRemapContract': OperationErrorKind.AutoRemapContract, 'OperationContract': OperationErrorKind.OperationContract, 'SemanticPreconditionContract': OperationErrorKind.SemanticPreconditionContract, 'CoordinateAppendRequiresValues': OperationErrorKind.CoordinateAppendRequiresValues, 'DerivedEffectContract': OperationErrorKind.DerivedEffectContract, 'DerivedPreservationMismatch': OperationErrorKind.DerivedPreservationMismatch, 'CipStateContract': OperationErrorKind.CipStateContract, 'InvalidPropertyList': OperationErrorKind.InvalidPropertyList, 'InvalidDerivedCache': OperationErrorKind.InvalidDerivedCache, 'InvalidAlgorithmResult': OperationErrorKind.InvalidAlgorithmResult, 'InvalidReconstructionOrigin': OperationErrorKind.InvalidReconstructionOrigin, 'Algorithm': OperationErrorKind.Algorithm})
values = mappingproxy({0: OperationErrorKind.AtomPropertyIndex, 1: OperationErrorKind.ReservedAtomPropertyKey, 2: OperationErrorKind.Fragments, 3: OperationErrorKind.Scaffold, 4: OperationErrorKind.ReactionRun, 5: OperationErrorKind.ReactionApply, 6: OperationErrorKind.Enumeration, 7: OperationErrorKind.Alignment, 8: OperationErrorKind.Conformer, 9: OperationErrorKind.Tautomer, 10: OperationErrorKind.InvalidTopology, 11: OperationErrorKind.InvalidTopologyEdit, 12: OperationErrorKind.InvalidCoordinates, 13: OperationErrorKind.InvalidProperty, 14: OperationErrorKind.AtomProperty, 15: OperationErrorKind.BondProperty, 16: OperationErrorKind.Valence, 17: OperationErrorKind.Radical, 18: OperationErrorKind.Rings, 19: OperationErrorKind.PotentialStereo, 20: OperationErrorKind.Stereo, 21: OperationErrorKind.CipLabeler, 22: OperationErrorKind.AtomCode, 23: OperationErrorKind.Transform, 24: OperationErrorKind.CoordinateInput, 25: OperationErrorKind.Coordinate2D, 26: OperationErrorKind.UffOptimization, 27: OperationErrorKind.MmffOptimization, 28: OperationErrorKind.Kekulize, 29: OperationErrorKind.Aromaticity, 30: OperationErrorKind.Sanitize, 31: OperationErrorKind.Hydrogen, 32: OperationErrorKind.EmptyFragments, 33: OperationErrorKind.UnsupportedFeature, 34: OperationErrorKind.Unsupported, 35: OperationErrorKind.OutputMismatch, 36: OperationErrorKind.AccessDenied, 37: OperationErrorKind.BlockCheckedOut, 38: OperationErrorKind.BlockNotCheckedOut, 39: OperationErrorKind.IncompleteCommit, 40: OperationErrorKind.MappingContract, 41: OperationErrorKind.InvalidTopologyMapping, 42: OperationErrorKind.AutoRemapContract, 43: OperationErrorKind.OperationContract, 44: OperationErrorKind.SemanticPreconditionContract, 45: OperationErrorKind.CoordinateAppendRequiresValues, 46: OperationErrorKind.DerivedEffectContract, 47: OperationErrorKind.DerivedPreservationMismatch, 48: OperationErrorKind.CipStateContract, 49: OperationErrorKind.InvalidPropertyList, 50: OperationErrorKind.InvalidDerivedCache, 51: OperationErrorKind.InvalidAlgorithmResult, 52: OperationErrorKind.InvalidReconstructionOrigin, 53: OperationErrorKind.Algorithm})
class cosmolkit.OperationInvariantEntry

Operation and its declared invariant validation profile.

Members (2)
operation: MoleculeOpSpec

Molecule operation whose invariant profile is described by this entry.

profile: str

Declared invariant or parity profile identifier.

class cosmolkit.OperationMappingRequirement

Read-only topology mapping requirement from an operation contract failure.

Members (1)
discriminant: int

Integer discriminant of the operation’s mapping requirement.

class cosmolkit.OperationSemanticPreconditions

Read-only mask of semantic preconditions missing for an operation.

Members (1)
bits: int

Bit mask of missing semantic preconditions.

class cosmolkit.OptimizationOutcome

Force-field optimization status with an energy only when parameters and an evaluated outcome are available.

Members (8)
converged: bool

Whether the optimizer reached its convergence criteria.

static converged_with_energy(energy) → OptimizationOutcome

Construct a converged outcome with its evaluated energy.

energy: float | None

Evaluated force-field energy; optimization outcomes without parameters return None.

static missing_parameters() → OptimizationOutcome

Construct an outcome indicating that required force-field parameters were unavailable.

needs_more: bool

Whether the native outcome reports nonconvergence requiring further optimization.

static not_converged_with_energy(energy) → OptimizationOutcome

Construct a nonconverged outcome retaining its last evaluated energy.

status: OptimizationStatus

converged, not converged or missing parameters.

Type:

Typed optimization status

status_code: int

Native optimization status code corresponding to the typed outcome.

exception cosmolkit.OptimizationStageError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

OptimizationStageError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: ForceFieldKernelError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: OptimizationStageErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.OptimizationStageErrorKind(value)

Discriminants of OptimizationStageErrorKind.

Members: Initialize, Minimize, FinalEnergy, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
FinalEnergy = OptimizationStageErrorKind.FinalEnergy
Initialize = OptimizationStageErrorKind.Initialize
Minimize = OptimizationStageErrorKind.Minimize
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Initialize': OptimizationStageErrorKind.Initialize, 'Minimize': OptimizationStageErrorKind.Minimize, 'FinalEnergy': OptimizationStageErrorKind.FinalEnergy})
values = mappingproxy({0: OptimizationStageErrorKind.Initialize, 1: OptimizationStageErrorKind.Minimize, 2: OptimizationStageErrorKind.FinalEnergy})
class cosmolkit.OptimizationStatus(value)

Typed OptimizationStatus values corresponding to the Rust enum.

Members: Converged, NotConverged, MissingParameters, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
Converged = OptimizationStatus.Converged
MissingParameters = OptimizationStatus.MissingParameters
NotConverged = OptimizationStatus.NotConverged
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Converged': OptimizationStatus.Converged, 'NotConverged': OptimizationStatus.NotConverged, 'MissingParameters': OptimizationStatus.MissingParameters})
values = mappingproxy({0: OptimizationStatus.Converged, 1: OptimizationStatus.NotConverged, 2: OptimizationStatus.MissingParameters})
exception cosmolkit.OrderedFragmentBuildError(*args, **kwargs)

Failure in the fragments domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

OrderedFragmentBuildError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property component_index: int | None

Component index reported by the native failure. Applies to OrderedFragmentBuildError.FastSubset, OrderedFragmentBuildError.SlowFullCopy. None when this payload is absent. Connected-component index that failed, or None for a whole-operation failure.

property component_labels: PathError | None

“error_payload”} Structured PathError payload of OrderedFragmentBuildError.ComponentLabels; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: StereoGroupError | MoleculePropertyError | BondValueError | AtomPropertyError | TemplateAttachmentOrderError | AtomPathSubsetCopyError | FullCopyComponentError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: OrderedFragmentBuildErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.OrderedFragmentBuildErrorKind(value)

Discriminants of OrderedFragmentBuildErrorKind.

Members: ComponentLabels, FastSubset, SlowFullCopy, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
ComponentLabels = OrderedFragmentBuildErrorKind.ComponentLabels
FastSubset = OrderedFragmentBuildErrorKind.FastSubset
SlowFullCopy = OrderedFragmentBuildErrorKind.SlowFullCopy
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ComponentLabels': OrderedFragmentBuildErrorKind.ComponentLabels, 'FastSubset': OrderedFragmentBuildErrorKind.FastSubset, 'SlowFullCopy': OrderedFragmentBuildErrorKind.SlowFullCopy})
values = mappingproxy({0: OrderedFragmentBuildErrorKind.ComponentLabels, 1: OrderedFragmentBuildErrorKind.FastSubset, 2: OrderedFragmentBuildErrorKind.SlowFullCopy})
class cosmolkit.ParityMatrixEntry

Operation, feature and reference profile in the generated parity matrix.

Members (4)
feature: FeatureSpec

Public feature declaration associated with this matrix entry.

operation: MoleculeOpSpec

Associated molecule operation; None when a support entry does not name an operation.

profile: str

Declared invariant or parity profile identifier.

rdkit_version: str | None

RDKit reference version recorded for this parity entry, or None if unspecified.

class cosmolkit.ParityPolicy(value)

Typed ParityPolicy values corresponding to the Rust enum.

Members: NotApplicable, RequiredWhenSupported, RequiredNow, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
NotApplicable = ParityPolicy.NotApplicable
RequiredNow = ParityPolicy.RequiredNow
RequiredWhenSupported = ParityPolicy.RequiredWhenSupported
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NotApplicable': ParityPolicy.NotApplicable, 'RequiredWhenSupported': ParityPolicy.RequiredWhenSupported, 'RequiredNow': ParityPolicy.RequiredNow})
values = mappingproxy({0: ParityPolicy.NotApplicable, 1: ParityPolicy.RequiredWhenSupported, 2: ParityPolicy.RequiredNow})
exception cosmolkit.ParseFloatError(*args, **kwargs)

ParseFloatError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (1)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

exception cosmolkit.ParserCarrierError(*args, **kwargs)

Failure in the parser_carrier domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ParserCarrierError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property model: str | None

Native parser model diagnostic, or None for another failure.

property source: PropertyStringError | AtomPropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: ParserCarrierErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ParserCarrierErrorKind(value)

Discriminants of ParserCarrierErrorKind.

Members: PropertyString, AtomProperty, Model, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
AtomProperty = ParserCarrierErrorKind.AtomProperty
Model = ParserCarrierErrorKind.Model
PropertyString = ParserCarrierErrorKind.PropertyString
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'PropertyString': ParserCarrierErrorKind.PropertyString, 'AtomProperty': ParserCarrierErrorKind.AtomProperty, 'Model': ParserCarrierErrorKind.Model})
values = mappingproxy({0: ParserCarrierErrorKind.PropertyString, 1: ParserCarrierErrorKind.AtomProperty, 2: ParserCarrierErrorKind.Model})
exception cosmolkit.ParserStereoOrderError(*args, **kwargs)

Failure in the parser_stereo_order domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ParserStereoOrderError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property bond_count: int | None

Readonly bond_count payload of the BondIndexOutOfRange error variant; None for other variants.

property bond_index: int | None

Readonly bond_index payload of the BondIndexOutOfRange error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property incident_count: int | None

Readonly incident_count payload of the ProbeLengthMismatch error variant; None for other variants.

property probe_count: int | None

Readonly probe_count payload of the ProbeLengthMismatch error variant; None for other variants.

property probe_index: int | None

Readonly probe_index payload of the ProbeMemberMissing error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: ParserStereoOrderErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ParserStereoOrderErrorKind(value)

Discriminants of ParserStereoOrderErrorKind.

Members: BondIndexOutOfRange, ProbeLengthMismatch, ProbeMemberMissing, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
BondIndexOutOfRange = ParserStereoOrderErrorKind.BondIndexOutOfRange
ProbeLengthMismatch = ParserStereoOrderErrorKind.ProbeLengthMismatch
ProbeMemberMissing = ParserStereoOrderErrorKind.ProbeMemberMissing
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'BondIndexOutOfRange': ParserStereoOrderErrorKind.BondIndexOutOfRange, 'ProbeLengthMismatch': ParserStereoOrderErrorKind.ProbeLengthMismatch, 'ProbeMemberMissing': ParserStereoOrderErrorKind.ProbeMemberMissing})
values = mappingproxy({0: ParserStereoOrderErrorKind.BondIndexOutOfRange, 1: ParserStereoOrderErrorKind.ProbeLengthMismatch, 2: ParserStereoOrderErrorKind.ProbeMemberMissing})
exception cosmolkit.PathError(*args, **kwargs)

Failure in the paths domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PathError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (19)
property actual: int | None

Observed value reported by the native check. Applies to PathError.IgnoredAtomMaskLength, PathError.ExtraInvariantLength. None when this payload is absent.

property atom: int | None

Atom identifier implicated in the failure. Applies to PathError.AtomOutOfRange, PathError.EqualShortestPathEndpoints, PathError.AtomPathOutOfRange. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to PathError.AtomOutOfRange, PathError.AtomPathOutOfRange. None when this payload is absent.

property carrier: int | None

Readonly carrier payload of the TemplateAttachmentRemap error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Required value reported by the native check. Applies to PathError.IgnoredAtomMaskLength, PathError.ExtraInvariantLength. None when this payload is absent.

property length: int | None

Readonly length payload of the LengthOverflow error variant; None for other variants.

property lower: int | None

Readonly lower payload of the InvalidLengthRange error variant; None for other variants.

property mapping: MappingValidationError | None

“error_payload”} Structured MappingValidationError payload of PathError.Mapping; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property matrix: MatrixError | None

“error_payload”} Structured MatrixError payload of PathError.Matrix; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property periodic_table: PeriodicTableError | None

“error_payload”} Structured PeriodicTableError payload of PathError.PeriodicTable; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property position: int | None

Readonly position payload of the AtomPathOutOfRange error variant; None for other variants.

property query_graph: QueryGraphError | None

“error_payload”} Structured QueryGraphError payload of PathError.QueryGraph; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property role: str | None

Readonly role payload of the AtomOutOfRange error variant; None for other variants.

property source: StereoGroupError | MoleculePropertyError | BondValueError | AtomPropertyError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of PathError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property upper: int | None

Readonly upper payload of the InvalidLengthRange error variant; None for other variants.

property variant: PathErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PathErrorKind(value)

Discriminants of PathErrorKind.

Members: StereoGroup, MoleculeProperty, BondProperty, AtomProperty, InvalidTopology, AtomOutOfRange, EqualShortestPathEndpoints, InvalidLengthRange, LengthOverflow, AtomPathOutOfRange, IgnoredAtomMaskLength, ExtraInvariantLength, PeriodicTable, InvalidSubsetTopology, QueryGraph, Mapping, TemplateAttachmentRemap, Matrix, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (21)
AtomOutOfRange = PathErrorKind.AtomOutOfRange
AtomPathOutOfRange = PathErrorKind.AtomPathOutOfRange
AtomProperty = PathErrorKind.AtomProperty
BondProperty = PathErrorKind.BondProperty
EqualShortestPathEndpoints = PathErrorKind.EqualShortestPathEndpoints
ExtraInvariantLength = PathErrorKind.ExtraInvariantLength
IgnoredAtomMaskLength = PathErrorKind.IgnoredAtomMaskLength
InvalidLengthRange = PathErrorKind.InvalidLengthRange
InvalidSubsetTopology = PathErrorKind.InvalidSubsetTopology
InvalidTopology = PathErrorKind.InvalidTopology
LengthOverflow = PathErrorKind.LengthOverflow
Mapping = PathErrorKind.Mapping
Matrix = PathErrorKind.Matrix
MoleculeProperty = PathErrorKind.MoleculeProperty
PeriodicTable = PathErrorKind.PeriodicTable
QueryGraph = PathErrorKind.QueryGraph
StereoGroup = PathErrorKind.StereoGroup
TemplateAttachmentRemap = PathErrorKind.TemplateAttachmentRemap
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': PathErrorKind.StereoGroup, 'MoleculeProperty': PathErrorKind.MoleculeProperty, 'BondProperty': PathErrorKind.BondProperty, 'AtomProperty': PathErrorKind.AtomProperty, 'InvalidTopology': PathErrorKind.InvalidTopology, 'AtomOutOfRange': PathErrorKind.AtomOutOfRange, 'EqualShortestPathEndpoints': PathErrorKind.EqualShortestPathEndpoints, 'InvalidLengthRange': PathErrorKind.InvalidLengthRange, 'LengthOverflow': PathErrorKind.LengthOverflow, 'AtomPathOutOfRange': PathErrorKind.AtomPathOutOfRange, 'IgnoredAtomMaskLength': PathErrorKind.IgnoredAtomMaskLength, 'ExtraInvariantLength': PathErrorKind.ExtraInvariantLength, 'PeriodicTable': PathErrorKind.PeriodicTable, 'InvalidSubsetTopology': PathErrorKind.InvalidSubsetTopology, 'QueryGraph': PathErrorKind.QueryGraph, 'Mapping': PathErrorKind.Mapping, 'TemplateAttachmentRemap': PathErrorKind.TemplateAttachmentRemap, 'Matrix': PathErrorKind.Matrix})
values = mappingproxy({0: PathErrorKind.StereoGroup, 1: PathErrorKind.MoleculeProperty, 2: PathErrorKind.BondProperty, 3: PathErrorKind.AtomProperty, 4: PathErrorKind.InvalidTopology, 5: PathErrorKind.AtomOutOfRange, 6: PathErrorKind.EqualShortestPathEndpoints, 7: PathErrorKind.InvalidLengthRange, 8: PathErrorKind.LengthOverflow, 9: PathErrorKind.AtomPathOutOfRange, 10: PathErrorKind.IgnoredAtomMaskLength, 11: PathErrorKind.ExtraInvariantLength, 12: PathErrorKind.PeriodicTable, 13: PathErrorKind.InvalidSubsetTopology, 14: PathErrorKind.QueryGraph, 15: PathErrorKind.Mapping, 16: PathErrorKind.TemplateAttachmentRemap, 17: PathErrorKind.Matrix})
exception cosmolkit.PatternFingerprintError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PatternFingerprintError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property left: int | None

Readonly left payload of the BitLengthMismatch error variant; None for other variants.

property reason: str | None

Readonly reason payload of the InvalidArguments error variant; None for other variants.

property right: int | None

Readonly right payload of the BitLengthMismatch error variant; None for other variants.

property source: TopologyValidationError | QueryGraphError | QueryAtomConversionError | RingFindingError | SmartsParseError | QueryCompileError | QueryMatchContextError | SubstructMatchError | FingerprintError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: PatternFingerprintErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PatternFingerprintErrorKind(value)

Discriminants of PatternFingerprintErrorKind.

Members: EmptyFingerprint, InvalidArguments, BitLengthMismatch, Topology, Query, QueryCarrier, Rings, Smarts, QueryCompile, QueryContext, Match, Value, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (15)
BitLengthMismatch = PatternFingerprintErrorKind.BitLengthMismatch
EmptyFingerprint = PatternFingerprintErrorKind.EmptyFingerprint
InvalidArguments = PatternFingerprintErrorKind.InvalidArguments
Match = PatternFingerprintErrorKind.Match
Query = PatternFingerprintErrorKind.Query
QueryCarrier = PatternFingerprintErrorKind.QueryCarrier
QueryCompile = PatternFingerprintErrorKind.QueryCompile
QueryContext = PatternFingerprintErrorKind.QueryContext
Rings = PatternFingerprintErrorKind.Rings
Smarts = PatternFingerprintErrorKind.Smarts
Topology = PatternFingerprintErrorKind.Topology
Value = PatternFingerprintErrorKind.Value
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyFingerprint': PatternFingerprintErrorKind.EmptyFingerprint, 'InvalidArguments': PatternFingerprintErrorKind.InvalidArguments, 'BitLengthMismatch': PatternFingerprintErrorKind.BitLengthMismatch, 'Topology': PatternFingerprintErrorKind.Topology, 'Query': PatternFingerprintErrorKind.Query, 'QueryCarrier': PatternFingerprintErrorKind.QueryCarrier, 'Rings': PatternFingerprintErrorKind.Rings, 'Smarts': PatternFingerprintErrorKind.Smarts, 'QueryCompile': PatternFingerprintErrorKind.QueryCompile, 'QueryContext': PatternFingerprintErrorKind.QueryContext, 'Match': PatternFingerprintErrorKind.Match, 'Value': PatternFingerprintErrorKind.Value})
values = mappingproxy({0: PatternFingerprintErrorKind.EmptyFingerprint, 1: PatternFingerprintErrorKind.InvalidArguments, 2: PatternFingerprintErrorKind.BitLengthMismatch, 3: PatternFingerprintErrorKind.Topology, 4: PatternFingerprintErrorKind.Query, 5: PatternFingerprintErrorKind.QueryCarrier, 6: PatternFingerprintErrorKind.Rings, 7: PatternFingerprintErrorKind.Smarts, 8: PatternFingerprintErrorKind.QueryCompile, 9: PatternFingerprintErrorKind.QueryContext, 10: PatternFingerprintErrorKind.Match, 11: PatternFingerprintErrorKind.Value})
class cosmolkit.PatternFingerprintParams(*, n_bits=Ellipsis, tautomeric=Ellipsis)

Parameters for the source-compatible Pattern fingerprint.

The default is a 2,048-bit ordinary Pattern fingerprint. Set tautomeric to reproduce the source’s tautomer-aware structural hashing. RDKit labels Pattern fingerprint version 1.0.0 experimental; COSMolKit preserves that upstream metadata while validating the modeled ordinary-molecule boundary exactly against the pinned source revision.

Members (2)
n_bits: int

Number of bits in the explicit result. Zero is rejected.

tautomeric: bool

Whether single, double, and aromatic bonds use tautomer-aware hashing.

class cosmolkit.PdbAtomFieldError

Read-only atom-record field diagnostic retaining invalid source bytes where applicable.

Members (5)
bytes: bytes | None

Unrepresentable chain-name or atom-name bytes; None for another field failure.

charge: PdbChargeError | None

Charge value rejected by the native operation. Applies to PdbAtomFieldError.Charge. None when this payload is absent.

len: int | None

Length reported by the native failure. Applies to PdbAtomFieldError.TooShort. None when this payload is absent.

residue_key: PdbResidueKeyError | None

Residue identifier involved in the failed lookup. Applies to PdbAtomFieldError.ResidueKey. None when this payload is absent.

variant: PdbAtomFieldErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbAtomFieldErrorKind(value)

Discriminants of PdbAtomFieldErrorKind.

Members: TooShort, SerialOutsideSourceDefinedRange, ChainNameNotRepresentable, AtomNameNotRepresentable, ResidueKey, Charge, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
AtomNameNotRepresentable = PdbAtomFieldErrorKind.AtomNameNotRepresentable
ChainNameNotRepresentable = PdbAtomFieldErrorKind.ChainNameNotRepresentable
Charge = PdbAtomFieldErrorKind.Charge
ResidueKey = PdbAtomFieldErrorKind.ResidueKey
SerialOutsideSourceDefinedRange = PdbAtomFieldErrorKind.SerialOutsideSourceDefinedRange
TooShort = PdbAtomFieldErrorKind.TooShort
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TooShort': PdbAtomFieldErrorKind.TooShort, 'SerialOutsideSourceDefinedRange': PdbAtomFieldErrorKind.SerialOutsideSourceDefinedRange, 'ChainNameNotRepresentable': PdbAtomFieldErrorKind.ChainNameNotRepresentable, 'AtomNameNotRepresentable': PdbAtomFieldErrorKind.AtomNameNotRepresentable, 'ResidueKey': PdbAtomFieldErrorKind.ResidueKey, 'Charge': PdbAtomFieldErrorKind.Charge})
values = mappingproxy({0: PdbAtomFieldErrorKind.TooShort, 1: PdbAtomFieldErrorKind.SerialOutsideSourceDefinedRange, 2: PdbAtomFieldErrorKind.ChainNameNotRepresentable, 3: PdbAtomFieldErrorKind.AtomNameNotRepresentable, 4: PdbAtomFieldErrorKind.ResidueKey, 5: PdbAtomFieldErrorKind.Charge})
class cosmolkit.PdbChargeError

Read-only diagnostic containing the invalid sign or digit of a PDB charge field.

Members (2)
digit: int

Original byte in the PDB charge magnitude position.

sign: int

Original byte in the PDB charge sign position.

class cosmolkit.PdbCisPepRecordError

Read-only diagnostic from a cis-peptide CISPEP record.

Members (6)
byte: int | None

Byte value or byte position reported by the native failure. Applies to PdbCisPepRecordError.ChainNameNotAscii. None when this payload is absent.

partner: int | None

Partner atom or endpoint involved in the native check. Applies to PdbCisPepRecordError.ChainNameNotAscii, PdbCisPepRecordError.ResidueAddress. None when this payload is absent. Disulfide connection partner identified by the native diagnostic.

record_len: int | None

Observed source-record length. Applies to PdbCisPepRecordError.RequiredFieldsPastRecord. None when this payload is absent.

required_len: int | None

Minimum record length required by the native parser. Applies to PdbCisPepRecordError.RequiredFieldsPastRecord. None when this payload is absent.

source: PdbResidueKeyError | None

Structured native error payload. Present for PdbCisPepRecordError.ResidueAddress; None when unavailable.

variant: PdbCisPepRecordErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbCisPepRecordErrorKind(value)

Discriminants of PdbCisPepRecordErrorKind.

Members: RequiredFieldsPastRecord, NoModelsAfterSourceDefault, SingleModelNumberUnavailable, ChainNameNotAscii, ResidueAddress, ModelNumberOutsideSourceDefinedRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
ChainNameNotAscii = PdbCisPepRecordErrorKind.ChainNameNotAscii
ModelNumberOutsideSourceDefinedRange = PdbCisPepRecordErrorKind.ModelNumberOutsideSourceDefinedRange
NoModelsAfterSourceDefault = PdbCisPepRecordErrorKind.NoModelsAfterSourceDefault
RequiredFieldsPastRecord = PdbCisPepRecordErrorKind.RequiredFieldsPastRecord
ResidueAddress = PdbCisPepRecordErrorKind.ResidueAddress
SingleModelNumberUnavailable = PdbCisPepRecordErrorKind.SingleModelNumberUnavailable
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'RequiredFieldsPastRecord': PdbCisPepRecordErrorKind.RequiredFieldsPastRecord, 'NoModelsAfterSourceDefault': PdbCisPepRecordErrorKind.NoModelsAfterSourceDefault, 'SingleModelNumberUnavailable': PdbCisPepRecordErrorKind.SingleModelNumberUnavailable, 'ChainNameNotAscii': PdbCisPepRecordErrorKind.ChainNameNotAscii, 'ResidueAddress': PdbCisPepRecordErrorKind.ResidueAddress, 'ModelNumberOutsideSourceDefinedRange': PdbCisPepRecordErrorKind.ModelNumberOutsideSourceDefinedRange})
values = mappingproxy({0: PdbCisPepRecordErrorKind.RequiredFieldsPastRecord, 1: PdbCisPepRecordErrorKind.NoModelsAfterSourceDefault, 2: PdbCisPepRecordErrorKind.SingleModelNumberUnavailable, 3: PdbCisPepRecordErrorKind.ChainNameNotAscii, 4: PdbCisPepRecordErrorKind.ResidueAddress, 5: PdbCisPepRecordErrorKind.ModelNumberOutsideSourceDefinedRange})
class cosmolkit.PdbConectError

Read-only diagnostic for a PDB CONECT serial outside the native numeric range.

Members (2)
field_offset: int | None

Offset of the failing field in the source record. Applies to PdbConectError.SourceSerialOutsideDefinedRange. None when this payload is absent.

variant: PdbConectErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbConectErrorKind(value)

Discriminants of PdbConectErrorKind.

Members: SourceSerialOutsideDefinedRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
SourceSerialOutsideDefinedRange = PdbConectErrorKind.SourceSerialOutsideDefinedRange
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SourceSerialOutsideDefinedRange': PdbConectErrorKind.SourceSerialOutsideDefinedRange})
values = mappingproxy({0: PdbConectErrorKind.SourceSerialOutsideDefinedRange})
class cosmolkit.PdbConnectionFinalizationError

Read-only connectivity finalization diagnostic retaining the responsible PDB record or resolution failure.

Members (5)
cis_pep_record: PdbCisPepRecordError | None

CISPEP record failure details, or None for another variant.

LINK record failure details, or None for another variant.

ssbond_record: PdbSsbondRecordError | None

SSBOND record failure details, or None for another variant.

ssbond_resolution: PdbSsbondResolutionError | None

Structured native error payload. Present for PdbConnectionFinalizationError.SsbondResolution; None when unavailable.

variant: PdbConnectionFinalizationErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbConnectionFinalizationErrorKind(value)

Discriminants of PdbConnectionFinalizationErrorKind.

Members: SsbondRecord, LinkRecord, CisPepRecord, SsbondResolution, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
CisPepRecord = PdbConnectionFinalizationErrorKind.CisPepRecord
LinkRecord = PdbConnectionFinalizationErrorKind.LinkRecord
SsbondRecord = PdbConnectionFinalizationErrorKind.SsbondRecord
SsbondResolution = PdbConnectionFinalizationErrorKind.SsbondResolution
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SsbondRecord': PdbConnectionFinalizationErrorKind.SsbondRecord, 'LinkRecord': PdbConnectionFinalizationErrorKind.LinkRecord, 'CisPepRecord': PdbConnectionFinalizationErrorKind.CisPepRecord, 'SsbondResolution': PdbConnectionFinalizationErrorKind.SsbondResolution})
values = mappingproxy({0: PdbConnectionFinalizationErrorKind.SsbondRecord, 1: PdbConnectionFinalizationErrorKind.LinkRecord, 2: PdbConnectionFinalizationErrorKind.CisPepRecord, 3: PdbConnectionFinalizationErrorKind.SsbondResolution})
class cosmolkit.PdbCrystalError

Read-only diagnostic from PDB crystal/cell metadata.

Members (4)
bio_structure_data: BioStructureError | None

Structured native error payload. Present for PdbCrystalError.BioStructureData; None when unavailable.

field_offset: int | None

Offset of the failing field in the source record. Applies to PdbCrystalError.TextFieldNotUtf8. None when this payload is absent.

valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbCrystalError.TextFieldNotUtf8. None when this payload is absent.

variant: PdbCrystalErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbCrystalErrorKind(value)

Discriminants of PdbCrystalErrorKind.

Members: BioStructureData, TextFieldNotUtf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
BioStructureData = PdbCrystalErrorKind.BioStructureData
TextFieldNotUtf8 = PdbCrystalErrorKind.TextFieldNotUtf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'BioStructureData': PdbCrystalErrorKind.BioStructureData, 'TextFieldNotUtf8': PdbCrystalErrorKind.TextFieldNotUtf8})
values = mappingproxy({0: PdbCrystalErrorKind.BioStructureData, 1: PdbCrystalErrorKind.TextFieldNotUtf8})
class cosmolkit.PdbDbRefError

Read-only diagnostic for a malformed PDB database-reference record, retaining the native variant and field offset.

Members (2)
field_offset: int | None

Offset of the failing field in the source record. Applies to PdbDbRefError.SourceIntegerOutsideDefinedRange. None when this payload is absent.

variant: PdbDbRefErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbDbRefErrorKind(value)

Discriminants of PdbDbRefErrorKind.

Members: SourceIntegerOutsideDefinedRange, MissingCurrentDbRef, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
MissingCurrentDbRef = PdbDbRefErrorKind.MissingCurrentDbRef
SourceIntegerOutsideDefinedRange = PdbDbRefErrorKind.SourceIntegerOutsideDefinedRange
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SourceIntegerOutsideDefinedRange': PdbDbRefErrorKind.SourceIntegerOutsideDefinedRange, 'MissingCurrentDbRef': PdbDbRefErrorKind.MissingCurrentDbRef})
values = mappingproxy({0: PdbDbRefErrorKind.SourceIntegerOutsideDefinedRange, 1: PdbDbRefErrorKind.MissingCurrentDbRef})
exception cosmolkit.PdbHeaderError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PdbHeaderError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property field_offset: int | None

Readonly field_offset payload of the TextFieldNotUtf8 error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valid_up_to: int | None

Readonly valid_up_to payload of the TextFieldNotUtf8 error variant; None for other variants.

property variant: PdbHeaderErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PdbHeaderErrorKind(value)

Discriminants of PdbHeaderErrorKind.

Members: TextFieldNotUtf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
TextFieldNotUtf8 = PdbHeaderErrorKind.TextFieldNotUtf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TextFieldNotUtf8': PdbHeaderErrorKind.TextFieldNotUtf8})
values = mappingproxy({0: PdbHeaderErrorKind.TextFieldNotUtf8})
class cosmolkit.PdbHelixError

Read-only HELIX-record diagnostic, including invalid chain, residue-address or integer fields.

Members (5)
field_offset: int | None

Offset of the failing field in the source record. Applies to PdbHelixError.ChainNameNotRepresentable, PdbHelixError.IntegerOutsideSourceDefinedRange. None when this payload is absent.

non_ascii: int | None

Non-ASCII source content reported by the parser. Applies to PdbHelixError.ChainNameNotRepresentable. None when this payload is absent.

residue_address: PdbResidueKeyError | None

Structured native error payload. Present for PdbHelixError.ResidueAddress; None when unavailable.

variant: PdbHelixErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

width: int | None

Width reported by the failing native check. Applies to PdbHelixError.ChainNameNotRepresentable, PdbHelixError.IntegerOutsideSourceDefinedRange. None when this payload is absent.

class cosmolkit.PdbHelixErrorKind(value)

Discriminants of PdbHelixErrorKind.

Members: ChainNameNotRepresentable, ResidueAddress, IntegerOutsideSourceDefinedRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
ChainNameNotRepresentable = PdbHelixErrorKind.ChainNameNotRepresentable
IntegerOutsideSourceDefinedRange = PdbHelixErrorKind.IntegerOutsideSourceDefinedRange
ResidueAddress = PdbHelixErrorKind.ResidueAddress
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ChainNameNotRepresentable': PdbHelixErrorKind.ChainNameNotRepresentable, 'ResidueAddress': PdbHelixErrorKind.ResidueAddress, 'IntegerOutsideSourceDefinedRange': PdbHelixErrorKind.IntegerOutsideSourceDefinedRange})
values = mappingproxy({0: PdbHelixErrorKind.ChainNameNotRepresentable, 1: PdbHelixErrorKind.ResidueAddress, 2: PdbHelixErrorKind.IntegerOutsideSourceDefinedRange})
exception cosmolkit.PdbInputFormatError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PdbInputFormatError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: str

Input source name whose contents were detected as CIF or mmJSON rather than PDB.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: PdbInputFormatErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PdbInputFormatErrorKind(value)

Discriminants of PdbInputFormatErrorKind.

Members: Cif, Mmjson, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Cif = PdbInputFormatErrorKind.Cif
Mmjson = PdbInputFormatErrorKind.Mmjson
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cif': PdbInputFormatErrorKind.Cif, 'Mmjson': PdbInputFormatErrorKind.Mmjson})
values = mappingproxy({0: PdbInputFormatErrorKind.Cif, 1: PdbInputFormatErrorKind.Mmjson})
class cosmolkit.PdbLinkNameCounter(value)

Typed PdbLinkNameCounter values corresponding to the Rust enum.

Members: Covale, MetalC, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Covale = PdbLinkNameCounter.Covale
MetalC = PdbLinkNameCounter.MetalC
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Covale': PdbLinkNameCounter.Covale, 'MetalC': PdbLinkNameCounter.MetalC})
values = mappingproxy({0: PdbLinkNameCounter.Covale, 1: PdbLinkNameCounter.MetalC})
class cosmolkit.PdbLinkRecordError

Read-only diagnostic from a PDB LINK connectivity record.

Members (6)
byte: int | None

Byte value or byte position reported by the native failure. Applies to PdbLinkRecordError.ChainNameNotAscii, PdbLinkRecordError.AtomNameNotAscii. None when this payload is absent.

counter: PdbLinkNameCounter | None

Counter value reported by the native failure. Applies to PdbLinkRecordError.NameCounterOutsideSourceDefinedRange. None when this payload is absent.

partner: int | None

Partner atom or endpoint involved in the native check. Applies to PdbLinkRecordError.ChainNameNotAscii, PdbLinkRecordError.AtomNameNotAscii, PdbLinkRecordError.ResidueAddress. None when this payload is absent. Disulfide connection partner identified by the native diagnostic.

source: PdbResidueKeyError | None

Structured native error payload. Present for PdbLinkRecordError.ResidueAddress; None when unavailable.

valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbLinkRecordError.LinkIdNotUtf8. None when this payload is absent.

variant: PdbLinkRecordErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbLinkRecordErrorKind(value)

Discriminants of PdbLinkRecordErrorKind.

Members: ChainNameNotAscii, AtomNameNotAscii, LinkIdNotUtf8, ResidueAddress, NameCounterOutsideSourceDefinedRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
AtomNameNotAscii = PdbLinkRecordErrorKind.AtomNameNotAscii
ChainNameNotAscii = PdbLinkRecordErrorKind.ChainNameNotAscii
LinkIdNotUtf8 = PdbLinkRecordErrorKind.LinkIdNotUtf8
NameCounterOutsideSourceDefinedRange = PdbLinkRecordErrorKind.NameCounterOutsideSourceDefinedRange
ResidueAddress = PdbLinkRecordErrorKind.ResidueAddress
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ChainNameNotAscii': PdbLinkRecordErrorKind.ChainNameNotAscii, 'AtomNameNotAscii': PdbLinkRecordErrorKind.AtomNameNotAscii, 'LinkIdNotUtf8': PdbLinkRecordErrorKind.LinkIdNotUtf8, 'ResidueAddress': PdbLinkRecordErrorKind.ResidueAddress, 'NameCounterOutsideSourceDefinedRange': PdbLinkRecordErrorKind.NameCounterOutsideSourceDefinedRange})
values = mappingproxy({0: PdbLinkRecordErrorKind.ChainNameNotAscii, 1: PdbLinkRecordErrorKind.AtomNameNotAscii, 2: PdbLinkRecordErrorKind.LinkIdNotUtf8, 3: PdbLinkRecordErrorKind.ResidueAddress, 4: PdbLinkRecordErrorKind.NameCounterOutsideSourceDefinedRange})
exception cosmolkit.PdbModelTransitionError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PdbModelTransitionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (9)
property chain: str | None

Structural chain involved in the failure. Applies to PdbModelTransitionError.NonpolymerSubchainCounterOutsideSourceIntRange. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property id: int | None

Identifier involved in the native failure. Applies to PdbModelTransitionError.ModelIdOutOfBounds. None when this payload is absent.

property model_count: int | None

Readonly model_count payload of the ModelIdOutOfBounds error variant; None for other variants.

property number: int | None

Readonly number payload of the DuplicateModelNumber error variant; None for other variants.

property offset: int | None

Readonly offset payload of the AnisouIntegerOutsideSourceIntRange error variant; None for other variants.

property source: BioStructureError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: PdbModelTransitionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PdbModelTransitionErrorKind(value)

Discriminants of PdbModelTransitionErrorKind.

Members: ModelWithoutEnd, DuplicateModelNumber, AtomBetweenModels, ModelNumberOutsideSourceIntRange, NonpolymerSubchainCounterOutsideSourceIntRange, AnisouWithoutAtom, DuplicateAnisou, AnisouIntegerOutsideSourceIntRange, ModelIdOutOfBounds, Structure, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (13)
AnisouIntegerOutsideSourceIntRange = PdbModelTransitionErrorKind.AnisouIntegerOutsideSourceIntRange
AnisouWithoutAtom = PdbModelTransitionErrorKind.AnisouWithoutAtom
AtomBetweenModels = PdbModelTransitionErrorKind.AtomBetweenModels
DuplicateAnisou = PdbModelTransitionErrorKind.DuplicateAnisou
DuplicateModelNumber = PdbModelTransitionErrorKind.DuplicateModelNumber
ModelIdOutOfBounds = PdbModelTransitionErrorKind.ModelIdOutOfBounds
ModelNumberOutsideSourceIntRange = PdbModelTransitionErrorKind.ModelNumberOutsideSourceIntRange
ModelWithoutEnd = PdbModelTransitionErrorKind.ModelWithoutEnd
NonpolymerSubchainCounterOutsideSourceIntRange = PdbModelTransitionErrorKind.NonpolymerSubchainCounterOutsideSourceIntRange
Structure = PdbModelTransitionErrorKind.Structure
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ModelWithoutEnd': PdbModelTransitionErrorKind.ModelWithoutEnd, 'DuplicateModelNumber': PdbModelTransitionErrorKind.DuplicateModelNumber, 'AtomBetweenModels': PdbModelTransitionErrorKind.AtomBetweenModels, 'ModelNumberOutsideSourceIntRange': PdbModelTransitionErrorKind.ModelNumberOutsideSourceIntRange, 'NonpolymerSubchainCounterOutsideSourceIntRange': PdbModelTransitionErrorKind.NonpolymerSubchainCounterOutsideSourceIntRange, 'AnisouWithoutAtom': PdbModelTransitionErrorKind.AnisouWithoutAtom, 'DuplicateAnisou': PdbModelTransitionErrorKind.DuplicateAnisou, 'AnisouIntegerOutsideSourceIntRange': PdbModelTransitionErrorKind.AnisouIntegerOutsideSourceIntRange, 'ModelIdOutOfBounds': PdbModelTransitionErrorKind.ModelIdOutOfBounds, 'Structure': PdbModelTransitionErrorKind.Structure})
values = mappingproxy({0: PdbModelTransitionErrorKind.ModelWithoutEnd, 1: PdbModelTransitionErrorKind.DuplicateModelNumber, 2: PdbModelTransitionErrorKind.AtomBetweenModels, 3: PdbModelTransitionErrorKind.ModelNumberOutsideSourceIntRange, 4: PdbModelTransitionErrorKind.NonpolymerSubchainCounterOutsideSourceIntRange, 5: PdbModelTransitionErrorKind.AnisouWithoutAtom, 6: PdbModelTransitionErrorKind.DuplicateAnisou, 7: PdbModelTransitionErrorKind.AnisouIntegerOutsideSourceIntRange, 8: PdbModelTransitionErrorKind.ModelIdOutOfBounds, 9: PdbModelTransitionErrorKind.Structure})
class cosmolkit.PdbModResError

Read-only modified-residue record diagnostic with source field and residue-address details.

Members (6)
field_offset: int | None

Offset of the failing field in the source record. Applies to PdbModResError.TextFieldNotUtf8. None when this payload is absent.

non_ascii: int | None

Non-ASCII source content reported by the parser. Applies to PdbModResError.ChainNameNotRepresentable. None when this payload is absent.

residue_address: PdbResidueKeyError | None

Structured native error payload. Present for PdbModResError.ResidueAddress; None when unavailable.

valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbModResError.TextFieldNotUtf8. None when this payload is absent.

variant: PdbModResErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

width: int | None

Width reported by the failing native check. Applies to PdbModResError.ChainNameNotRepresentable. None when this payload is absent.

class cosmolkit.PdbModResErrorKind(value)

Discriminants of PdbModResErrorKind.

Members: ChainNameNotRepresentable, ResidueAddress, TextFieldNotUtf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
ChainNameNotRepresentable = PdbModResErrorKind.ChainNameNotRepresentable
ResidueAddress = PdbModResErrorKind.ResidueAddress
TextFieldNotUtf8 = PdbModResErrorKind.TextFieldNotUtf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ChainNameNotRepresentable': PdbModResErrorKind.ChainNameNotRepresentable, 'ResidueAddress': PdbModResErrorKind.ResidueAddress, 'TextFieldNotUtf8': PdbModResErrorKind.TextFieldNotUtf8})
values = mappingproxy({0: PdbModResErrorKind.ChainNameNotRepresentable, 1: PdbModResErrorKind.ResidueAddress, 2: PdbModResErrorKind.TextFieldNotUtf8})
class cosmolkit.PdbMtrixError

Read-only diagnostic for invalid text in a PDB non-crystallographic matrix record.

Members (3)
field_offset: int | None

Offset of the failing field in the source record. Applies to PdbMtrixError.TextFieldNotUtf8. None when this payload is absent.

valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbMtrixError.TextFieldNotUtf8. None when this payload is absent.

variant: PdbMtrixErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbMtrixErrorKind(value)

Discriminants of PdbMtrixErrorKind.

Members: TextFieldNotUtf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
TextFieldNotUtf8 = PdbMtrixErrorKind.TextFieldNotUtf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TextFieldNotUtf8': PdbMtrixErrorKind.TextFieldNotUtf8})
values = mappingproxy({0: PdbMtrixErrorKind.TextFieldNotUtf8})
exception cosmolkit.PdbPostprocessError(*args, **kwargs)

Failure in the pdb domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PdbPostprocessError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: AtomPropertyError | TopologyValidationError | CoordinateValidationError | ValenceError | TopologyEditError | PropertyUIntReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Value rejected or reported by the native operation. Applies to PdbPostprocessError.Unsupported, PdbPostprocessError.InvalidState. None when this payload is absent.

property variant: PdbPostprocessErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PdbPostprocessErrorKind(value)

Discriminants of PdbPostprocessErrorKind.

Members: AtomProperty, Unsupported, InvalidState, Topology, Coordinates, Valence, TopologyEdit, PropertyUInt, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
AtomProperty = PdbPostprocessErrorKind.AtomProperty
Coordinates = PdbPostprocessErrorKind.Coordinates
InvalidState = PdbPostprocessErrorKind.InvalidState
PropertyUInt = PdbPostprocessErrorKind.PropertyUInt
Topology = PdbPostprocessErrorKind.Topology
TopologyEdit = PdbPostprocessErrorKind.TopologyEdit
Unsupported = PdbPostprocessErrorKind.Unsupported
Valence = PdbPostprocessErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'AtomProperty': PdbPostprocessErrorKind.AtomProperty, 'Unsupported': PdbPostprocessErrorKind.Unsupported, 'InvalidState': PdbPostprocessErrorKind.InvalidState, 'Topology': PdbPostprocessErrorKind.Topology, 'Coordinates': PdbPostprocessErrorKind.Coordinates, 'Valence': PdbPostprocessErrorKind.Valence, 'TopologyEdit': PdbPostprocessErrorKind.TopologyEdit, 'PropertyUInt': PdbPostprocessErrorKind.PropertyUInt})
values = mappingproxy({0: PdbPostprocessErrorKind.AtomProperty, 1: PdbPostprocessErrorKind.Unsupported, 2: PdbPostprocessErrorKind.InvalidState, 3: PdbPostprocessErrorKind.Topology, 4: PdbPostprocessErrorKind.Coordinates, 5: PdbPostprocessErrorKind.Valence, 6: PdbPostprocessErrorKind.TopologyEdit, 7: PdbPostprocessErrorKind.PropertyUInt})
exception cosmolkit.PdbReaderCause(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PdbReaderCause is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (16)
property atom_fields: PdbAtomFieldError | None

“error_payload”} Atom-field diagnostic for AtomFields failures; None for other PDB reader variants.

Type:

{“role”

property conect: PdbConectError | None

“error_payload”} CONECT connectivity diagnostic, or None for another PDB reader variant.

Type:

{“role”

property crystal: PdbCrystalError | None

“error_payload”} Crystallographic record diagnostic, or None for another PDB reader variant.

Type:

{“role”

property db_ref: PdbDbRefError | None

“error_payload”} DBREF sequence-reference diagnostic, or None for another PDB reader variant.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property finalization: PdbStructureFinalizationError | None

“error_payload”} Structure finalization diagnostic, or None for another PDB reader variant.

Type:

{“role”

property header: PdbHeaderError | None

“error_payload”} Structured PdbHeaderError payload of PdbReaderCause.Header; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property helix: PdbHelixError | None

“error_payload”} HELIX secondary-structure diagnostic, or None for another PDB reader variant.

Type:

{“role”

property input_format: PdbInputFormatError | None

“error_payload”} Structured PdbInputFormatError payload of PdbReaderCause.InputFormat; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property mod_res: PdbModResError | None

“error_payload”} MODRES modified-residue diagnostic, or None for another PDB reader variant.

Type:

{“role”

property model_transition: PdbModelTransitionError | None

“error_payload”} Structured PdbModelTransitionError payload of PdbReaderCause.ModelTransition; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property mtrix: PdbMtrixError | None

“error_payload”} MTRIX noncrystallographic transform diagnostic, or None for another PDB reader variant.

Type:

{“role”

property remark: PdbRemarkError | None

“error_payload”} Structured PdbRemarkError payload of PdbReaderCause.Remark; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property sheet: PdbSheetError | None

“error_payload”} SHEET secondary-structure diagnostic, or None for another PDB reader variant.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: PdbReaderCauseKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PdbReaderCauseKind(value)

Discriminants of PdbReaderCauseKind.

Members: LineNumberOutsideSourceIntRange, InputFormat, AtomFields, ModelTransition, Remark, Conect, ModRes, Helix, Sheet, Header, DbRef, Mtrix, Crystal, Finalization, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (17)
AtomFields = PdbReaderCauseKind.AtomFields
Conect = PdbReaderCauseKind.Conect
Crystal = PdbReaderCauseKind.Crystal
DbRef = PdbReaderCauseKind.DbRef
Finalization = PdbReaderCauseKind.Finalization
Header = PdbReaderCauseKind.Header
Helix = PdbReaderCauseKind.Helix
InputFormat = PdbReaderCauseKind.InputFormat
LineNumberOutsideSourceIntRange = PdbReaderCauseKind.LineNumberOutsideSourceIntRange
ModRes = PdbReaderCauseKind.ModRes
ModelTransition = PdbReaderCauseKind.ModelTransition
Mtrix = PdbReaderCauseKind.Mtrix
Remark = PdbReaderCauseKind.Remark
Sheet = PdbReaderCauseKind.Sheet
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'LineNumberOutsideSourceIntRange': PdbReaderCauseKind.LineNumberOutsideSourceIntRange, 'InputFormat': PdbReaderCauseKind.InputFormat, 'AtomFields': PdbReaderCauseKind.AtomFields, 'ModelTransition': PdbReaderCauseKind.ModelTransition, 'Remark': PdbReaderCauseKind.Remark, 'Conect': PdbReaderCauseKind.Conect, 'ModRes': PdbReaderCauseKind.ModRes, 'Helix': PdbReaderCauseKind.Helix, 'Sheet': PdbReaderCauseKind.Sheet, 'Header': PdbReaderCauseKind.Header, 'DbRef': PdbReaderCauseKind.DbRef, 'Mtrix': PdbReaderCauseKind.Mtrix, 'Crystal': PdbReaderCauseKind.Crystal, 'Finalization': PdbReaderCauseKind.Finalization})
values = mappingproxy({0: PdbReaderCauseKind.LineNumberOutsideSourceIntRange, 1: PdbReaderCauseKind.InputFormat, 2: PdbReaderCauseKind.AtomFields, 3: PdbReaderCauseKind.ModelTransition, 4: PdbReaderCauseKind.Remark, 5: PdbReaderCauseKind.Conect, 6: PdbReaderCauseKind.ModRes, 7: PdbReaderCauseKind.Helix, 8: PdbReaderCauseKind.Sheet, 9: PdbReaderCauseKind.Header, 10: PdbReaderCauseKind.DbRef, 11: PdbReaderCauseKind.Mtrix, 12: PdbReaderCauseKind.Crystal, 13: PdbReaderCauseKind.Finalization})
class cosmolkit.PdbReadFlags

PdbReadFlags native option bit mask. Combine named constants with the bitwise OR operator; bits exposes its integer representation.

Members (7)
KEEP_ALTERNATE_AND_PSEUDO_ATOMS = <cosmolkit.PdbReadFlags object>
NONE = <cosmolkit.PdbReadFlags object>
STANDARD_RESIDUE_BOND_ORDERS = <cosmolkit.PdbReadFlags object>
bits: int

Integer representation of this option mask.

contains(flags) → bool

Whether every bit in the supplied mask is present.

static from_bits(bits) → PdbReadFlags

Construct a mask from the native integer flag representation.

is_empty: bool

Whether the mask contains no enabled options.

class cosmolkit.PdbRemark200Error

Read-only parsing diagnostic for experimental REMARK 200 records.

Members (3)
software: PdbRemark3Error | None

Software metadata involved in the failed write. Applies to PdbRemark200Error.Software. None when this payload is absent.

valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbRemark200Error.TextNotUtf8. None when this payload is absent.

variant: PdbRemark200ErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbRemark200ErrorKind(value)

Discriminants of PdbRemark200ErrorKind.

Members: IntegerOutsideSourceDefinedRange, TextNotUtf8, MissingExperimentalRows, UndefinedPhNumericScreening, Software, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
IntegerOutsideSourceDefinedRange = PdbRemark200ErrorKind.IntegerOutsideSourceDefinedRange
MissingExperimentalRows = PdbRemark200ErrorKind.MissingExperimentalRows
Software = PdbRemark200ErrorKind.Software
TextNotUtf8 = PdbRemark200ErrorKind.TextNotUtf8
UndefinedPhNumericScreening = PdbRemark200ErrorKind.UndefinedPhNumericScreening
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'IntegerOutsideSourceDefinedRange': PdbRemark200ErrorKind.IntegerOutsideSourceDefinedRange, 'TextNotUtf8': PdbRemark200ErrorKind.TextNotUtf8, 'MissingExperimentalRows': PdbRemark200ErrorKind.MissingExperimentalRows, 'UndefinedPhNumericScreening': PdbRemark200ErrorKind.UndefinedPhNumericScreening, 'Software': PdbRemark200ErrorKind.Software})
values = mappingproxy({0: PdbRemark200ErrorKind.IntegerOutsideSourceDefinedRange, 1: PdbRemark200ErrorKind.TextNotUtf8, 2: PdbRemark200ErrorKind.MissingExperimentalRows, 3: PdbRemark200ErrorKind.UndefinedPhNumericScreening, 4: PdbRemark200ErrorKind.Software})
class cosmolkit.PdbRemark350Error

Read-only parsing diagnostic for biological-assembly REMARK 350 records.

Members (6)
field_offset: int | None

Offset of the failing field in the source record. Applies to PdbRemark350Error.TextNotUtf8. None when this payload is absent.

offset: int | None

Source offset reported by the native parser. Applies to PdbRemark350Error.SourceUndefinedAccess. None when this payload is absent.

record_length: int | None

Length of the source record involved in the failed parse. Applies to PdbRemark350Error.SourceUndefinedAccess. None when this payload is absent.

valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbRemark350Error.TextNotUtf8. None when this payload is absent.

variant: PdbRemark350ErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

width: int | None

Width reported by the failing native check. Applies to PdbRemark350Error.SourceUndefinedAccess. None when this payload is absent.

class cosmolkit.PdbRemark350ErrorKind(value)

Discriminants of PdbRemark350ErrorKind.

Members: IntegerOutsideSourceDefinedRange, SourceUndefinedAccess, TextNotUtf8, StateInvariantLost, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
IntegerOutsideSourceDefinedRange = PdbRemark350ErrorKind.IntegerOutsideSourceDefinedRange
SourceUndefinedAccess = PdbRemark350ErrorKind.SourceUndefinedAccess
StateInvariantLost = PdbRemark350ErrorKind.StateInvariantLost
TextNotUtf8 = PdbRemark350ErrorKind.TextNotUtf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'IntegerOutsideSourceDefinedRange': PdbRemark350ErrorKind.IntegerOutsideSourceDefinedRange, 'SourceUndefinedAccess': PdbRemark350ErrorKind.SourceUndefinedAccess, 'TextNotUtf8': PdbRemark350ErrorKind.TextNotUtf8, 'StateInvariantLost': PdbRemark350ErrorKind.StateInvariantLost})
values = mappingproxy({0: PdbRemark350ErrorKind.IntegerOutsideSourceDefinedRange, 1: PdbRemark350ErrorKind.SourceUndefinedAccess, 2: PdbRemark350ErrorKind.TextNotUtf8, 3: PdbRemark350ErrorKind.StateInvariantLost})
class cosmolkit.PdbRemark3Error

Read-only parsing diagnostic for PDB refinement REMARK 3 records.

Members (3)
valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbRemark3Error.TextNotUtf8. None when this payload is absent.

variant: PdbRemark3ErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

width: int | None

Width reported by the failing native check. Applies to PdbRemark3Error.TlsChainIdNotRepresentable. None when this payload is absent.

class cosmolkit.PdbRemark3ErrorKind(value)

Discriminants of PdbRemark3ErrorKind.

Members: IntegerOutsideSourceDefinedRange, TextNotUtf8, MissingContinuationTarget, TlsChainIdNotRepresentable, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
IntegerOutsideSourceDefinedRange = PdbRemark3ErrorKind.IntegerOutsideSourceDefinedRange
MissingContinuationTarget = PdbRemark3ErrorKind.MissingContinuationTarget
TextNotUtf8 = PdbRemark3ErrorKind.TextNotUtf8
TlsChainIdNotRepresentable = PdbRemark3ErrorKind.TlsChainIdNotRepresentable
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'IntegerOutsideSourceDefinedRange': PdbRemark3ErrorKind.IntegerOutsideSourceDefinedRange, 'TextNotUtf8': PdbRemark3ErrorKind.TextNotUtf8, 'MissingContinuationTarget': PdbRemark3ErrorKind.MissingContinuationTarget, 'TlsChainIdNotRepresentable': PdbRemark3ErrorKind.TlsChainIdNotRepresentable})
values = mappingproxy({0: PdbRemark3ErrorKind.IntegerOutsideSourceDefinedRange, 1: PdbRemark3ErrorKind.TextNotUtf8, 2: PdbRemark3ErrorKind.MissingContinuationTarget, 3: PdbRemark3ErrorKind.TlsChainIdNotRepresentable})
exception cosmolkit.PdbRemarkError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PdbRemarkError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property line_len: int | None

Readonly line_len payload of the LineLengthOutsideBuffer error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valid_up_to: int | None

Readonly valid_up_to payload of the TextFieldNotUtf8 error variant; None for other variants.

property variant: PdbRemarkErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PdbRemarkErrorKind(value)

Discriminants of PdbRemarkErrorKind.

Members: LineLengthOutsideBuffer, TextFieldNotUtf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
LineLengthOutsideBuffer = PdbRemarkErrorKind.LineLengthOutsideBuffer
TextFieldNotUtf8 = PdbRemarkErrorKind.TextFieldNotUtf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'LineLengthOutsideBuffer': PdbRemarkErrorKind.LineLengthOutsideBuffer, 'TextFieldNotUtf8': PdbRemarkErrorKind.TextFieldNotUtf8})
values = mappingproxy({0: PdbRemarkErrorKind.LineLengthOutsideBuffer, 1: PdbRemarkErrorKind.TextFieldNotUtf8})
class cosmolkit.PdbRemarkFinalizationError

Read-only diagnostic from converting parsed remarks into structure metadata.

Members (5)
remark200: PdbRemark200Error | None

REMARK 200 experimental-data failure details, or None for another variant.

remark3: PdbRemark3Error | None

REMARK 3 refinement failure details, or None for another variant.

remark350: PdbRemark350Error | None

REMARK 350 assembly failure details, or None for another variant.

remark_metadata: PdbRemarkMetadataError | None

General remark-metadata failure details, or None for another variant.

variant: PdbRemarkFinalizationErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbRemarkFinalizationErrorKind(value)

Discriminants of PdbRemarkFinalizationErrorKind.

Members: IntegerOutsideSourceDefinedRange, Remark3, Remark200, RemarkMetadata, Remark350, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
IntegerOutsideSourceDefinedRange = PdbRemarkFinalizationErrorKind.IntegerOutsideSourceDefinedRange
Remark200 = PdbRemarkFinalizationErrorKind.Remark200
Remark3 = PdbRemarkFinalizationErrorKind.Remark3
Remark350 = PdbRemarkFinalizationErrorKind.Remark350
RemarkMetadata = PdbRemarkFinalizationErrorKind.RemarkMetadata
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'IntegerOutsideSourceDefinedRange': PdbRemarkFinalizationErrorKind.IntegerOutsideSourceDefinedRange, 'Remark3': PdbRemarkFinalizationErrorKind.Remark3, 'Remark200': PdbRemarkFinalizationErrorKind.Remark200, 'RemarkMetadata': PdbRemarkFinalizationErrorKind.RemarkMetadata, 'Remark350': PdbRemarkFinalizationErrorKind.Remark350})
values = mappingproxy({0: PdbRemarkFinalizationErrorKind.IntegerOutsideSourceDefinedRange, 1: PdbRemarkFinalizationErrorKind.Remark3, 2: PdbRemarkFinalizationErrorKind.Remark200, 3: PdbRemarkFinalizationErrorKind.RemarkMetadata, 4: PdbRemarkFinalizationErrorKind.Remark350})
class cosmolkit.PdbRemarkMetadataError

Read-only diagnostic from retained PDB remark metadata.

Members (3)
offset: int | None

Source offset reported by the native parser. Applies to PdbRemarkMetadataError.TextBoundaryNotUtf8. None when this payload is absent.

remark_length: int | None

Length of the remark involved in the failed parse. Applies to PdbRemarkMetadataError.UndefinedResolutionField. None when this payload is absent.

variant: PdbRemarkMetadataErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbRemarkMetadataErrorKind(value)

Discriminants of PdbRemarkMetadataErrorKind.

Members: IntegerOutsideSourceDefinedRange, UndefinedResolutionField, TextBoundaryNotUtf8, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
IntegerOutsideSourceDefinedRange = PdbRemarkMetadataErrorKind.IntegerOutsideSourceDefinedRange
TextBoundaryNotUtf8 = PdbRemarkMetadataErrorKind.TextBoundaryNotUtf8
UndefinedResolutionField = PdbRemarkMetadataErrorKind.UndefinedResolutionField
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'IntegerOutsideSourceDefinedRange': PdbRemarkMetadataErrorKind.IntegerOutsideSourceDefinedRange, 'UndefinedResolutionField': PdbRemarkMetadataErrorKind.UndefinedResolutionField, 'TextBoundaryNotUtf8': PdbRemarkMetadataErrorKind.TextBoundaryNotUtf8})
values = mappingproxy({0: PdbRemarkMetadataErrorKind.IntegerOutsideSourceDefinedRange, 1: PdbRemarkMetadataErrorKind.UndefinedResolutionField, 2: PdbRemarkMetadataErrorKind.TextBoundaryNotUtf8})
exception cosmolkit.PdbResidueKeyError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PdbResidueKeyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property byte: int | None

Byte value or byte position reported by the native failure. Applies to PdbResidueKeyError.ResidueNameNotAscii, PdbResidueKeyError.SegmentNotAscii. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: PdbResidueKeyErrorKind

Exact Rust error variant, independent of the human-readable message.

property width: int | None

Width reported by the failing native check. Applies to PdbResidueKeyError.ResidueNameTooWide, PdbResidueKeyError.SegmentTooWide, PdbResidueKeyError.SegmentNotRepresentable. None when this payload is absent.

class cosmolkit.PdbResidueKeyErrorKind(value)

Discriminants of PdbResidueKeyErrorKind.

Members: SequenceIdNotRepresentable, ResidueNameTooWide, ResidueNameNotAscii, SegmentTooWide, SegmentNotAscii, SegmentNotRepresentable, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
ResidueNameNotAscii = PdbResidueKeyErrorKind.ResidueNameNotAscii
ResidueNameTooWide = PdbResidueKeyErrorKind.ResidueNameTooWide
SegmentNotAscii = PdbResidueKeyErrorKind.SegmentNotAscii
SegmentNotRepresentable = PdbResidueKeyErrorKind.SegmentNotRepresentable
SegmentTooWide = PdbResidueKeyErrorKind.SegmentTooWide
SequenceIdNotRepresentable = PdbResidueKeyErrorKind.SequenceIdNotRepresentable
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SequenceIdNotRepresentable': PdbResidueKeyErrorKind.SequenceIdNotRepresentable, 'ResidueNameTooWide': PdbResidueKeyErrorKind.ResidueNameTooWide, 'ResidueNameNotAscii': PdbResidueKeyErrorKind.ResidueNameNotAscii, 'SegmentTooWide': PdbResidueKeyErrorKind.SegmentTooWide, 'SegmentNotAscii': PdbResidueKeyErrorKind.SegmentNotAscii, 'SegmentNotRepresentable': PdbResidueKeyErrorKind.SegmentNotRepresentable})
values = mappingproxy({0: PdbResidueKeyErrorKind.SequenceIdNotRepresentable, 1: PdbResidueKeyErrorKind.ResidueNameTooWide, 2: PdbResidueKeyErrorKind.ResidueNameNotAscii, 3: PdbResidueKeyErrorKind.SegmentTooWide, 4: PdbResidueKeyErrorKind.SegmentNotAscii, 5: PdbResidueKeyErrorKind.SegmentNotRepresentable})
class cosmolkit.PdbSeqId(seq_num, ins_code=None)

Author residue sequence number paired with an optional insertion code.

Members (2)
ins_code: str | None

Insertion-code character, or None if absent.

seq_num: int

Author residue sequence number.

class cosmolkit.PdbSheetError

Read-only SHEET-record diagnostic retaining source positions and nested record details.

Members (7)
field_offset: int | None

Offset of the failing field in the source record. Applies to PdbSheetError.TextFieldNotUtf8, PdbSheetError.ChainNameNotRepresentable, PdbSheetError.IntegerOutsideSourceDefinedRange. None when this payload is absent.

non_ascii: int | None

Non-ASCII source content reported by the parser. Applies to PdbSheetError.ChainNameNotRepresentable. None when this payload is absent.

sequence_offset: int | None

Position in the input sequence reported by the failure. Applies to PdbSheetError.ResidueAddress. None when this payload is absent.

source: PdbResidueKeyError | None

Structured native error payload. Present for PdbSheetError.ResidueAddress; None when unavailable.

valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbSheetError.TextFieldNotUtf8. None when this payload is absent.

variant: PdbSheetErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

width: int | None

Width reported by the failing native check. Applies to PdbSheetError.ChainNameNotRepresentable, PdbSheetError.IntegerOutsideSourceDefinedRange. None when this payload is absent.

class cosmolkit.PdbSheetErrorKind(value)

Discriminants of PdbSheetErrorKind.

Members: TextFieldNotUtf8, ChainNameNotRepresentable, ResidueAddress, IntegerOutsideSourceDefinedRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
ChainNameNotRepresentable = PdbSheetErrorKind.ChainNameNotRepresentable
IntegerOutsideSourceDefinedRange = PdbSheetErrorKind.IntegerOutsideSourceDefinedRange
ResidueAddress = PdbSheetErrorKind.ResidueAddress
TextFieldNotUtf8 = PdbSheetErrorKind.TextFieldNotUtf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TextFieldNotUtf8': PdbSheetErrorKind.TextFieldNotUtf8, 'ChainNameNotRepresentable': PdbSheetErrorKind.ChainNameNotRepresentable, 'ResidueAddress': PdbSheetErrorKind.ResidueAddress, 'IntegerOutsideSourceDefinedRange': PdbSheetErrorKind.IntegerOutsideSourceDefinedRange})
values = mappingproxy({0: PdbSheetErrorKind.TextFieldNotUtf8, 1: PdbSheetErrorKind.ChainNameNotRepresentable, 2: PdbSheetErrorKind.ResidueAddress, 3: PdbSheetErrorKind.IntegerOutsideSourceDefinedRange})
class cosmolkit.PdbSsbondRecordError

Read-only diagnostic from a disulfide-bond SSBOND record.

Members (4)
byte: int | None

Byte value or byte position reported by the native failure. Applies to PdbSsbondRecordError.ChainNameNotAscii. None when this payload is absent.

partner: int | None

Partner atom or endpoint involved in the native check. Applies to PdbSsbondRecordError.ChainNameNotAscii, PdbSsbondRecordError.ResidueAddress. None when this payload is absent. Disulfide connection partner identified by the native diagnostic.

source: PdbResidueKeyError | None

Structured native error payload. Present for PdbSsbondRecordError.ResidueAddress; None when unavailable.

variant: PdbSsbondRecordErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbSsbondRecordErrorKind(value)

Discriminants of PdbSsbondRecordErrorKind.

Members: EmptyRecord, ChainNameNotAscii, ResidueAddress, CounterOutsideSourceIntRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
ChainNameNotAscii = PdbSsbondRecordErrorKind.ChainNameNotAscii
CounterOutsideSourceIntRange = PdbSsbondRecordErrorKind.CounterOutsideSourceIntRange
EmptyRecord = PdbSsbondRecordErrorKind.EmptyRecord
ResidueAddress = PdbSsbondRecordErrorKind.ResidueAddress
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyRecord': PdbSsbondRecordErrorKind.EmptyRecord, 'ChainNameNotAscii': PdbSsbondRecordErrorKind.ChainNameNotAscii, 'ResidueAddress': PdbSsbondRecordErrorKind.ResidueAddress, 'CounterOutsideSourceIntRange': PdbSsbondRecordErrorKind.CounterOutsideSourceIntRange})
values = mappingproxy({0: PdbSsbondRecordErrorKind.EmptyRecord, 1: PdbSsbondRecordErrorKind.ChainNameNotAscii, 2: PdbSsbondRecordErrorKind.ResidueAddress, 3: PdbSsbondRecordErrorKind.CounterOutsideSourceIntRange})
exception cosmolkit.PdbSsbondResolutionError(*args, **kwargs)

PdbSsbondResolutionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property atom_name: str

Atom name that could not be resolved for the disulfide connection.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property partner: int

Disulfide connection partner identified by the native diagnostic.

class cosmolkit.PdbStructureFinalizationError

Read-only structure finalization diagnostic, including chemical-component and structure-validation failures.

Members (11)
actual: int | None

Observed value reported by the native check. Applies to PdbStructureFinalizationError.StagingRowOrder. None when this payload is absent.

ccd: PdbResidueKeyError | None

Structured native error payload. Present for PdbStructureFinalizationError.Ccd; None when unavailable.

connection: PdbConnectionFinalizationError | None

Structural connection involved in the failure. Applies to PdbStructureFinalizationError.Connection. None when this payload is absent.

expected: int | None

Required value reported by the native check. Applies to PdbStructureFinalizationError.StagingRowOrder. None when this payload is absent.

field: str | None

Field whose content or type caused the failure. Applies to PdbStructureFinalizationError.SourceIdNotRepresentable, PdbStructureFinalizationError.Utf8. None when this payload is absent.

model: PdbModelTransitionError | None

Structural model involved in the failure. Applies to PdbStructureFinalizationError.Model. None when this payload is absent.

remarks: PdbRemarkFinalizationError | None

Remark records involved in the parsing failure. Applies to PdbStructureFinalizationError.Remarks. None when this payload is absent.

structure: BioStructureError | None

Structured native error payload. Present for PdbStructureFinalizationError.Structure; None when unavailable.

table: str | None

Table involved in the failed lookup or consistency check. Applies to PdbStructureFinalizationError.StagingRowOrder. None when this payload is absent.

valid_up_to: int | None

Length in bytes of the valid UTF-8 prefix before the encoding error. Applies to PdbStructureFinalizationError.Utf8. None when this payload is absent.

variant: PdbStructureFinalizationErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PdbStructureFinalizationErrorKind(value)

Discriminants of PdbStructureFinalizationErrorKind.

Members: Model, Connection, Remarks, Ccd, NoModelAfterDefault, SourceIdNotRepresentable, Utf8, Structure, StagingRowOrder, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
Ccd = PdbStructureFinalizationErrorKind.Ccd
Connection = PdbStructureFinalizationErrorKind.Connection
Model = PdbStructureFinalizationErrorKind.Model
NoModelAfterDefault = PdbStructureFinalizationErrorKind.NoModelAfterDefault
Remarks = PdbStructureFinalizationErrorKind.Remarks
SourceIdNotRepresentable = PdbStructureFinalizationErrorKind.SourceIdNotRepresentable
StagingRowOrder = PdbStructureFinalizationErrorKind.StagingRowOrder
Structure = PdbStructureFinalizationErrorKind.Structure
Utf8 = PdbStructureFinalizationErrorKind.Utf8
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Model': PdbStructureFinalizationErrorKind.Model, 'Connection': PdbStructureFinalizationErrorKind.Connection, 'Remarks': PdbStructureFinalizationErrorKind.Remarks, 'Ccd': PdbStructureFinalizationErrorKind.Ccd, 'NoModelAfterDefault': PdbStructureFinalizationErrorKind.NoModelAfterDefault, 'SourceIdNotRepresentable': PdbStructureFinalizationErrorKind.SourceIdNotRepresentable, 'Utf8': PdbStructureFinalizationErrorKind.Utf8, 'Structure': PdbStructureFinalizationErrorKind.Structure, 'StagingRowOrder': PdbStructureFinalizationErrorKind.StagingRowOrder})
values = mappingproxy({0: PdbStructureFinalizationErrorKind.Model, 1: PdbStructureFinalizationErrorKind.Connection, 2: PdbStructureFinalizationErrorKind.Remarks, 3: PdbStructureFinalizationErrorKind.Ccd, 4: PdbStructureFinalizationErrorKind.NoModelAfterDefault, 5: PdbStructureFinalizationErrorKind.SourceIdNotRepresentable, 6: PdbStructureFinalizationErrorKind.Utf8, 7: PdbStructureFinalizationErrorKind.Structure, 8: PdbStructureFinalizationErrorKind.StagingRowOrder})
exception cosmolkit.PdbWriteError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PdbWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property dimension: CoordinateDimension | None

Readonly dimension payload of the MissingCoordinate error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property feature: str | None

Readonly feature payload of the Unsupported error variant; None for other variants.

property id: int | None

Identifier involved in the native failure. Applies to PdbWriteError.ConformerNotFound, PdbWriteError.MissingCoordinate. None when this payload is absent.

property property_error: PropertyStringError | None

“error_payload”} Structured PropertyStringError payload of PdbWriteError.Property; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: TopologyValidationError | CoordinateValidationError | KekulizeError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property three_d: int | None

Readonly three_d payload of the AmbiguousCoordinates error variant; None for other variants.

property two_d: int | None

Readonly two_d payload of the AmbiguousCoordinates error variant; None for other variants.

property variant: PdbWriteErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PdbWriteErrorKind(value)

Discriminants of PdbWriteErrorKind.

Members: Property, ConformerNotFound, Unsupported, Topology, Coordinates, AmbiguousCoordinates, MissingCoordinate, ConflictingCoordinateSelection, Kekulize, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
AmbiguousCoordinates = PdbWriteErrorKind.AmbiguousCoordinates
ConflictingCoordinateSelection = PdbWriteErrorKind.ConflictingCoordinateSelection
ConformerNotFound = PdbWriteErrorKind.ConformerNotFound
Coordinates = PdbWriteErrorKind.Coordinates
Kekulize = PdbWriteErrorKind.Kekulize
MissingCoordinate = PdbWriteErrorKind.MissingCoordinate
Property = PdbWriteErrorKind.Property
Topology = PdbWriteErrorKind.Topology
Unsupported = PdbWriteErrorKind.Unsupported
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Property': PdbWriteErrorKind.Property, 'ConformerNotFound': PdbWriteErrorKind.ConformerNotFound, 'Unsupported': PdbWriteErrorKind.Unsupported, 'Topology': PdbWriteErrorKind.Topology, 'Coordinates': PdbWriteErrorKind.Coordinates, 'AmbiguousCoordinates': PdbWriteErrorKind.AmbiguousCoordinates, 'MissingCoordinate': PdbWriteErrorKind.MissingCoordinate, 'ConflictingCoordinateSelection': PdbWriteErrorKind.ConflictingCoordinateSelection, 'Kekulize': PdbWriteErrorKind.Kekulize})
values = mappingproxy({0: PdbWriteErrorKind.Property, 1: PdbWriteErrorKind.ConformerNotFound, 2: PdbWriteErrorKind.Unsupported, 3: PdbWriteErrorKind.Topology, 4: PdbWriteErrorKind.Coordinates, 5: PdbWriteErrorKind.AmbiguousCoordinates, 6: PdbWriteErrorKind.MissingCoordinate, 7: PdbWriteErrorKind.ConflictingCoordinateSelection, 8: PdbWriteErrorKind.Kekulize})
class cosmolkit.PdbWriteFlags

PdbWriteFlags native option bit mask. Combine named constants with the bitwise OR operator; bits exposes its integer representation.

Members (10)
BIDIRECTIONAL_CONECT = <cosmolkit.PdbWriteFlags object>
MASTER = <cosmolkit.PdbWriteFlags object>
NONE = <cosmolkit.PdbWriteFlags object>
NO_BOND_ORDER = <cosmolkit.PdbWriteFlags object>
OMIT_SINGLE_CONECT = <cosmolkit.PdbWriteFlags object>
TER = <cosmolkit.PdbWriteFlags object>
bits: int

Integer representation of this option mask.

contains(flags) → bool

Whether every bit in the supplied mask is present.

static from_bits(bits) → PdbWriteFlags

Construct a mask from the native integer flag representation.

is_empty: bool

Whether the mask contains no enabled options.

class cosmolkit.PdbWriteParams(*, coordinate_selection=Ellipsis, all_conformers=Ellipsis, flavor=Ellipsis)

Public exporter policy: unique-or-explicit coordinates, or all stored sets. All-set output uses 2D storage order followed by 3D storage order; IDs are not assumed contiguous. PDB stores 2D positions with z=0 and cannot retain the coordinate dimension or arbitrary CK conformer identifiers.

Members (3)
all_conformers: bool

Write every stored coordinate set rather than a single selected set.

coordinate_selection: MolCoordinateSelection

Select a stored 2D or 3D coordinate set when not exporting all conformers.

flavor: PdbWriteFlags

PDB connectivity and record-format flags.

exception cosmolkit.PeriodicTableError(*args, **kwargs)

PeriodicTableError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property element: int

Atomic number involved in the failed lookup.

property isotope: int

Isotope mass number involved in the failed lookup.

property variant: PeriodicTableErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PeriodicTableErrorKind(value)

Discriminants of PeriodicTableErrorKind.

Members: UnknownIsotope, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
UnknownIsotope = PeriodicTableErrorKind.UnknownIsotope
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnknownIsotope': PeriodicTableErrorKind.UnknownIsotope})
values = mappingproxy({0: PeriodicTableErrorKind.UnknownIsotope})
exception cosmolkit.PickleError(*args, **kwargs)

Failure in the serialization domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PickleError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (14)
property actual: int | None

Readonly actual payload of the DataLengthMismatch error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the DataLengthMismatch error variant; None for other variants.

property length: int | None

Length relevant to the failed bounds check. Present for PickleError.TooManyAtoms, PickleError.TooManyBonds, PickleError.StringTooLong; None when unavailable.

property major: int | None

Readonly major payload of the UnsupportedArchiveVersion error variant; None for other variants.

property message: str | None

Native diagnostic message. Present for PickleError.InvalidArchive, PickleError.InvalidMolecule; None when unavailable.

property minor: int | None

Readonly minor payload of the UnsupportedArchiveVersion error variant; None for other variants.

property section: int | None

Binary or textual input section containing the failure. Present for PickleError.UnsupportedSectionVersion, PickleError.MissingRequiredSection, PickleError.DuplicateSection, PickleError.UnknownRequiredSection; None when unavailable.

property source: StereoGroupError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property type_name: str | None

Readonly type_name payload of the InvalidEnumValue error variant; None for other variants.

property value: int | None

Readonly value payload of the InvalidEnumValue error variant; None for other variants.

property variant: PickleErrorKind

Exact Rust error variant, independent of the human-readable message.

property version: int | None

Input format version associated with the failure. Present for PickleError.UnsupportedVersion, PickleError.UnsupportedSectionVersion; None when unavailable.

class cosmolkit.PickleErrorKind(value)

Discriminants of PickleErrorKind.

Members: StereoGroup, UnexpectedEof, UnsupportedVersion, UnsupportedArchiveVersion, UnsupportedSectionVersion, InvalidArchive, MissingRequiredSection, DuplicateSection, UnknownRequiredSection, DataLengthMismatch, InvalidEnumValue, InvalidMolecule, TooManyAtoms, TooManyBonds, StringTooLong, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (18)
DataLengthMismatch = PickleErrorKind.DataLengthMismatch
DuplicateSection = PickleErrorKind.DuplicateSection
InvalidArchive = PickleErrorKind.InvalidArchive
InvalidEnumValue = PickleErrorKind.InvalidEnumValue
InvalidMolecule = PickleErrorKind.InvalidMolecule
MissingRequiredSection = PickleErrorKind.MissingRequiredSection
StereoGroup = PickleErrorKind.StereoGroup
StringTooLong = PickleErrorKind.StringTooLong
TooManyAtoms = PickleErrorKind.TooManyAtoms
TooManyBonds = PickleErrorKind.TooManyBonds
UnexpectedEof = PickleErrorKind.UnexpectedEof
UnknownRequiredSection = PickleErrorKind.UnknownRequiredSection
UnsupportedArchiveVersion = PickleErrorKind.UnsupportedArchiveVersion
UnsupportedSectionVersion = PickleErrorKind.UnsupportedSectionVersion
UnsupportedVersion = PickleErrorKind.UnsupportedVersion
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': PickleErrorKind.StereoGroup, 'UnexpectedEof': PickleErrorKind.UnexpectedEof, 'UnsupportedVersion': PickleErrorKind.UnsupportedVersion, 'UnsupportedArchiveVersion': PickleErrorKind.UnsupportedArchiveVersion, 'UnsupportedSectionVersion': PickleErrorKind.UnsupportedSectionVersion, 'InvalidArchive': PickleErrorKind.InvalidArchive, 'MissingRequiredSection': PickleErrorKind.MissingRequiredSection, 'DuplicateSection': PickleErrorKind.DuplicateSection, 'UnknownRequiredSection': PickleErrorKind.UnknownRequiredSection, 'DataLengthMismatch': PickleErrorKind.DataLengthMismatch, 'InvalidEnumValue': PickleErrorKind.InvalidEnumValue, 'InvalidMolecule': PickleErrorKind.InvalidMolecule, 'TooManyAtoms': PickleErrorKind.TooManyAtoms, 'TooManyBonds': PickleErrorKind.TooManyBonds, 'StringTooLong': PickleErrorKind.StringTooLong})
values = mappingproxy({0: PickleErrorKind.StereoGroup, 1: PickleErrorKind.UnexpectedEof, 2: PickleErrorKind.UnsupportedVersion, 3: PickleErrorKind.UnsupportedArchiveVersion, 4: PickleErrorKind.UnsupportedSectionVersion, 5: PickleErrorKind.InvalidArchive, 6: PickleErrorKind.MissingRequiredSection, 7: PickleErrorKind.DuplicateSection, 8: PickleErrorKind.UnknownRequiredSection, 9: PickleErrorKind.DataLengthMismatch, 10: PickleErrorKind.InvalidEnumValue, 11: PickleErrorKind.InvalidMolecule, 12: PickleErrorKind.TooManyAtoms, 13: PickleErrorKind.TooManyBonds, 14: PickleErrorKind.StringTooLong})
exception cosmolkit.PoisonError(*args, **kwargs)

PoisonError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (1)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

class cosmolkit.PolymerKind(value)

Typed PolymerKind values corresponding to the Rust enum.

Members: Unknown, PeptideL, PeptideD, Dna, Rna, DnaRnaHybrid, SaccharideD, SaccharideL, Pna, CyclicPseudoPeptide, Other, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (14)
CyclicPseudoPeptide = PolymerKind.CyclicPseudoPeptide
Dna = PolymerKind.Dna
DnaRnaHybrid = PolymerKind.DnaRnaHybrid
Other = PolymerKind.Other
PeptideD = PolymerKind.PeptideD
PeptideL = PolymerKind.PeptideL
Pna = PolymerKind.Pna
Rna = PolymerKind.Rna
SaccharideD = PolymerKind.SaccharideD
SaccharideL = PolymerKind.SaccharideL
Unknown = PolymerKind.Unknown
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unknown': PolymerKind.Unknown, 'PeptideL': PolymerKind.PeptideL, 'PeptideD': PolymerKind.PeptideD, 'Dna': PolymerKind.Dna, 'Rna': PolymerKind.Rna, 'DnaRnaHybrid': PolymerKind.DnaRnaHybrid, 'SaccharideD': PolymerKind.SaccharideD, 'SaccharideL': PolymerKind.SaccharideL, 'Pna': PolymerKind.Pna, 'CyclicPseudoPeptide': PolymerKind.CyclicPseudoPeptide, 'Other': PolymerKind.Other})
values = mappingproxy({0: PolymerKind.Unknown, 1: PolymerKind.PeptideL, 2: PolymerKind.PeptideD, 3: PolymerKind.Dna, 4: PolymerKind.Rna, 5: PolymerKind.DnaRnaHybrid, 6: PolymerKind.SaccharideD, 7: PolymerKind.SaccharideL, 8: PolymerKind.Pna, 9: PolymerKind.CyclicPseudoPeptide, 10: PolymerKind.Other})
class cosmolkit.PotentialStereoCenter

Atom-or-bond location of a potential stereochemical element.

Members (2)
index: int

Zero-based atom or bond index, interpreted according to kind.

kind: str

Whether the stereochemical center is an atom or a bond, returned as ‘atom’ or ‘bond’.

class cosmolkit.PotentialStereoDescriptor(value)

Typed PotentialStereoDescriptor values corresponding to the Rust enum.

Members: None, TetrahedralClockwise, TetrahedralCounterclockwise, BondCis, BondTrans, BondAtropCw, BondAtropCcw, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (17)
BOND_ATROP_CCW = PotentialStereoDescriptor.BondAtropCcw
BOND_ATROP_CW = PotentialStereoDescriptor.BondAtropCw
BOND_CIS = PotentialStereoDescriptor.BondCis
BOND_TRANS = PotentialStereoDescriptor.BondTrans
BondAtropCcw = PotentialStereoDescriptor.BondAtropCcw
BondAtropCw = PotentialStereoDescriptor.BondAtropCw
BondCis = PotentialStereoDescriptor.BondCis
BondTrans = PotentialStereoDescriptor.BondTrans
NONE = PotentialStereoDescriptor.None_
None_ = PotentialStereoDescriptor.None_
TETRAHEDRAL_CLOCKWISE = PotentialStereoDescriptor.TetrahedralClockwise
TETRAHEDRAL_COUNTERCLOCKWISE = PotentialStereoDescriptor.TetrahedralCounterclockwise
TetrahedralClockwise = PotentialStereoDescriptor.TetrahedralClockwise
TetrahedralCounterclockwise = PotentialStereoDescriptor.TetrahedralCounterclockwise
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'None_': PotentialStereoDescriptor.None_, 'NONE': PotentialStereoDescriptor.None_, 'TetrahedralClockwise': PotentialStereoDescriptor.TetrahedralClockwise, 'TETRAHEDRAL_CLOCKWISE': PotentialStereoDescriptor.TetrahedralClockwise, 'TetrahedralCounterclockwise': PotentialStereoDescriptor.TetrahedralCounterclockwise, 'TETRAHEDRAL_COUNTERCLOCKWISE': PotentialStereoDescriptor.TetrahedralCounterclockwise, 'BondCis': PotentialStereoDescriptor.BondCis, 'BOND_CIS': PotentialStereoDescriptor.BondCis, 'BondTrans': PotentialStereoDescriptor.BondTrans, 'BOND_TRANS': PotentialStereoDescriptor.BondTrans, 'BondAtropCw': PotentialStereoDescriptor.BondAtropCw, 'BOND_ATROP_CW': PotentialStereoDescriptor.BondAtropCw, 'BondAtropCcw': PotentialStereoDescriptor.BondAtropCcw, 'BOND_ATROP_CCW': PotentialStereoDescriptor.BondAtropCcw})
values = mappingproxy({0: PotentialStereoDescriptor.None_, 1: PotentialStereoDescriptor.TetrahedralClockwise, 2: PotentialStereoDescriptor.TetrahedralCounterclockwise, 3: PotentialStereoDescriptor.BondCis, 4: PotentialStereoDescriptor.BondTrans, 5: PotentialStereoDescriptor.BondAtropCw, 6: PotentialStereoDescriptor.BondAtropCcw})
exception cosmolkit.PotentialStereoError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PotentialStereoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (20)
property actual: int | None

Readonly actual payload of the InvalidValence error variant; None for other variants.

property atom: int | None

Atom identifier implicated in the failure. Applies to PotentialStereoError.InvalidPropertyKind, PotentialStereoError.InvalidRingStereoReference, PotentialStereoError.EmptyRingStereoReferences, PotentialStereoError.InvalidValenceValue, PotentialStereoError.AtomOutOfRange, PotentialStereoError.InvalidAtomDegree, PotentialStereoError.InvalidChiralPermutation. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to PotentialStereoError.InvalidValence, PotentialStereoError.AtomOutOfRange. None when this payload is absent.

property bond: int | None

Bond identifier implicated in the failure. Applies to PotentialStereoError.InvalidBondDegree, PotentialStereoError.InvalidStereoReferences, PotentialStereoError.UnsupportedBondOrder, PotentialStereoError.AtropisomerDependencyUnavailable. None when this payload is absent.

property degree: int | None

Neighbor count reported by the native check. Applies to PotentialStereoError.InvalidAtomDegree, PotentialStereoError.InvalidBondDegree. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property endpoint: str | None

Readonly endpoint payload of the InvalidBondDegree error variant; None for other variants.

property field: str | None

Field whose content or type caused the failure. Applies to PotentialStereoError.InvalidValence, PotentialStereoError.InvalidValenceValue. None when this payload is absent.

property iterations: int | None

Readonly iterations payload of the RefinementDidNotConverge error variant; None for other variants.

property kind: PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to PotentialStereoError.InvalidPropertyKind. None when this payload is absent.

Type:

{“role”

property limit: int | None

Readonly limit payload of the InvalidRingInfo error variant; None for other variants.

property order: BondOrder | None

Readonly order payload of the UnsupportedBondOrder error variant; None for other variants.

property permutation: int | None

Readonly permutation payload of the InvalidChiralPermutation error variant; None for other variants.

property property: str | None

Readonly property payload of the InvalidPropertyKind error variant; None for other variants.

property reason: str | None

Native explanation for rejecting the operation. Applies to PotentialStereoError.InvalidRingInfo, PotentialStereoError.InvalidStereoReferences. None when this payload is absent.

property row: int | None

Readonly row payload of the InvalidRingInfo error variant; None for other variants.

property source: RingFindingError | CanonicalRankError | TopologyValidationError | ValenceError | StereoOrderError | DoubleBondStereoError | BondValueError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: int | None

Value rejected or reported by the native operation. Applies to PotentialStereoError.InvalidRingStereoReference, PotentialStereoError.InvalidValenceValue, PotentialStereoError.InvalidRingInfo. None when this payload is absent.

property variant: PotentialStereoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PotentialStereoErrorKind(value)

Discriminants of PotentialStereoErrorKind.

Members: InvalidPropertyKind, InvalidRingStereoReference, EmptyRingStereoReferences, Ring, Rank, InvalidTopology, InvalidValence, InvalidValenceValue, AtomOutOfRange, InvalidRingInfo, InvalidAtomDegree, InvalidBondDegree, InvalidStereoReferences, UnsupportedBondOrder, InvalidChiralPermutation, AtropisomerDependencyUnavailable, RefinementDidNotConverge, Valence, StereoOrder, DoubleStereo, BondValue, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (24)
AtomOutOfRange = PotentialStereoErrorKind.AtomOutOfRange
AtropisomerDependencyUnavailable = PotentialStereoErrorKind.AtropisomerDependencyUnavailable
BondValue = PotentialStereoErrorKind.BondValue
DoubleStereo = PotentialStereoErrorKind.DoubleStereo
EmptyRingStereoReferences = PotentialStereoErrorKind.EmptyRingStereoReferences
InvalidAtomDegree = PotentialStereoErrorKind.InvalidAtomDegree
InvalidBondDegree = PotentialStereoErrorKind.InvalidBondDegree
InvalidChiralPermutation = PotentialStereoErrorKind.InvalidChiralPermutation
InvalidPropertyKind = PotentialStereoErrorKind.InvalidPropertyKind
InvalidRingInfo = PotentialStereoErrorKind.InvalidRingInfo
InvalidRingStereoReference = PotentialStereoErrorKind.InvalidRingStereoReference
InvalidStereoReferences = PotentialStereoErrorKind.InvalidStereoReferences
InvalidTopology = PotentialStereoErrorKind.InvalidTopology
InvalidValence = PotentialStereoErrorKind.InvalidValence
InvalidValenceValue = PotentialStereoErrorKind.InvalidValenceValue
Rank = PotentialStereoErrorKind.Rank
RefinementDidNotConverge = PotentialStereoErrorKind.RefinementDidNotConverge
Ring = PotentialStereoErrorKind.Ring
StereoOrder = PotentialStereoErrorKind.StereoOrder
UnsupportedBondOrder = PotentialStereoErrorKind.UnsupportedBondOrder
Valence = PotentialStereoErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidPropertyKind': PotentialStereoErrorKind.InvalidPropertyKind, 'InvalidRingStereoReference': PotentialStereoErrorKind.InvalidRingStereoReference, 'EmptyRingStereoReferences': PotentialStereoErrorKind.EmptyRingStereoReferences, 'Ring': PotentialStereoErrorKind.Ring, 'Rank': PotentialStereoErrorKind.Rank, 'InvalidTopology': PotentialStereoErrorKind.InvalidTopology, 'InvalidValence': PotentialStereoErrorKind.InvalidValence, 'InvalidValenceValue': PotentialStereoErrorKind.InvalidValenceValue, 'AtomOutOfRange': PotentialStereoErrorKind.AtomOutOfRange, 'InvalidRingInfo': PotentialStereoErrorKind.InvalidRingInfo, 'InvalidAtomDegree': PotentialStereoErrorKind.InvalidAtomDegree, 'InvalidBondDegree': PotentialStereoErrorKind.InvalidBondDegree, 'InvalidStereoReferences': PotentialStereoErrorKind.InvalidStereoReferences, 'UnsupportedBondOrder': PotentialStereoErrorKind.UnsupportedBondOrder, 'InvalidChiralPermutation': PotentialStereoErrorKind.InvalidChiralPermutation, 'AtropisomerDependencyUnavailable': PotentialStereoErrorKind.AtropisomerDependencyUnavailable, 'RefinementDidNotConverge': PotentialStereoErrorKind.RefinementDidNotConverge, 'Valence': PotentialStereoErrorKind.Valence, 'StereoOrder': PotentialStereoErrorKind.StereoOrder, 'DoubleStereo': PotentialStereoErrorKind.DoubleStereo, 'BondValue': PotentialStereoErrorKind.BondValue})
values = mappingproxy({0: PotentialStereoErrorKind.InvalidPropertyKind, 1: PotentialStereoErrorKind.InvalidRingStereoReference, 2: PotentialStereoErrorKind.EmptyRingStereoReferences, 3: PotentialStereoErrorKind.Ring, 4: PotentialStereoErrorKind.Rank, 5: PotentialStereoErrorKind.InvalidTopology, 6: PotentialStereoErrorKind.InvalidValence, 7: PotentialStereoErrorKind.InvalidValenceValue, 8: PotentialStereoErrorKind.AtomOutOfRange, 9: PotentialStereoErrorKind.InvalidRingInfo, 10: PotentialStereoErrorKind.InvalidAtomDegree, 11: PotentialStereoErrorKind.InvalidBondDegree, 12: PotentialStereoErrorKind.InvalidStereoReferences, 13: PotentialStereoErrorKind.UnsupportedBondOrder, 14: PotentialStereoErrorKind.InvalidChiralPermutation, 15: PotentialStereoErrorKind.AtropisomerDependencyUnavailable, 16: PotentialStereoErrorKind.RefinementDidNotConverge, 17: PotentialStereoErrorKind.Valence, 18: PotentialStereoErrorKind.StereoOrder, 19: PotentialStereoErrorKind.DoubleStereo, 20: PotentialStereoErrorKind.BondValue})
class cosmolkit.PotentialStereoInfo(stereo_type, specified, centered_on, descriptor, permutation, controlling_atoms)

Geometric type, specification state and controlling atoms for a potential stereochemical element.

Members (6)
centered_on: PotentialStereoCenter

Atom or bond identifying the stereochemical center.

controlling_atoms: list[int | None]

Ordered controlling atom indices, with None for source sentinel positions.

descriptor: PotentialStereoDescriptor

Native stereochemical descriptor for this element.

permutation: int

Permutation index used for non-tetrahedral stereochemistry.

specified: PotentialStereoSpecified

Whether stereochemistry is specified, unspecified or explicitly unknown.

stereo_type: PotentialStereoType

Geometric type of the potential stereochemical element.

class cosmolkit.PotentialStereoParams(*, clean=Ellipsis, flag_possible=Ellipsis, allow_nontetrahedral=Ellipsis)

Options for identifying possible stereochemical centers and bonds.

Members (3)
allow_nontetrahedral: bool

Consider supported non-tetrahedral stereochemical geometries.

clean: bool

Remove invalid existing stereochemical annotations.

flag_possible: bool

Flag potential stereochemical elements even when unspecified.

class cosmolkit.PotentialStereoResult(stereo, atom_ranks, ring_relations, cleaned_molecule)

Potential stereochemical elements, atom ranks, ring relationships and optional cleaned molecule.

Members (4)
atom_ranks: list[int]

Native atom ranks used during potential stereochemistry detection.

cleaned_molecule: Molecule | None

COW molecular value with cleaned stereochemistry, or None when no cleaned value was produced.

ring_relations: list[RingStereoRelation]

Independent list of ring stereochemistry relationships.

stereo: list[PotentialStereoInfo]

Independent list of identified potential stereochemical elements.

class cosmolkit.PotentialStereoSpecified(value)

Typed PotentialStereoSpecified values corresponding to the Rust enum.

Members: Unspecified, Specified, Unknown, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (9)
SPECIFIED = PotentialStereoSpecified.Specified
Specified = PotentialStereoSpecified.Specified
UNKNOWN = PotentialStereoSpecified.Unknown
UNSPECIFIED = PotentialStereoSpecified.Unspecified
Unknown = PotentialStereoSpecified.Unknown
Unspecified = PotentialStereoSpecified.Unspecified
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unspecified': PotentialStereoSpecified.Unspecified, 'UNSPECIFIED': PotentialStereoSpecified.Unspecified, 'Specified': PotentialStereoSpecified.Specified, 'SPECIFIED': PotentialStereoSpecified.Specified, 'Unknown': PotentialStereoSpecified.Unknown, 'UNKNOWN': PotentialStereoSpecified.Unknown})
values = mappingproxy({0: PotentialStereoSpecified.Unspecified, 1: PotentialStereoSpecified.Specified, 2: PotentialStereoSpecified.Unknown})
class cosmolkit.PotentialStereoType(value)

Typed PotentialStereoType values corresponding to the Rust enum.

Members: AtomTetrahedral, AtomSquarePlanar, AtomTrigonalBipyramidal, AtomOctahedral, BondDouble, BondCumuleneEven, BondAtropisomer, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (17)
ATOM_OCTAHEDRAL = PotentialStereoType.AtomOctahedral
ATOM_SQUAREPLANAR = PotentialStereoType.AtomSquarePlanar
ATOM_TETRAHEDRAL = PotentialStereoType.AtomTetrahedral
ATOM_TRIGONALBIPYRAMIDAL = PotentialStereoType.AtomTrigonalBipyramidal
AtomOctahedral = PotentialStereoType.AtomOctahedral
AtomSquarePlanar = PotentialStereoType.AtomSquarePlanar
AtomTetrahedral = PotentialStereoType.AtomTetrahedral
AtomTrigonalBipyramidal = PotentialStereoType.AtomTrigonalBipyramidal
BOND_ATROPISOMER = PotentialStereoType.BondAtropisomer
BOND_CUMULENE_EVEN = PotentialStereoType.BondCumuleneEven
BOND_DOUBLE = PotentialStereoType.BondDouble
BondAtropisomer = PotentialStereoType.BondAtropisomer
BondCumuleneEven = PotentialStereoType.BondCumuleneEven
BondDouble = PotentialStereoType.BondDouble
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'AtomTetrahedral': PotentialStereoType.AtomTetrahedral, 'ATOM_TETRAHEDRAL': PotentialStereoType.AtomTetrahedral, 'AtomSquarePlanar': PotentialStereoType.AtomSquarePlanar, 'ATOM_SQUAREPLANAR': PotentialStereoType.AtomSquarePlanar, 'AtomTrigonalBipyramidal': PotentialStereoType.AtomTrigonalBipyramidal, 'ATOM_TRIGONALBIPYRAMIDAL': PotentialStereoType.AtomTrigonalBipyramidal, 'AtomOctahedral': PotentialStereoType.AtomOctahedral, 'ATOM_OCTAHEDRAL': PotentialStereoType.AtomOctahedral, 'BondDouble': PotentialStereoType.BondDouble, 'BOND_DOUBLE': PotentialStereoType.BondDouble, 'BondCumuleneEven': PotentialStereoType.BondCumuleneEven, 'BOND_CUMULENE_EVEN': PotentialStereoType.BondCumuleneEven, 'BondAtropisomer': PotentialStereoType.BondAtropisomer, 'BOND_ATROPISOMER': PotentialStereoType.BondAtropisomer})
values = mappingproxy({0: PotentialStereoType.AtomTetrahedral, 1: PotentialStereoType.AtomSquarePlanar, 2: PotentialStereoType.AtomTrigonalBipyramidal, 3: PotentialStereoType.AtomOctahedral, 4: PotentialStereoType.BondDouble, 5: PotentialStereoType.BondCumuleneEven, 6: PotentialStereoType.BondAtropisomer})
exception cosmolkit.PropertyCacheError(*args, **kwargs)

Failure in the property_cache domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PropertyCacheError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: ValenceError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError

“error_payload”} Valence value rejected by the native check. Applies to PropertyCacheError.Valence.

Type:

{“role”

property variant: PropertyCacheErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PropertyCacheErrorKind(value)

Discriminants of PropertyCacheErrorKind.

Members: Valence, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
Valence = PropertyCacheErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Valence': PropertyCacheErrorKind.Valence})
values = mappingproxy({0: PropertyCacheErrorKind.Valence})
exception cosmolkit.PropertyIntReadError(*args, **kwargs)

Failure in the property domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PropertyIntReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property kind: PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to PropertyIntReadError.InvalidKind. None when this payload is absent.

Type:

{“role”

property magnitude: int | None

Readonly magnitude payload of the SignedTextOverflow error variant; None for other variants.

property negative: bool | None

Readonly negative payload of the SignedTextOverflow error variant; None for other variants.

property source: UIntLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: int | str | None

Value rejected or reported by the native operation. Applies to PropertyIntReadError.UnsignedOverflow, PropertyIntReadError.SignedTextOverflow, PropertyIntReadError.Lexical, PropertyIntReadError.InvalidKind. None when this payload is absent.

property variant: PropertyIntReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PropertyIntReadErrorKind(value)

Discriminants of PropertyIntReadErrorKind.

Members: UnsignedOverflow, InvalidKind, SignedTextOverflow, Lexical, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
InvalidKind = PropertyIntReadErrorKind.InvalidKind
Lexical = PropertyIntReadErrorKind.Lexical
SignedTextOverflow = PropertyIntReadErrorKind.SignedTextOverflow
UnsignedOverflow = PropertyIntReadErrorKind.UnsignedOverflow
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnsignedOverflow': PropertyIntReadErrorKind.UnsignedOverflow, 'InvalidKind': PropertyIntReadErrorKind.InvalidKind, 'SignedTextOverflow': PropertyIntReadErrorKind.SignedTextOverflow, 'Lexical': PropertyIntReadErrorKind.Lexical})
values = mappingproxy({0: PropertyIntReadErrorKind.UnsignedOverflow, 1: PropertyIntReadErrorKind.InvalidKind, 2: PropertyIntReadErrorKind.SignedTextOverflow, 3: PropertyIntReadErrorKind.Lexical})
exception cosmolkit.PropertyStringError(*args, **kwargs)

PropertyStringError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property kind: PropertyValueKind

Preserve the actual canonical Rust method; this is not a discriminator.

property variant: PropertyStringErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.PropertyStringErrorKind(value)

Discriminants of PropertyStringErrorKind.

Members: UnsupportedKind, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
UnsupportedKind = PropertyStringErrorKind.UnsupportedKind
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnsupportedKind': PropertyStringErrorKind.UnsupportedKind})
values = mappingproxy({0: PropertyStringErrorKind.UnsupportedKind})
exception cosmolkit.PropertyUIntReadError(*args, **kwargs)

Failure in the property domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PropertyUIntReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property kind: PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to PropertyUIntReadError.InvalidKind. None when this payload is absent.

Type:

{“role”

property source: UIntLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: int | str | None

Value rejected or reported by the native operation. Applies to PropertyUIntReadError.Negative, PropertyUIntReadError.Lexical, PropertyUIntReadError.InvalidKind. None when this payload is absent.

property variant: PropertyUIntReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PropertyUIntReadErrorKind(value)

Discriminants of PropertyUIntReadErrorKind.

Members: Negative, InvalidKind, Lexical, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
InvalidKind = PropertyUIntReadErrorKind.InvalidKind
Lexical = PropertyUIntReadErrorKind.Lexical
Negative = PropertyUIntReadErrorKind.Negative
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Negative': PropertyUIntReadErrorKind.Negative, 'InvalidKind': PropertyUIntReadErrorKind.InvalidKind, 'Lexical': PropertyUIntReadErrorKind.Lexical})
values = mappingproxy({0: PropertyUIntReadErrorKind.Negative, 1: PropertyUIntReadErrorKind.InvalidKind, 2: PropertyUIntReadErrorKind.Lexical})
exception cosmolkit.PropertyULongReadError(*args, **kwargs)

Failure in the property domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PropertyULongReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property kind: PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to PropertyULongReadError.InvalidKind. None when this payload is absent.

Type:

{“role”

property source: UIntLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: int | str | None

Value rejected or reported by the native operation. Applies to PropertyULongReadError.Negative, PropertyULongReadError.Lexical, PropertyULongReadError.LexicalOverflow, PropertyULongReadError.InvalidKind. None when this payload is absent.

property variant: PropertyULongReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PropertyULongReadErrorKind(value)

Discriminants of PropertyULongReadErrorKind.

Members: Negative, InvalidKind, LexicalOverflow, Lexical, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
InvalidKind = PropertyULongReadErrorKind.InvalidKind
Lexical = PropertyULongReadErrorKind.Lexical
LexicalOverflow = PropertyULongReadErrorKind.LexicalOverflow
Negative = PropertyULongReadErrorKind.Negative
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Negative': PropertyULongReadErrorKind.Negative, 'InvalidKind': PropertyULongReadErrorKind.InvalidKind, 'LexicalOverflow': PropertyULongReadErrorKind.LexicalOverflow, 'Lexical': PropertyULongReadErrorKind.Lexical})
values = mappingproxy({0: PropertyULongReadErrorKind.Negative, 1: PropertyULongReadErrorKind.InvalidKind, 2: PropertyULongReadErrorKind.LexicalOverflow, 3: PropertyULongReadErrorKind.Lexical})
class cosmolkit.PropertyValue

Explicitly tagged molecular property value. Typed reads require the matching stored variant and do not coerce other kinds.

Members (14)
static Bool(value) → PropertyValue

Create a Boolean property value.

static Double(value) → PropertyValue

Create a double-precision floating-point property value.

static Int(value) → PropertyValue

Create a signed 32-bit integer property value.

static IntVector(value) → PropertyValue

Create a vector of signed 32-bit integer property values.

static String(value) → PropertyValue

Create a String property value from Python text.

static StringVector(value) → PropertyValue

Create a vector of string property values.

static UInt(value) → PropertyValue

Create an unsigned 32-bit integer property value.

as_bool() → bool

Read a Bool value; raise PropertyValueError for a different stored variant.

as_double() → float

Read a Double value; raise PropertyValueError for a different stored variant.

as_int() → int

Read a signed integer property without coercing another stored kind.

as_int_vector() → list[int]

Read an integer-vector property as an independent list; reject a different kind.

as_string() → str

Read a String property as text; reject a different stored kind.

as_uint() → int

Read an unsigned integer property without coercing another stored kind.

kind: PropertyValueKind

Stored property variant, without numeric or textual coercion.

exception cosmolkit.PropertyValueError(*args, **kwargs)

PropertyValueError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property actual: PropertyValueKind

Property value kind actually stored.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property expected: PropertyValueKind

Property value kind required by the attempted typed read.

class cosmolkit.PropertyValueKind(value)

Typed PropertyValueKind values corresponding to the Rust enum.

Members: String, Int, UInt, IntVector, StringVector, Double, Bool, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (10)
Bool = PropertyValueKind.Bool
Double = PropertyValueKind.Double
Int = PropertyValueKind.Int
IntVector = PropertyValueKind.IntVector
String = PropertyValueKind.String
StringVector = PropertyValueKind.StringVector
UInt = PropertyValueKind.UInt
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'String': PropertyValueKind.String, 'Int': PropertyValueKind.Int, 'UInt': PropertyValueKind.UInt, 'IntVector': PropertyValueKind.IntVector, 'StringVector': PropertyValueKind.StringVector, 'Double': PropertyValueKind.Double, 'Bool': PropertyValueKind.Bool})
values = mappingproxy({0: PropertyValueKind.String, 1: PropertyValueKind.Int, 2: PropertyValueKind.UInt, 3: PropertyValueKind.IntVector, 4: PropertyValueKind.StringVector, 5: PropertyValueKind.Double, 6: PropertyValueKind.Bool})
class cosmolkit.ProteinAtomRef

Readonly ProteinAtomRef retaining its protein owner. It remains a stable view when another COW value is modified.

Members (7)
altloc: AltLocLabel | None

Alternate-location label, or None for an unlabelled atom.

element: Element

Chemical element of the represented atom.

id: int

Local row identifier within the retained protein structure.

name: AtomName

Source atom or residue name.

position: list[float]

Cartesian position as an (x, y, z) tuple.

residue: ProteinResidueRef

Parent residue view retaining the same protein owner.

row: BioAtomRow

Detached copy of this view’s underlying metadata row.

class cosmolkit.ProteinChainRef

Readonly ProteinChainRef retaining its protein owner. It remains a stable view when another COW value is modified.

Members (6)
atoms: list[ProteinAtomRef]

Atom views retaining the protein owner, in stored order.

id: int

Local row identifier within the retained protein structure.

kind: ChainKind

Native classification of the represented chain or residue.

residues: list[ProteinResidueRef]

Residue views retaining the protein owner, in stored order.

row: BioChainRow

Detached copy of this view’s underlying metadata row.

source: ChainSourceIds

Source-format identifiers, distinct from local row identifiers.

exception cosmolkit.ProteinProjectionError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ProteinProjectionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property cause: BioStructureError | None

“error_source”} Actual underlying BioStructureError, identical to __cause__, or None.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Readonly index payload of the NonAminoAcidResidue error variant; None for other variants.

property source: int | None

Readonly source payload of the MissingEntityMapping error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: ProteinProjectionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ProteinProjectionErrorKind(value)

Discriminants of ProteinProjectionErrorKind.

Members: Structure, MissingEntityMapping, NonAminoAcidResidue, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
MissingEntityMapping = ProteinProjectionErrorKind.MissingEntityMapping
NonAminoAcidResidue = ProteinProjectionErrorKind.NonAminoAcidResidue
Structure = ProteinProjectionErrorKind.Structure
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Structure': ProteinProjectionErrorKind.Structure, 'MissingEntityMapping': ProteinProjectionErrorKind.MissingEntityMapping, 'NonAminoAcidResidue': ProteinProjectionErrorKind.NonAminoAcidResidue})
values = mappingproxy({0: ProteinProjectionErrorKind.Structure, 1: ProteinProjectionErrorKind.MissingEntityMapping, 2: ProteinProjectionErrorKind.NonAminoAcidResidue})
exception cosmolkit.ProteinReadError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ProteinReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: BioReadError | BioPdbReadError | BioMmcifReadError | ProteinProjectionError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: ProteinReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ProteinReadErrorKind(value)

Discriminants of ProteinReadErrorKind.

Members: Structure, Pdb, Mmcif, Projection, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
Mmcif = ProteinReadErrorKind.Mmcif
Pdb = ProteinReadErrorKind.Pdb
Projection = ProteinReadErrorKind.Projection
Structure = ProteinReadErrorKind.Structure
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Structure': ProteinReadErrorKind.Structure, 'Pdb': ProteinReadErrorKind.Pdb, 'Mmcif': ProteinReadErrorKind.Mmcif, 'Projection': ProteinReadErrorKind.Projection})
values = mappingproxy({0: ProteinReadErrorKind.Structure, 1: ProteinReadErrorKind.Pdb, 2: ProteinReadErrorKind.Mmcif, 3: ProteinReadErrorKind.Projection})
class cosmolkit.ProteinResidueRef

Readonly ProteinResidueRef retaining its protein owner. It remains a stable view when another COW value is modified.

Members (11)
atoms: list[ProteinAtomRef]

Atom views retaining the protein owner, in stored order.

chain: ProteinChainRef

Parent chain view retaining the same protein owner.

code: ResidueCode

Native residue code.

fasta_code: str

Residue character appropriate for FASTA output.

id: int

Local row identifier within the retained protein structure.

info: ResidueInfo

Residue classification and code information.

is_standard: bool

Whether the native residue classification marks this residue as standard.

kind: ResidueKind

Native classification of the represented chain or residue.

name: str

Source atom or residue name.

one_letter_code: str

One-letter residue code returned by the native residue classification.

row: BioResidueRow

Detached copy of this view’s underlying metadata row.

class cosmolkit.ProteinSelectionSummary

Read-only chain, residue and atom counts for a protein selection.

Members (3)
atoms: int

Number of atoms represented by this selection summary.

chains: int

Number of chains represented by this selection summary.

residues: int

Number of residues represented by this selection summary.

exception cosmolkit.PruningError(*args, **kwargs)

Failure in the conformer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

PruningError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property context: QueryMatchContextError | None

“error_payload”} Structured native error payload. Present for PruningError.Context; None when unavailable.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property hydrogens: HydrogenError | None

“error_payload”} Hydrogen count or hydrogen-related payload reported by the native check. Applies to PruningError.Hydrogens. None when this payload is absent.

Type:

{“role”

property matching: SubstructMatchError | None

“error_payload”} Structured native error payload. Present for PruningError.Match; None when unavailable.

Type:

{“role”

property message: str | None

Detailed native diagnostic message. Applies to PruningError.Input. None when this payload is absent.

property projection: QueryGraphError | None

“error_payload”} Structured native error payload. Present for PruningError.Projection; None when unavailable.

Type:

{“role”

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | StereoOrderError | AtomPropertyError | PropertyIntReadError | TemplateAttachmentOrderError | MappingValidationError | PropertyUIntReadError | CanonicalRankError | DoubleBondStereoError | MoleculePropertyError | CxQueryLoweringError | QueryGraphError | ParserCarrierError | ThreadCountError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property terminal: AlignmentError | None

“error_payload”} Structured native error payload. Present for PruningError.Terminal; None when unavailable.

Type:

{“role”

property variant: PruningErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.PruningErrorKind(value)

Discriminants of PruningErrorKind.

Members: Hydrogens, Projection, Terminal, Match, Context, Input, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
Context = PruningErrorKind.Context
Hydrogens = PruningErrorKind.Hydrogens
Input = PruningErrorKind.Input
Match = PruningErrorKind.Match
Projection = PruningErrorKind.Projection
Terminal = PruningErrorKind.Terminal
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Hydrogens': PruningErrorKind.Hydrogens, 'Projection': PruningErrorKind.Projection, 'Terminal': PruningErrorKind.Terminal, 'Match': PruningErrorKind.Match, 'Context': PruningErrorKind.Context, 'Input': PruningErrorKind.Input})
values = mappingproxy({0: PruningErrorKind.Hydrogens, 1: PruningErrorKind.Projection, 2: PruningErrorKind.Terminal, 3: PruningErrorKind.Match, 4: PruningErrorKind.Context, 5: PruningErrorKind.Input})
class cosmolkit.QueryAtom

Detached native query-atom value passed to substructure callbacks; not a molecular Atom.

Members (9)
atom_map: int | None

Optional query atom-map number.

atomic_number: int

Stored query atom atomic number; a wildcard may use zero.

explicit_hydrogens: int

Explicit hydrogen count stored on the query atom.

formal_charge: int

Formal charge stored on the query atom.

id: int

Zero-based atom identifier in the query graph.

is_aromatic: bool

Whether the query atom carries an aromatic flag.

isotope: int | None

Explicit isotope mass number, or None when unspecified.

no_implicit: bool

Whether implicit hydrogen inference is disabled.

radical_electrons: int

Radical electron count stored on the query atom.

exception cosmolkit.QueryAtomConversionError(*args, **kwargs)

Failure in the model domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

QueryAtomConversionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property atom: int | None

Readonly atom payload of the NonElementAtomicNumber error variant; None for other variants.

property atomic_number: int | None

Readonly atomic_number payload of the NonElementAtomicNumber error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: QueryAtomConversionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.QueryAtomConversionErrorKind(value)

Discriminants of QueryAtomConversionErrorKind.

Members: NonElementAtomicNumber, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
NonElementAtomicNumber = QueryAtomConversionErrorKind.NonElementAtomicNumber
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NonElementAtomicNumber': QueryAtomConversionErrorKind.NonElementAtomicNumber})
values = mappingproxy({0: QueryAtomConversionErrorKind.NonElementAtomicNumber})
exception cosmolkit.QueryCompileError(*args, **kwargs)

QueryCompileError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property message: str

Explanation of why the query graph could not be compiled.

property variant: QueryCompileErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.QueryCompileErrorKind(value)

Discriminants of QueryCompileErrorKind.

Members: InvalidGraph, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
InvalidGraph = QueryCompileErrorKind.InvalidGraph
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidGraph': QueryCompileErrorKind.InvalidGraph})
values = mappingproxy({0: QueryCompileErrorKind.InvalidGraph})
class cosmolkit.QueryGraph

Parsed chemical query graph used for substructure matching; distinct from a concrete molecular graph.

Members (5)
static from_smarts(text: str, *, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None, parse_name: bool | None = None, merge_hs: bool | None = None, skip_cleanup: bool | None = None, debug_parse: bool | None = None, replacements: dict[str, str] | None = None) → QueryGraph
static from_smarts(text: str, params: SmartsParseParams | None = None) → QueryGraph

Parse SMARTS into a query graph; accept a parameter object or keyword options, not both.

static from_smarts_with_params(text, params) → QueryGraph

Parse SMARTS into a query graph using the supplied parsing parameters.

name: str | None

Query name retained from the input, or None if absent.

num_atoms: int

Number of query atoms.

num_bonds: int

Number of query bonds.

exception cosmolkit.QueryGraphError(*args, **kwargs)

Failure in the model domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

QueryGraphError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property atom: int | None

Atom identifier implicated in the failure. Applies to QueryGraphError.TemplateAttachmentOrder, QueryGraphError.StereoGroupAtomOutOfRange, QueryGraphError.SubstanceGroupAtomOutOfRange. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to QueryGraphError.StereoAtomOutOfRange, QueryGraphError.StereoGroupAtomOutOfRange, QueryGraphError.SubstanceGroupAtomOutOfRange. None when this payload is absent.

property begin: int | None

Beginning endpoint reported by the native check. Applies to QueryGraphError.StereoAtomOutOfRange. None when this payload is absent.

property bond: int | None

Bond identifier implicated in the failure. Applies to QueryGraphError.InvalidBondEndpoint, QueryGraphError.StereoAtomOutOfRange, QueryGraphError.StereoGroupBondOutOfRange, QueryGraphError.SubstanceGroupBondOutOfRange. None when this payload is absent.

property bond_count: int | None

Bond count used when validating the reported bond reference. Applies to QueryGraphError.StereoGroupBondOutOfRange, QueryGraphError.SubstanceGroupBondOutOfRange. None when this payload is absent.

property coordinate_validation: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of QueryGraphError.CoordinateValidation; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Ending endpoint reported by the native check. Applies to QueryGraphError.StereoAtomOutOfRange. None when this payload is absent.

property id: int | None

Identifier involved in the native failure. Applies to QueryGraphError.AtomIdMismatch, QueryGraphError.BondIdMismatch, QueryGraphError.SubstanceGroupIdMismatch. None when this payload is absent.

property parent: int | None

Parent group or row involved in the failed relationship check. Applies to QueryGraphError.SubstanceGroupParentOutOfRange. None when this payload is absent.

property position: int | None

Position reported by the native failure. Applies to QueryGraphError.AtomIdMismatch, QueryGraphError.BondIdMismatch, QueryGraphError.SubstanceGroupIdMismatch. None when this payload is absent.

property sgroup: int | None

Substance-group index involved in the failure. Applies to QueryGraphError.SubstanceGroupAtomOutOfRange, QueryGraphError.SubstanceGroupBondOutOfRange, QueryGraphError.SubstanceGroupParentOutOfRange. None when this payload is absent.

property source: StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: QueryGraphErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.QueryGraphErrorKind(value)

Discriminants of QueryGraphErrorKind.

Members: StereoGroup, AtomIdMismatch, TemplateAttachmentOrder, BondIdMismatch, InvalidBondEndpoint, StereoAtomOutOfRange, StereoGroupAtomOutOfRange, StereoGroupBondOutOfRange, SubstanceGroupIdMismatch, SubstanceGroupAtomOutOfRange, SubstanceGroupBondOutOfRange, SubstanceGroupParentOutOfRange, CoordinateValidation, AdjacencyMismatch, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (17)
AdjacencyMismatch = QueryGraphErrorKind.AdjacencyMismatch
AtomIdMismatch = QueryGraphErrorKind.AtomIdMismatch
BondIdMismatch = QueryGraphErrorKind.BondIdMismatch
CoordinateValidation = QueryGraphErrorKind.CoordinateValidation
InvalidBondEndpoint = QueryGraphErrorKind.InvalidBondEndpoint
StereoAtomOutOfRange = QueryGraphErrorKind.StereoAtomOutOfRange
StereoGroup = QueryGraphErrorKind.StereoGroup
StereoGroupAtomOutOfRange = QueryGraphErrorKind.StereoGroupAtomOutOfRange
StereoGroupBondOutOfRange = QueryGraphErrorKind.StereoGroupBondOutOfRange
SubstanceGroupAtomOutOfRange = QueryGraphErrorKind.SubstanceGroupAtomOutOfRange
SubstanceGroupBondOutOfRange = QueryGraphErrorKind.SubstanceGroupBondOutOfRange
SubstanceGroupIdMismatch = QueryGraphErrorKind.SubstanceGroupIdMismatch
SubstanceGroupParentOutOfRange = QueryGraphErrorKind.SubstanceGroupParentOutOfRange
TemplateAttachmentOrder = QueryGraphErrorKind.TemplateAttachmentOrder
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': QueryGraphErrorKind.StereoGroup, 'AtomIdMismatch': QueryGraphErrorKind.AtomIdMismatch, 'TemplateAttachmentOrder': QueryGraphErrorKind.TemplateAttachmentOrder, 'BondIdMismatch': QueryGraphErrorKind.BondIdMismatch, 'InvalidBondEndpoint': QueryGraphErrorKind.InvalidBondEndpoint, 'StereoAtomOutOfRange': QueryGraphErrorKind.StereoAtomOutOfRange, 'StereoGroupAtomOutOfRange': QueryGraphErrorKind.StereoGroupAtomOutOfRange, 'StereoGroupBondOutOfRange': QueryGraphErrorKind.StereoGroupBondOutOfRange, 'SubstanceGroupIdMismatch': QueryGraphErrorKind.SubstanceGroupIdMismatch, 'SubstanceGroupAtomOutOfRange': QueryGraphErrorKind.SubstanceGroupAtomOutOfRange, 'SubstanceGroupBondOutOfRange': QueryGraphErrorKind.SubstanceGroupBondOutOfRange, 'SubstanceGroupParentOutOfRange': QueryGraphErrorKind.SubstanceGroupParentOutOfRange, 'CoordinateValidation': QueryGraphErrorKind.CoordinateValidation, 'AdjacencyMismatch': QueryGraphErrorKind.AdjacencyMismatch})
values = mappingproxy({0: QueryGraphErrorKind.StereoGroup, 1: QueryGraphErrorKind.AtomIdMismatch, 2: QueryGraphErrorKind.TemplateAttachmentOrder, 3: QueryGraphErrorKind.BondIdMismatch, 4: QueryGraphErrorKind.InvalidBondEndpoint, 5: QueryGraphErrorKind.StereoAtomOutOfRange, 6: QueryGraphErrorKind.StereoGroupAtomOutOfRange, 7: QueryGraphErrorKind.StereoGroupBondOutOfRange, 8: QueryGraphErrorKind.SubstanceGroupIdMismatch, 9: QueryGraphErrorKind.SubstanceGroupAtomOutOfRange, 10: QueryGraphErrorKind.SubstanceGroupBondOutOfRange, 11: QueryGraphErrorKind.SubstanceGroupParentOutOfRange, 12: QueryGraphErrorKind.CoordinateValidation, 13: QueryGraphErrorKind.AdjacencyMismatch})
exception cosmolkit.QueryMatchContextError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

QueryMatchContextError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (11)
property actual: int | None

Observed value reported by the native check. Applies to QueryMatchContextError.ValenceRows, QueryMatchContextError.RingMembershipRows. None when this payload is absent.

property atom: int | None

Atom identifier implicated in the failure. Applies to QueryMatchContextError.ValencePrecondition, QueryMatchContextError.RingPrecondition. None when this payload is absent.

property bond: int | None

Bond identifier implicated in the failure. Applies to QueryMatchContextError.RingPrecondition. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Required value reported by the native check. Applies to QueryMatchContextError.ValenceRows, QueryMatchContextError.RingMembershipRows. None when this payload is absent.

property field: str | None

Field whose content or type caused the failure. Applies to QueryMatchContextError.ValenceRows, QueryMatchContextError.ValencePrecondition, QueryMatchContextError.RingMembershipRows. None when this payload is absent.

property getter: str | None

Accessor involved in the reported failure. Applies to QueryMatchContextError.ValencePrecondition, QueryMatchContextError.RingPrecondition. None when this payload is absent.

property source: TopologyValidationError | RingFindingError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of QueryMatchContextError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: QueryMatchContextErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.QueryMatchContextErrorKind(value)

Discriminants of QueryMatchContextErrorKind.

Members: InvalidTopology, ValenceRows, Valence, ValencePrecondition, RingPrecondition, UninitializedRings, RingMembershipRows, Rings, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
InvalidTopology = QueryMatchContextErrorKind.InvalidTopology
RingMembershipRows = QueryMatchContextErrorKind.RingMembershipRows
RingPrecondition = QueryMatchContextErrorKind.RingPrecondition
Rings = QueryMatchContextErrorKind.Rings
UninitializedRings = QueryMatchContextErrorKind.UninitializedRings
Valence = QueryMatchContextErrorKind.Valence
ValencePrecondition = QueryMatchContextErrorKind.ValencePrecondition
ValenceRows = QueryMatchContextErrorKind.ValenceRows
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': QueryMatchContextErrorKind.InvalidTopology, 'ValenceRows': QueryMatchContextErrorKind.ValenceRows, 'Valence': QueryMatchContextErrorKind.Valence, 'ValencePrecondition': QueryMatchContextErrorKind.ValencePrecondition, 'RingPrecondition': QueryMatchContextErrorKind.RingPrecondition, 'UninitializedRings': QueryMatchContextErrorKind.UninitializedRings, 'RingMembershipRows': QueryMatchContextErrorKind.RingMembershipRows, 'Rings': QueryMatchContextErrorKind.Rings})
values = mappingproxy({0: QueryMatchContextErrorKind.InvalidTopology, 1: QueryMatchContextErrorKind.ValenceRows, 2: QueryMatchContextErrorKind.Valence, 3: QueryMatchContextErrorKind.ValencePrecondition, 4: QueryMatchContextErrorKind.RingPrecondition, 5: QueryMatchContextErrorKind.UninitializedRings, 6: QueryMatchContextErrorKind.RingMembershipRows, 7: QueryMatchContextErrorKind.Rings})
exception cosmolkit.QueryStateError(*args, **kwargs)

Failure in the model domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

QueryStateError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property actual: int | tuple[int, int] | None

Observed value reported by the native check. Applies to QueryStateError.AtomCount, QueryStateError.BondCount, QueryStateError.AppendedRowCount, QueryStateError.AtomId, QueryStateError.BondId, QueryStateError.BondEndpoints. None when this payload is absent.

property atom: int | None

Readonly atom payload of the NonElementAtomIdentity error variant; None for other variants.

property atomic_number: int | None

Readonly atomic_number payload of the NonElementAtomIdentity error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property entity: str | None

Structural entity involved in the failure. Applies to QueryStateError.AppendedRow, QueryStateError.AppendedRowCount. None when this payload is absent.

property expected: int | tuple[int, int] | None

Required value reported by the native check. Applies to QueryStateError.AtomCount, QueryStateError.BondCount, QueryStateError.AppendedRowCount, QueryStateError.AtomId, QueryStateError.BondId, QueryStateError.BondEndpoints. None when this payload is absent.

property position: int | None

Position reported by the native failure. Applies to QueryStateError.NonElementAtomIdentity, QueryStateError.AtomId, QueryStateError.BondId, QueryStateError.BondEndpoints, QueryStateError.AppendedRow. None when this payload is absent.

property source: MappingValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: QueryStateErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.QueryStateErrorKind(value)

Discriminants of QueryStateErrorKind.

Members: NonElementAtomIdentity, AtomCount, BondCount, AtomId, BondId, BondEndpoints, Mapping, AppendedRow, AppendedRowCount, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
AppendedRow = QueryStateErrorKind.AppendedRow
AppendedRowCount = QueryStateErrorKind.AppendedRowCount
AtomCount = QueryStateErrorKind.AtomCount
AtomId = QueryStateErrorKind.AtomId
BondCount = QueryStateErrorKind.BondCount
BondEndpoints = QueryStateErrorKind.BondEndpoints
BondId = QueryStateErrorKind.BondId
Mapping = QueryStateErrorKind.Mapping
NonElementAtomIdentity = QueryStateErrorKind.NonElementAtomIdentity
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NonElementAtomIdentity': QueryStateErrorKind.NonElementAtomIdentity, 'AtomCount': QueryStateErrorKind.AtomCount, 'BondCount': QueryStateErrorKind.BondCount, 'AtomId': QueryStateErrorKind.AtomId, 'BondId': QueryStateErrorKind.BondId, 'BondEndpoints': QueryStateErrorKind.BondEndpoints, 'Mapping': QueryStateErrorKind.Mapping, 'AppendedRow': QueryStateErrorKind.AppendedRow, 'AppendedRowCount': QueryStateErrorKind.AppendedRowCount})
values = mappingproxy({0: QueryStateErrorKind.NonElementAtomIdentity, 1: QueryStateErrorKind.AtomCount, 2: QueryStateErrorKind.BondCount, 3: QueryStateErrorKind.AtomId, 4: QueryStateErrorKind.BondId, 5: QueryStateErrorKind.BondEndpoints, 6: QueryStateErrorKind.Mapping, 7: QueryStateErrorKind.AppendedRow, 8: QueryStateErrorKind.AppendedRowCount})
exception cosmolkit.RadicalError(*args, **kwargs)

Failure in the radicals domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

RadicalError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (9)
property atom: int | None

Readonly atom payload of the RadicalCountOutOfRange error variant; None for other variants.

property atomic_number: int | None

Readonly atomic_number payload of the PeriodicTableLookup error variant; None for other variants.

property count: int | None

Readonly count payload of the RadicalCountOutOfRange error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property field: str | None

Readonly field payload of the PeriodicTableLookup error variant; None for other variants.

property source: TopologyValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of RadicalError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: RadicalErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.RadicalErrorKind(value)

Discriminants of RadicalErrorKind.

Members: InvalidTopology, PeriodicTableLookup, Valence, RadicalCountOutOfRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
InvalidTopology = RadicalErrorKind.InvalidTopology
PeriodicTableLookup = RadicalErrorKind.PeriodicTableLookup
RadicalCountOutOfRange = RadicalErrorKind.RadicalCountOutOfRange
Valence = RadicalErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': RadicalErrorKind.InvalidTopology, 'PeriodicTableLookup': RadicalErrorKind.PeriodicTableLookup, 'Valence': RadicalErrorKind.Valence, 'RadicalCountOutOfRange': RadicalErrorKind.RadicalCountOutOfRange})
values = mappingproxy({0: RadicalErrorKind.InvalidTopology, 1: RadicalErrorKind.PeriodicTableLookup, 2: RadicalErrorKind.Valence, 3: RadicalErrorKind.RadicalCountOutOfRange})
class cosmolkit.RandomSmilesWriteParams(*, isomeric_smiles=Ellipsis, kekule=Ellipsis, all_bonds_explicit=Ellipsis, all_hydrogens_explicit=Ellipsis)

Source options accepted by RDKit’s random-SMILES vector writer.

Members (4)
all_bonds_explicit: bool

Write explicit bond symbols where implicit notation would otherwise suffice.

all_hydrogens_explicit: bool

Write hydrogen counts explicitly in atom notation.

isomeric_smiles: bool

Include isotope and stereochemical distinctions in random SMILES.

kekule: bool

Write Kekule bond orders instead of aromatic notation.

class cosmolkit.Reaction

Ordered reactant, product and agent templates with native matching configuration. run() returns product sets; with_* methods preserve the source reaction.

Members (35)
agent_template(index) → QueryGraph

Return the agent template at a zero-based index; invalid indices raise ReactionModelError.

agent_templates: list[QueryGraph]

Agent query templates in stored order, retaining their reaction owner.

static from_smirks(text: str, *, use_smiles: bool | None = None, sanitize: bool | None = None, replacements: dict[str, str] | None = None, allow_cxsmiles: bool | None = None, strict_cxsmiles: bool | None = None) → Reaction
static from_smirks(text: str, params: ReactionParseParams | None = None) → Reaction

Parse SMIRKS into reaction templates using a parameter object or mutually exclusive keyword options.

static from_smirks_with_params(text, params) → Reaction

Parse SMIRKS using explicit reaction-parse parameters.

static from_templates(reactants, products, agents) → Reaction

Construct a reaction from ordered reactant, product and agent query templates.

implicit_properties: bool

Whether native implicit-property handling is enabled.

is_initialized: bool

Whether native reaction template initialization has completed.

match_params: SubstructMatchParams

Return an independent copy of this reaction’s match configuration with its native callbacks retained.

num_agent_templates: int

Number of agent query templates.

num_product_templates: int

Number of product query templates.

num_reactant_templates: int

Number of reactant query templates.

product_template(index) → QueryGraph

Return the product template at a zero-based index; invalid indices raise ReactionModelError.

product_templates: list[QueryGraph]

Product query templates in stored order, retaining their reaction owner.

reactant_template(index) → QueryGraph

Return the reactant template at a zero-based index; invalid indices raise ReactionModelError.

reactant_templates: list[QueryGraph]

Reactant query templates in stored order, retaining their reaction owner.

run(reactants: _typeshed.SupportsGetItem[int, Molecule], *, max_products: SupportsIndex | None = None, coordinate_selections: _typeshed.SupportsGetItem[int, ReactionCoordinateSelection] | None = None, copy_atom_properties: bool | None = None) → list[list[Molecule]]
run(reactants: _typeshed.SupportsGetItem[int, Molecule], params: ReactionRunParams | None = None) → list[list[Molecule]]

Apply reaction templates to ordered reactants and return product sets. Supply ReactionRunParams or chemical keyword options, not both.

set_match_params(params) → None

Assign a value copy of substructure-match parameters, retaining configured callbacks for reaction matching.

to_cx_smirks(*, canonical: bool | None = None, isomeric_smiles: bool | None = None, rooted_at_atom: SupportsIndex | None = None, include_dative_bonds: bool | None = None, include_cx: bool | None = None, cx_fields: CxSmilesFields | str | None = None, coordinate_selections: _typeshed.SupportsGetItem[int, ReactionCoordinateSelection] | None = None) → str
to_cx_smirks(params: ReactionWriteParams | None = None) → str

Write reaction templates with CXSMIRKS extensions using a parameter object or mutually exclusive keywords.

to_cx_smirks_with_params(params) → str

Write reaction templates with CXSMIRKS extensions using explicit writer parameters.

to_smirks(*, canonical: bool | None = None, isomeric_smiles: bool | None = None, rooted_at_atom: SupportsIndex | None = None, include_dative_bonds: bool | None = None, include_cx: bool | None = None, cx_fields: CxSmilesFields | str | None = None, coordinate_selections: _typeshed.SupportsGetItem[int, ReactionCoordinateSelection] | None = None) → str
to_smirks(params: ReactionWriteParams | None = None) → str

Write reaction templates as SMIRKS using a parameter object or mutually exclusive keyword options.

to_smirks_with_params(params) → str

Write reaction templates as SMIRKS using explicit writer parameters.

validate(*, silent: bool | None = None) → ReactionValidationReport
validate(params: ReactionValidationParams | None = None) → ReactionValidationReport

Return native reaction-template validation findings without modifying this reaction.

validate_with_params(params) → ReactionValidationReport

Return native reaction-template validation findings using explicit validation parameters.

with_agent_template(template) → Reaction

Return a new reaction with the agent template appended.

with_implicit_properties(enabled) → Reaction

Return a new reaction with implicit-property handling enabled or disabled.

with_initialized(*, silent: bool | None = None) → Reaction
with_initialized(params: ReactionValidationParams | None = None) → Reaction

Return a new reaction with native template initialization applied; validation failures propagate.

with_initialized_with_params(params) → Reaction

Return a new initialized reaction using explicit validation parameters.

with_match_params(params) → Reaction

Return an independent reaction with the supplied match configuration; leave this reaction unchanged.

with_product_template(template) → Reaction

Return a new reaction with the product template appended.

with_reactant_template(template) → Reaction

Return a new reaction with the reactant template appended.

without_agents() → ReactionTemplateRemoval

Return a removal result containing a reaction without agent templates and the removed templates.

without_unmapped_products(*, threshold_unmapped_atoms: SupportsFloat | SupportsIndex | None = None, move_to_agent_templates: bool | None = None) → ReactionTemplateRemoval
without_unmapped_products(params: ReactionTemplateRemovalParams | None = None) → ReactionTemplateRemoval

Return a removal result for product templates selected by the native unmapped-atom threshold policy.

without_unmapped_products_with_params(params) → ReactionTemplateRemoval

Return a product-template removal result using explicit removal parameters.

without_unmapped_reactants(*, threshold_unmapped_atoms: SupportsFloat | SupportsIndex | None = None, move_to_agent_templates: bool | None = None) → ReactionTemplateRemoval
without_unmapped_reactants(params: ReactionTemplateRemovalParams | None = None) → ReactionTemplateRemoval

Return a removal result for reactant templates selected by the native unmapped-atom threshold policy.

without_unmapped_reactants_with_params(params) → ReactionTemplateRemoval

Return a reactant-template removal result using explicit removal parameters.

exception cosmolkit.ReactionApplyError(*args, **kwargs)

Failure in the reaction domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ReactionApplyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (12)
property atom: int | None

Readonly atom payload of the AddsProductAtom error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property edit: TopologyEditError | None

“error_payload”} Structured TopologyEditError payload of ReactionApplyError.Edit; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property initialization: ReactionInitializationError | None

“error_payload”} Structured ReactionInitializationError payload of ReactionApplyError.Initialization; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property matching: ReactionRunError | None

“error_payload”} Structured ReactionRunError payload of ReactionApplyError.Matching; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property product: ReactionProductError | None

“error_payload”} Structured ReactionProductError payload of ReactionApplyError.Product; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property products: int | None

Readonly products payload of the ApplicabilityArity error variant; None for other variants.

property reactants: int | None

Readonly reactants payload of the ApplicabilityArity error variant; None for other variants.

property source: ReactionProductError | ReactionValidationError | SubstructMatchError | StereoGroupError | CoordinateValidationError | MoleculePropertyError | AtomPropertyError | TemplateAttachmentOrderError | RingFindingError | PropertyIntReadError | TopologyValidationError | BondValueError | TopologyEditError | PropertyULongReadError | PropertyUIntReadError | PropertyValueError | RequiredPropertyStringError | PropertyStringError | LegacyStereoError | PotentialStereoError | ParserStereoOrderError | StereoOrderError | SmilesStereoError | AtropisomerError | ParserCarrierError | KekulizeError | SanitizeError | HydrogenError | UIntLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property source_text: PropertyStringError | None

“error_payload”} Structured PropertyStringError payload of ReactionApplyError.SourceText; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: ReactionApplyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ReactionApplyErrorKind(value)

Discriminants of ReactionApplyErrorKind.

Members: SourceText, Initialization, ApplicabilityArity, AddsProductAtom, Matching, Product, Edit, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (10)
AddsProductAtom = ReactionApplyErrorKind.AddsProductAtom
ApplicabilityArity = ReactionApplyErrorKind.ApplicabilityArity
Edit = ReactionApplyErrorKind.Edit
Initialization = ReactionApplyErrorKind.Initialization
Matching = ReactionApplyErrorKind.Matching
Product = ReactionApplyErrorKind.Product
SourceText = ReactionApplyErrorKind.SourceText
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SourceText': ReactionApplyErrorKind.SourceText, 'Initialization': ReactionApplyErrorKind.Initialization, 'ApplicabilityArity': ReactionApplyErrorKind.ApplicabilityArity, 'AddsProductAtom': ReactionApplyErrorKind.AddsProductAtom, 'Matching': ReactionApplyErrorKind.Matching, 'Product': ReactionApplyErrorKind.Product, 'Edit': ReactionApplyErrorKind.Edit})
values = mappingproxy({0: ReactionApplyErrorKind.SourceText, 1: ReactionApplyErrorKind.Initialization, 2: ReactionApplyErrorKind.ApplicabilityArity, 3: ReactionApplyErrorKind.AddsProductAtom, 4: ReactionApplyErrorKind.Matching, 5: ReactionApplyErrorKind.Product, 6: ReactionApplyErrorKind.Edit})
class cosmolkit.ReactionApplyParams(*, remove_unmatched_atoms=Ellipsis)

Options for applying a reaction to one molecular value.

Members (1)
remove_unmatched_atoms: bool

Remove atoms not matched by the reaction’s reactant template.

class cosmolkit.ReactionApplyResult(molecule, changed)

Resulting molecular value and change indicator for single-molecule reaction application.

Members (2)
changed: bool

Whether reaction application changed the molecular value.

molecule: Molecule

COW molecular value resulting from reaction application.

class cosmolkit.ReactionCoordinateSelection

Explicit or automatic selection of the coordinates used by a reaction.

Members (7)
static auto() → ReactionCoordinateSelection

Use the canonical automatic reaction coordinate selection.

id: int | None

Selected conformer identifier, or None for automatic selection.

is_2d: bool

Whether an explicit 2D conformer is selected.

is_3d: bool

Whether an explicit 3D conformer is selected.

is_auto: bool

Whether automatic coordinate selection is requested.

static three_d(id) → ReactionCoordinateSelection

Select the stored 3D conformer with this identifier.

static two_d(id) → ReactionCoordinateSelection

Select the stored 2D conformer with this identifier.

exception cosmolkit.ReactionInitializationError(*args, **kwargs)

Failure in the reaction domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ReactionInitializationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property report: ReactionValidationReport | None

“error_payload”} Validation report for an invalid reaction, or None for another initialization failure.

Type:

{“role”

property source: ReactionValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: ReactionInitializationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ReactionInitializationErrorKind(value)

Discriminants of ReactionInitializationErrorKind.

Members: Validation, Invalid, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Invalid = ReactionInitializationErrorKind.Invalid
Validation = ReactionInitializationErrorKind.Validation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Validation': ReactionInitializationErrorKind.Validation, 'Invalid': ReactionInitializationErrorKind.Invalid})
values = mappingproxy({0: ReactionInitializationErrorKind.Validation, 1: ReactionInitializationErrorKind.Invalid})
exception cosmolkit.ReactionModelError(*args, **kwargs)

Failure in the reaction domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ReactionModelError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property count: int | None

Readonly count payload of the TemplateIndex error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Readonly index payload of the TemplateIndex error variant; None for other variants.

property role: ReactionRole

Template role involved in the native reaction-model error.

property source: QueryGraphError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property template: int | None

Readonly template payload of the Template error variant; None for other variants.

property variant: ReactionModelErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ReactionModelErrorKind(value)

Discriminants of ReactionModelErrorKind.

Members: Template, TemplateIndex, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Template = ReactionModelErrorKind.Template
TemplateIndex = ReactionModelErrorKind.TemplateIndex
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Template': ReactionModelErrorKind.Template, 'TemplateIndex': ReactionModelErrorKind.TemplateIndex})
values = mappingproxy({0: ReactionModelErrorKind.Template, 1: ReactionModelErrorKind.TemplateIndex})
exception cosmolkit.ReactionParseError(*args, **kwargs)

Failure in the reaction domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ReactionParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (17)
property atom: int | None

Atom index involved in the failure. Present for ReactionParseError.TemplateAtomBounds, ReactionParseError.StereoInversionFlag, ReactionParseError.StereoOrder; None when unavailable.

property atom_count: int | None

Readonly atom_count payload of the TemplateAtomBounds error variant; None for other variants.

property count: int | None

Count observed when the failure occurred. Present for ReactionParseError.Separators, ReactionParseError.MultiStep; None when unavailable.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the ComponentBounds error variant; None for other variants.

property flag: int | None

Readonly flag payload of the StereoInversionFlag error variant; None for other variants.

property product: int | None

Product-template index associated with the failure. Present for ReactionParseError.StereoDegreeArithmetic, ReactionParseError.StereoInversionFlag, ReactionParseError.StereoOrder; None when unavailable.

property reactant: int | None

Readonly reactant payload of the StereoDegreeArithmetic error variant; None for other variants.

property role: ReactionRole | None

Role of the affected reaction template or transformation participant. Present for ReactionParseError.ParserCleanup, ReactionParseError.TemplateAtomBounds, ReactionParseError.Smarts, ReactionParseError.Smiles, ReactionParseError.ComponentEncoding, ReactionParseError.Model, ReactionParseError.CxParse, ReactionParseError.CxLowering; None when unavailable.

property source: SmartsParseError | SmilesParseError | Utf8Error | QueryGraphError | ReactionValidationError | CxParseError | CxQueryLoweringError | StereoOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property start: int | None

Readonly start payload of the ComponentBounds error variant; None for other variants.

property start_atom: int | None

Starting atom offset for the reaction template. Present for ReactionParseError.CxParse, ReactionParseError.CxLowering; None when unavailable.

property start_bond: int | None

Starting bond offset for the reaction template. Present for ReactionParseError.CxParse, ReactionParseError.CxLowering; None when unavailable.

property template: int | None

Index of the affected reaction template. Present for ReactionParseError.ParserCleanup, ReactionParseError.TemplateAtomBounds, ReactionParseError.Smarts, ReactionParseError.Smiles, ReactionParseError.ComponentEncoding, ReactionParseError.Model, ReactionParseError.CxParse, ReactionParseError.CxLowering; None when unavailable.

property text: str | None

Original input text retained by the error. Present for ReactionParseError.Smarts, ReactionParseError.Smiles, ReactionParseError.ComponentEncoding; None when unavailable.

property variant: ReactionParseErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ReactionParseErrorKind(value)

Discriminants of ReactionParseErrorKind.

Members: ParserCleanup, TemplateAtomBounds, StereoDegreeArithmetic, StereoInversionFlag, TemplateProperty, Separators, MultiStep, ComponentBounds, OffsetOverflow, Smarts, Smiles, ComponentEncoding, Model, AgentFragments, CxParse, CxLowering, StereoOrder, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (20)
AgentFragments = ReactionParseErrorKind.AgentFragments
ComponentBounds = ReactionParseErrorKind.ComponentBounds
ComponentEncoding = ReactionParseErrorKind.ComponentEncoding
CxLowering = ReactionParseErrorKind.CxLowering
CxParse = ReactionParseErrorKind.CxParse
Model = ReactionParseErrorKind.Model
MultiStep = ReactionParseErrorKind.MultiStep
OffsetOverflow = ReactionParseErrorKind.OffsetOverflow
ParserCleanup = ReactionParseErrorKind.ParserCleanup
Separators = ReactionParseErrorKind.Separators
Smarts = ReactionParseErrorKind.Smarts
Smiles = ReactionParseErrorKind.Smiles
StereoDegreeArithmetic = ReactionParseErrorKind.StereoDegreeArithmetic
StereoInversionFlag = ReactionParseErrorKind.StereoInversionFlag
StereoOrder = ReactionParseErrorKind.StereoOrder
TemplateAtomBounds = ReactionParseErrorKind.TemplateAtomBounds
TemplateProperty = ReactionParseErrorKind.TemplateProperty
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ParserCleanup': ReactionParseErrorKind.ParserCleanup, 'TemplateAtomBounds': ReactionParseErrorKind.TemplateAtomBounds, 'StereoDegreeArithmetic': ReactionParseErrorKind.StereoDegreeArithmetic, 'StereoInversionFlag': ReactionParseErrorKind.StereoInversionFlag, 'TemplateProperty': ReactionParseErrorKind.TemplateProperty, 'Separators': ReactionParseErrorKind.Separators, 'MultiStep': ReactionParseErrorKind.MultiStep, 'ComponentBounds': ReactionParseErrorKind.ComponentBounds, 'OffsetOverflow': ReactionParseErrorKind.OffsetOverflow, 'Smarts': ReactionParseErrorKind.Smarts, 'Smiles': ReactionParseErrorKind.Smiles, 'ComponentEncoding': ReactionParseErrorKind.ComponentEncoding, 'Model': ReactionParseErrorKind.Model, 'AgentFragments': ReactionParseErrorKind.AgentFragments, 'CxParse': ReactionParseErrorKind.CxParse, 'CxLowering': ReactionParseErrorKind.CxLowering, 'StereoOrder': ReactionParseErrorKind.StereoOrder})
values = mappingproxy({0: ReactionParseErrorKind.ParserCleanup, 1: ReactionParseErrorKind.TemplateAtomBounds, 2: ReactionParseErrorKind.StereoDegreeArithmetic, 3: ReactionParseErrorKind.StereoInversionFlag, 4: ReactionParseErrorKind.TemplateProperty, 5: ReactionParseErrorKind.Separators, 6: ReactionParseErrorKind.MultiStep, 7: ReactionParseErrorKind.ComponentBounds, 8: ReactionParseErrorKind.OffsetOverflow, 9: ReactionParseErrorKind.Smarts, 10: ReactionParseErrorKind.Smiles, 11: ReactionParseErrorKind.ComponentEncoding, 12: ReactionParseErrorKind.Model, 13: ReactionParseErrorKind.AgentFragments, 14: ReactionParseErrorKind.CxParse, 15: ReactionParseErrorKind.CxLowering, 16: ReactionParseErrorKind.StereoOrder})
class cosmolkit.ReactionParseParams(*, use_smiles=Ellipsis, sanitize=Ellipsis, replacements=Ellipsis, allow_cxsmiles=Ellipsis, strict_cxsmiles=Ellipsis)

Reaction SMARTS/SMILES parsing, sanitization and CX extension options.

Members (5)
allow_cxsmiles: bool

Recognize and parse reaction CXSMILES extensions.

replacements: collections.abc.Mapping[str, str]

Text replacements expanded before component parsing.

sanitize: bool

Sanitize parsed molecular templates.

strict_cxsmiles: bool

Declared by RDKit but not consumed by parseReaction. This flag does not suppress reaction-global CX exceptions.

use_smiles: bool

Parse reaction components as SMILES rather than SMARTS.

exception cosmolkit.ReactionProductError(*args, **kwargs)

Failure in the reaction domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ReactionProductError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (27)
property adjacency: AdjacencyError | None

“error_payload”} Structured AdjacencyError payload of ReactionProductError.Adjacency; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property atom: int | None

Atom identifier implicated in the failure. Applies to ReactionProductError.StereoGetter, ReactionProductError.PropertyInt, ReactionProductError.PropertyUInt, ReactionProductError.MissingProperty. None when this payload is absent.

property atom_property: AtomPropertyError | None

“error_payload”} Structured AtomPropertyError payload of ReactionProductError.AtomProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property bond: int | None

Bond identifier implicated in the failure. Applies to ReactionProductError.Invariant, ReactionProductError.QueryReactantBond. None when this payload is absent.

property bond_value: BondValueError | None

“error_payload”} Structured BondValueError payload of ReactionProductError.BondValue; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property carrier_identity: QueryAtomConversionError | None

“error_payload”} Structured QueryAtomConversionError payload of ReactionProductError.CarrierIdentity; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property coordinate: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of ReactionProductError.Coordinate; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property coordinate_selection: SmilesParseError | None

“error_payload”} Structured SmilesParseError payload of ReactionProductError.CoordinateSelection; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property detail: str | None

Readonly detail payload of the Invariant error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property double_bond_stereo: DoubleBondStereoError | None

“error_payload”} Structured DoubleBondStereoError payload of ReactionProductError.DoubleBondStereo; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property index: int | None

Readonly index payload of the RowOverflow error variant; None for other variants.

property key: str | None

Property key involved in the failure. Applies to ReactionProductError.PropertyInt, ReactionProductError.PropertyUInt, ReactionProductError.MissingProperty. None when this payload is absent.

property kind: str | None

Readonly kind payload of the RowOverflow error variant; None for other variants.

property molecule_property: MoleculePropertyError | None

“error_payload”} Structured MoleculePropertyError payload of ReactionProductError.MoleculeProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property product_atom: int | None

Readonly product_atom payload of the Invariant error variant; None for other variants.

property reactant_atom: int | None

Readonly reactant_atom payload of the Invariant error variant; None for other variants.

property ring_finding: RingFindingError | None

“error_payload”} Structured RingFindingError payload of ReactionProductError.RingFinding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | CoordinateValidationError | MoleculePropertyError | AtomPropertyError | TemplateAttachmentOrderError | RingFindingError | PropertyIntReadError | TopologyValidationError | BondValueError | TopologyEditError | PropertyULongReadError | PropertyUIntReadError | PropertyValueError | RequiredPropertyStringError | PropertyStringError | LegacyStereoError | PotentialStereoError | ParserStereoOrderError | StereoOrderError | SmilesStereoError | AtropisomerError | ParserCarrierError | KekulizeError | SanitizeError | HydrogenError | UIntLexicalReadError | SubstructMatchError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property source_uint: PropertyUIntReadError | None

“error_payload”} Structured PropertyUIntReadError payload of ReactionProductError.SourceUInt; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property stage: str | None

Readonly stage payload of the Invariant error variant; None for other variants.

property stereo_order: StereoOrderError | None

“error_payload”} Structured StereoOrderError payload of ReactionProductError.StereoOrder; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property template_property: ReactionValidationError | None

“error_payload”} Structured ReactionValidationError payload of ReactionProductError.TemplateProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property topology_edit: TopologyEditError | None

“error_payload”} Structured TopologyEditError payload of ReactionProductError.TopologyEdit; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of ReactionProductError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: ReactionProductErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ReactionProductErrorKind(value)

Discriminants of ReactionProductErrorKind.

Members: StereoGroup, Coordinate, TopologyEdit, Adjacency, RingFinding, SourceUInt, Valence, StereoOrder, DoubleBondStereo, StereoGetter, CoordinateSelection, CarrierIdentity, PropertyInt, PropertyUInt, MissingProperty, MoleculeProperty, AtomProperty, BondValue, TemplateProperty, Invariant, RowOverflow, QueryReactantBond, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (25)
Adjacency = ReactionProductErrorKind.Adjacency
AtomProperty = ReactionProductErrorKind.AtomProperty
BondValue = ReactionProductErrorKind.BondValue
CarrierIdentity = ReactionProductErrorKind.CarrierIdentity
Coordinate = ReactionProductErrorKind.Coordinate
CoordinateSelection = ReactionProductErrorKind.CoordinateSelection
DoubleBondStereo = ReactionProductErrorKind.DoubleBondStereo
Invariant = ReactionProductErrorKind.Invariant
MissingProperty = ReactionProductErrorKind.MissingProperty
MoleculeProperty = ReactionProductErrorKind.MoleculeProperty
PropertyInt = ReactionProductErrorKind.PropertyInt
PropertyUInt = ReactionProductErrorKind.PropertyUInt
QueryReactantBond = ReactionProductErrorKind.QueryReactantBond
RingFinding = ReactionProductErrorKind.RingFinding
RowOverflow = ReactionProductErrorKind.RowOverflow
SourceUInt = ReactionProductErrorKind.SourceUInt
StereoGetter = ReactionProductErrorKind.StereoGetter
StereoGroup = ReactionProductErrorKind.StereoGroup
StereoOrder = ReactionProductErrorKind.StereoOrder
TemplateProperty = ReactionProductErrorKind.TemplateProperty
TopologyEdit = ReactionProductErrorKind.TopologyEdit
Valence = ReactionProductErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': ReactionProductErrorKind.StereoGroup, 'Coordinate': ReactionProductErrorKind.Coordinate, 'TopologyEdit': ReactionProductErrorKind.TopologyEdit, 'Adjacency': ReactionProductErrorKind.Adjacency, 'RingFinding': ReactionProductErrorKind.RingFinding, 'SourceUInt': ReactionProductErrorKind.SourceUInt, 'Valence': ReactionProductErrorKind.Valence, 'StereoOrder': ReactionProductErrorKind.StereoOrder, 'DoubleBondStereo': ReactionProductErrorKind.DoubleBondStereo, 'StereoGetter': ReactionProductErrorKind.StereoGetter, 'CoordinateSelection': ReactionProductErrorKind.CoordinateSelection, 'CarrierIdentity': ReactionProductErrorKind.CarrierIdentity, 'PropertyInt': ReactionProductErrorKind.PropertyInt, 'PropertyUInt': ReactionProductErrorKind.PropertyUInt, 'MissingProperty': ReactionProductErrorKind.MissingProperty, 'MoleculeProperty': ReactionProductErrorKind.MoleculeProperty, 'AtomProperty': ReactionProductErrorKind.AtomProperty, 'BondValue': ReactionProductErrorKind.BondValue, 'TemplateProperty': ReactionProductErrorKind.TemplateProperty, 'Invariant': ReactionProductErrorKind.Invariant, 'RowOverflow': ReactionProductErrorKind.RowOverflow, 'QueryReactantBond': ReactionProductErrorKind.QueryReactantBond})
values = mappingproxy({0: ReactionProductErrorKind.StereoGroup, 1: ReactionProductErrorKind.Coordinate, 2: ReactionProductErrorKind.TopologyEdit, 3: ReactionProductErrorKind.Adjacency, 4: ReactionProductErrorKind.RingFinding, 5: ReactionProductErrorKind.SourceUInt, 6: ReactionProductErrorKind.Valence, 7: ReactionProductErrorKind.StereoOrder, 8: ReactionProductErrorKind.DoubleBondStereo, 9: ReactionProductErrorKind.StereoGetter, 10: ReactionProductErrorKind.CoordinateSelection, 11: ReactionProductErrorKind.CarrierIdentity, 12: ReactionProductErrorKind.PropertyInt, 13: ReactionProductErrorKind.PropertyUInt, 14: ReactionProductErrorKind.MissingProperty, 15: ReactionProductErrorKind.MoleculeProperty, 16: ReactionProductErrorKind.AtomProperty, 17: ReactionProductErrorKind.BondValue, 18: ReactionProductErrorKind.TemplateProperty, 19: ReactionProductErrorKind.Invariant, 20: ReactionProductErrorKind.RowOverflow, 21: ReactionProductErrorKind.QueryReactantBond})
class cosmolkit.ReactionRole(value)

Typed ReactionRole values corresponding to the Rust enum.

Members: Reactant, Product, Agent, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
Agent = ReactionRole.Agent
Product = ReactionRole.Product
Reactant = ReactionRole.Reactant
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Reactant': ReactionRole.Reactant, 'Product': ReactionRole.Product, 'Agent': ReactionRole.Agent})
values = mappingproxy({0: ReactionRole.Reactant, 1: ReactionRole.Product, 2: ReactionRole.Agent})
exception cosmolkit.ReactionRunError(*args, **kwargs)

Failure in the reaction domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ReactionRunError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property actual: int | None

Observed value reported by the native check. Applies to ReactionRunError.CoordinateSelectionArity, ReactionRunError.ReactantArity, ReactionRunError.CombinationSize. None when this payload is absent.

property atom: int | None

Readonly atom payload of the MatchAtomIndex error variant; None for other variants.

property atom_count: int | None

Readonly atom_count payload of the MatchAtomIndex error variant; None for other variants.

property count: int | None

Count reported by the native failure. Applies to ReactionRunError.ReactantTemplateIndex, ReactionRunError.CombinationLevel. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Required value reported by the native check. Applies to ReactionRunError.CoordinateSelectionArity, ReactionRunError.ReactantArity, ReactionRunError.CombinationSize. None when this payload is absent.

property index: int | None

Readonly index payload of the ReactantTemplateIndex error variant; None for other variants.

property initialization: ReactionInitializationError | None

“error_payload”} Structured ReactionInitializationError payload of ReactionRunError.Initialization; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property level: int | None

Readonly level payload of the CombinationLevel error variant; None for other variants.

property reactant: int | None

Reactant index involved in the failed reaction match. Applies to ReactionRunError.Matching, ReactionRunError.MatchAtomIndex. None when this payload is absent.

property set: int | None

Readonly set payload of the Product error variant; None for other variants.

property source: ReactionProductError | ReactionValidationError | SubstructMatchError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property template: int | None

Reaction template index involved in the failure. Applies to ReactionRunError.Product, ReactionRunError.Matching, ReactionRunError.MatchAtomIndex. None when this payload is absent.

property variant: ReactionRunErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ReactionRunErrorKind(value)

Discriminants of ReactionRunErrorKind.

Members: Product, CoordinateSelectionArity, Initialization, NeedsInitialization, ReactantArity, ReactantTemplateIndex, Matching, MatchAtomIndex, CombinationLevel, CombinationSize, EmptyCombinationLevels, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (14)
CombinationLevel = ReactionRunErrorKind.CombinationLevel
CombinationSize = ReactionRunErrorKind.CombinationSize
CoordinateSelectionArity = ReactionRunErrorKind.CoordinateSelectionArity
EmptyCombinationLevels = ReactionRunErrorKind.EmptyCombinationLevels
Initialization = ReactionRunErrorKind.Initialization
MatchAtomIndex = ReactionRunErrorKind.MatchAtomIndex
Matching = ReactionRunErrorKind.Matching
NeedsInitialization = ReactionRunErrorKind.NeedsInitialization
Product = ReactionRunErrorKind.Product
ReactantArity = ReactionRunErrorKind.ReactantArity
ReactantTemplateIndex = ReactionRunErrorKind.ReactantTemplateIndex
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Product': ReactionRunErrorKind.Product, 'CoordinateSelectionArity': ReactionRunErrorKind.CoordinateSelectionArity, 'Initialization': ReactionRunErrorKind.Initialization, 'NeedsInitialization': ReactionRunErrorKind.NeedsInitialization, 'ReactantArity': ReactionRunErrorKind.ReactantArity, 'ReactantTemplateIndex': ReactionRunErrorKind.ReactantTemplateIndex, 'Matching': ReactionRunErrorKind.Matching, 'MatchAtomIndex': ReactionRunErrorKind.MatchAtomIndex, 'CombinationLevel': ReactionRunErrorKind.CombinationLevel, 'CombinationSize': ReactionRunErrorKind.CombinationSize, 'EmptyCombinationLevels': ReactionRunErrorKind.EmptyCombinationLevels})
values = mappingproxy({0: ReactionRunErrorKind.Product, 1: ReactionRunErrorKind.CoordinateSelectionArity, 2: ReactionRunErrorKind.Initialization, 3: ReactionRunErrorKind.NeedsInitialization, 4: ReactionRunErrorKind.ReactantArity, 5: ReactionRunErrorKind.ReactantTemplateIndex, 6: ReactionRunErrorKind.Matching, 7: ReactionRunErrorKind.MatchAtomIndex, 8: ReactionRunErrorKind.CombinationLevel, 9: ReactionRunErrorKind.CombinationSize, 10: ReactionRunErrorKind.EmptyCombinationLevels})
class cosmolkit.ReactionRunParams(*, max_products=Ellipsis, coordinate_selections=Ellipsis, copy_atom_properties=Ellipsis)

Options for ordered multiple-reagent reaction execution.

Members (3)
coordinate_selections: tuple[ReactionCoordinateSelection, ...]

Empty selects Auto for each input; otherwise input arity must match.

copy_atom_properties: bool

fill missing product user properties from atom origins. False preserves native behavior; it never clears existing properties.

Type:

CK extension

max_products: int

RDKit default 1000; zero leaves matching and combinations unlimited.

class cosmolkit.ReactionSingleRunParams(*, coordinate_selection=Ellipsis)

Coordinate selection for executing one reaction template against one input.

Members (1)
coordinate_selection: ReactionCoordinateSelection

Automatic or explicit input-conformer selection.

class cosmolkit.ReactionTemplateRemoval

Result of template removal containing the resulting reaction and removed query templates.

Members (2)
reaction: Reaction

Reaction after template removal, retaining ownership of the removal result.

removed_templates: list[QueryGraph]

Removed query templates in native removal order.

class cosmolkit.ReactionTemplateRemovalParams(*, threshold_unmapped_atoms=Ellipsis, move_to_agent_templates=Ellipsis)

Source removal threshold. The name is retained from RDKit even though the predicate compares mapped-property count divided by heavy-atom count.

Members (2)
move_to_agent_templates: bool

Move removed templates into the agent list.

threshold_unmapped_atoms: float

Native removal threshold comparing mapped-property count to heavy-atom count.

exception cosmolkit.ReactionValidationError(*args, **kwargs)

Failure in the reaction domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ReactionValidationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (11)
property atom: int

Atom identifier implicated in the failure. Applies to ReactionValidationError.Property, ReactionValidationError.MapOverflow, ReactionValidationError.AtomBounds, ReactionValidationError.MissingReactingAtom, ReactionValidationError.QueryArithmetic, ReactionValidationError.Annotation.

property atom_count: int | None

Readonly atom_count payload of the AtomBounds error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property map: int | None

Readonly map payload of the MissingReactingAtom error variant; None for other variants.

property property: str | None

Property name involved in the failure. Applies to ReactionValidationError.Property, ReactionValidationError.MapOverflow, ReactionValidationError.Annotation. None when this payload is absent.

property role: ReactionRole | None

Reaction template role implicated in the failure. Applies to ReactionValidationError.Property, ReactionValidationError.MapOverflow, ReactionValidationError.AtomBounds. None when this payload is absent.

property source: PropertyIntReadError | AtomPropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property template: int

Reaction template index involved in the failure. Applies to ReactionValidationError.Property, ReactionValidationError.MapOverflow, ReactionValidationError.AtomBounds, ReactionValidationError.MissingReactingAtom, ReactionValidationError.QueryArithmetic, ReactionValidationError.Annotation.

property value: int | None

Readonly value payload of the MapOverflow error variant; None for other variants.

property variant: ReactionValidationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ReactionValidationErrorKind(value)

Discriminants of ReactionValidationErrorKind.

Members: Property, MapOverflow, AtomBounds, MissingReactingAtom, QueryArithmetic, Annotation, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
Annotation = ReactionValidationErrorKind.Annotation
AtomBounds = ReactionValidationErrorKind.AtomBounds
MapOverflow = ReactionValidationErrorKind.MapOverflow
MissingReactingAtom = ReactionValidationErrorKind.MissingReactingAtom
Property = ReactionValidationErrorKind.Property
QueryArithmetic = ReactionValidationErrorKind.QueryArithmetic
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Property': ReactionValidationErrorKind.Property, 'MapOverflow': ReactionValidationErrorKind.MapOverflow, 'AtomBounds': ReactionValidationErrorKind.AtomBounds, 'MissingReactingAtom': ReactionValidationErrorKind.MissingReactingAtom, 'QueryArithmetic': ReactionValidationErrorKind.QueryArithmetic, 'Annotation': ReactionValidationErrorKind.Annotation})
values = mappingproxy({0: ReactionValidationErrorKind.Property, 1: ReactionValidationErrorKind.MapOverflow, 2: ReactionValidationErrorKind.AtomBounds, 3: ReactionValidationErrorKind.MissingReactingAtom, 4: ReactionValidationErrorKind.QueryArithmetic, 5: ReactionValidationErrorKind.Annotation})
class cosmolkit.ReactionValidationIssue(kind, severity, role, template, atom, map, maps, detail)

One structured reaction-template validation diagnostic.

Members (8)
atom: int | None

Zero-based atom index within the template, or None.

detail: str

Native human-readable explanation of the issue.

kind: ReactionValidationIssueKind

Native category of the reaction validation issue.

map: int | None

Atom-map number associated with the issue, or None.

maps: list[int]

Atom-map numbers associated with the issue.

role: ReactionRole | None

Affected reactant, product or agent role, or None when not template-specific.

severity: ReactionValidationSeverity

Whether the issue is a warning or an error.

template: int | None

Zero-based template index within the affected role, or None.

class cosmolkit.ReactionValidationIssueKind(value)

Typed ReactionValidationIssueKind values corresponding to the Rust enum.

Members: MissingReactants, MissingProducts, DuplicateReactantMap, UnmappedReactant, DuplicateProductMap, MissingProductMapReactant, UnmappedProduct, UnmappedReactantMaps, MultipleCharge, MultipleHydrogenCount, MultipleMass, MultipleIsotope, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (15)
DuplicateProductMap = ReactionValidationIssueKind.DuplicateProductMap
DuplicateReactantMap = ReactionValidationIssueKind.DuplicateReactantMap
MissingProductMapReactant = ReactionValidationIssueKind.MissingProductMapReactant
MissingProducts = ReactionValidationIssueKind.MissingProducts
MissingReactants = ReactionValidationIssueKind.MissingReactants
MultipleCharge = ReactionValidationIssueKind.MultipleCharge
MultipleHydrogenCount = ReactionValidationIssueKind.MultipleHydrogenCount
MultipleIsotope = ReactionValidationIssueKind.MultipleIsotope
MultipleMass = ReactionValidationIssueKind.MultipleMass
UnmappedProduct = ReactionValidationIssueKind.UnmappedProduct
UnmappedReactant = ReactionValidationIssueKind.UnmappedReactant
UnmappedReactantMaps = ReactionValidationIssueKind.UnmappedReactantMaps
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingReactants': ReactionValidationIssueKind.MissingReactants, 'MissingProducts': ReactionValidationIssueKind.MissingProducts, 'DuplicateReactantMap': ReactionValidationIssueKind.DuplicateReactantMap, 'UnmappedReactant': ReactionValidationIssueKind.UnmappedReactant, 'DuplicateProductMap': ReactionValidationIssueKind.DuplicateProductMap, 'MissingProductMapReactant': ReactionValidationIssueKind.MissingProductMapReactant, 'UnmappedProduct': ReactionValidationIssueKind.UnmappedProduct, 'UnmappedReactantMaps': ReactionValidationIssueKind.UnmappedReactantMaps, 'MultipleCharge': ReactionValidationIssueKind.MultipleCharge, 'MultipleHydrogenCount': ReactionValidationIssueKind.MultipleHydrogenCount, 'MultipleMass': ReactionValidationIssueKind.MultipleMass, 'MultipleIsotope': ReactionValidationIssueKind.MultipleIsotope})
values = mappingproxy({0: ReactionValidationIssueKind.MissingReactants, 1: ReactionValidationIssueKind.MissingProducts, 2: ReactionValidationIssueKind.DuplicateReactantMap, 3: ReactionValidationIssueKind.UnmappedReactant, 4: ReactionValidationIssueKind.DuplicateProductMap, 5: ReactionValidationIssueKind.MissingProductMapReactant, 6: ReactionValidationIssueKind.UnmappedProduct, 7: ReactionValidationIssueKind.UnmappedReactantMaps, 8: ReactionValidationIssueKind.MultipleCharge, 9: ReactionValidationIssueKind.MultipleHydrogenCount, 10: ReactionValidationIssueKind.MultipleMass, 11: ReactionValidationIssueKind.MultipleIsotope})
class cosmolkit.ReactionValidationParams(*, silent=Ellipsis)

Diagnostic-output policy for native reaction validation.

Members (1)
silent: bool

Suppress native diagnostic logging while retaining the structured validation report.

class cosmolkit.ReactionValidationReport(warnings, errors)

Validation warnings and errors for a reaction definition.

Members (5)
errors: list[ReactionValidationIssue]

Independent list of validation errors.

is_valid: bool

Whether the report contains no validation errors.

num_errors: int

Number of validation errors.

num_warnings: int

Number of validation warnings.

warnings: list[ReactionValidationIssue]

Independent list of validation warnings.

class cosmolkit.ReactionValidationSeverity(value)

Typed ReactionValidationSeverity values corresponding to the Rust enum.

Members: Warning, Error, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Error = ReactionValidationSeverity.Error
Warning = ReactionValidationSeverity.Warning
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Warning': ReactionValidationSeverity.Warning, 'Error': ReactionValidationSeverity.Error})
values = mappingproxy({0: ReactionValidationSeverity.Warning, 1: ReactionValidationSeverity.Error})
exception cosmolkit.ReactionWriteError(*args, **kwargs)

Failure in the reaction domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ReactionWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property actual: int | None

Readonly actual payload of the CoordinateSelectionArity error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the CoordinateSelectionArity error variant; None for other variants.

property role: ReactionRole | None

Role of the affected reaction template or transformation participant. Present for ReactionWriteError.Template, ReactionWriteError.Connectivity; None when unavailable.

property source: SmartsWriteError | PathError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property template: int | None

Index of the affected reaction template. Present for ReactionWriteError.Template, ReactionWriteError.Connectivity; None when unavailable.

property variant: ReactionWriteErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ReactionWriteErrorKind(value)

Discriminants of ReactionWriteErrorKind.

Members: Cx, Template, Connectivity, CoordinateSelectionArity, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
Connectivity = ReactionWriteErrorKind.Connectivity
CoordinateSelectionArity = ReactionWriteErrorKind.CoordinateSelectionArity
Cx = ReactionWriteErrorKind.Cx
Template = ReactionWriteErrorKind.Template
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cx': ReactionWriteErrorKind.Cx, 'Template': ReactionWriteErrorKind.Template, 'Connectivity': ReactionWriteErrorKind.Connectivity, 'CoordinateSelectionArity': ReactionWriteErrorKind.CoordinateSelectionArity})
values = mappingproxy({0: ReactionWriteErrorKind.Cx, 1: ReactionWriteErrorKind.Template, 2: ReactionWriteErrorKind.Connectivity, 3: ReactionWriteErrorKind.CoordinateSelectionArity})
class cosmolkit.ReactionWriteParams(*, canonical=Ellipsis, isomeric_smiles=Ellipsis, rooted_at_atom=Ellipsis, include_dative_bonds=Ellipsis, include_cx=Ellipsis, cx_fields=Ellipsis, coordinate_selections=Ellipsis)

Source-consumed SMARTS/CX options; canonical sorts strings within each role.

Members (7)
canonical: bool

Canonicalize component output and sort strings within each reaction role.

coordinate_selections: tuple[ReactionCoordinateSelection, ...]

Per template in original reactant, agent, product insertion order.

cx_fields: CxSmilesFields

Bit mask of CXSMILES extensions to write.

include_cx: bool

Include the selected CXSMILES extension fields.

include_dative_bonds: bool

Write dative bonds using their explicit notation.

isomeric_smiles: bool

Include isotope and stereochemical information.

rooted_at_atom: int | None

Optional starting atom index for template output.

class cosmolkit.RecursiveStructureQuery

Read-only recursive SMARTS query retained by its owning diagnostic.

Members (4)
initialized: bool

Whether the recursive query has an initialized graph.

query_graph: QueryGraph | None

Initialized recursive query graph, or None when not initialized.

serial_number: int

Native recursive-query serial identifier.

source_smarts: str | None

Original recursive SMARTS text, or None if not retained.

class cosmolkit.RemoveHsParams(*, remove_degree_zero=Ellipsis, remove_higher_degrees=Ellipsis, remove_only_h_neighbors=Ellipsis, remove_isotopes=Ellipsis, remove_and_track_isotopes=Ellipsis, remove_dummy_neighbors=Ellipsis, remove_defining_bond_stereo=Ellipsis, remove_with_wedged_bond=Ellipsis, remove_with_query=Ellipsis, remove_mapped=Ellipsis, remove_in_sgroups=Ellipsis, show_warnings=Ellipsis, remove_nonimplicit=Ellipsis, update_explicit_count=Ellipsis, remove_hydrides=Ellipsis, remove_nontetrahedral_neighbors=Ellipsis, sanitize=Ellipsis)

Parameters corresponding to RDKit’s MolOps::RemoveHsParameters.

Members (17)
remove_and_track_isotopes: bool

Remove isotopic hydrogens while retaining isotope tracking for subsequent hydrogen addition.

remove_defining_bond_stereo: bool

Allow removal of hydrogens used to define bond stereochemistry.

remove_degree_zero: bool

Allow removal of isolated hydrogen atoms.

remove_dummy_neighbors: bool

Allow removal of hydrogens attached to dummy atoms.

remove_higher_degrees: bool

Allow removal of hydrogens with more than one neighbor.

remove_hydrides: bool

Allow removal of negatively charged hydrogen atoms.

remove_in_sgroups: bool

Allow source-eligible hydrogen removal within substance groups.

remove_isotopes: bool

Allow removal of isotopically labeled hydrogen atoms.

remove_mapped: bool

Allow removal of hydrogen atoms carrying atom-map numbers.

remove_nonimplicit: bool

Remove eligible explicit hydrogen atoms, not just hydrogens treated as implicit.

remove_nontetrahedral_neighbors: bool

Allow removal of hydrogens neighboring atoms with non-tetrahedral stereo.

remove_only_h_neighbors: bool

Allow removal of hydrogens whose neighbors are all hydrogen atoms.

remove_with_query: bool

Allow removal of hydrogen atoms carrying queries.

remove_with_wedged_bond: bool

Allow removal of hydrogens attached by wedged bonds.

sanitize: bool

Run the complete default sanitize pipeline after source-eligible non-implicit removal. RDKit exposes this as the overload’s separate sanitize argument; the canonical COSMolKit parameter value keeps the observable option explicit across languages. When false, actual pre-removal source scalar values survive; intermediate calculations needed by removal still run. True alone is not proof of strict chemical validity when no sanitize branch executes.

show_warnings: bool

Emit warnings for hydrogen-removal conditions reported by the native algorithm.

update_explicit_count: bool

Update explicit hydrogen counts on the remaining neighboring atoms.

class cosmolkit.Replace3DCoordinatesParams(*, conformer_id=Ellipsis)

Explicit stored-conformer selection for replacing 3D coordinates.

Members (1)
conformer_id: int

Actual ThreeD conformer ID; the default selects ID0 and never falls back.

exception cosmolkit.RequiredPropertyStringError(*args, **kwargs)

RequiredPropertyStringError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property conversion: PropertyStringError | None

“error_payload”} Structured PropertyStringError payload of RequiredPropertyStringError.Conversion; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property missing: MissingPropertyError | None

“error_payload”} Structured MissingPropertyError payload of RequiredPropertyStringError.Missing; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: RequiredPropertyStringErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.RequiredPropertyStringErrorKind(value)

Discriminants of RequiredPropertyStringErrorKind.

Members: Missing, Conversion, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Conversion = RequiredPropertyStringErrorKind.Conversion
Missing = RequiredPropertyStringErrorKind.Missing
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Missing': RequiredPropertyStringErrorKind.Missing, 'Conversion': RequiredPropertyStringErrorKind.Conversion})
values = mappingproxy({0: RequiredPropertyStringErrorKind.Missing, 1: RequiredPropertyStringErrorKind.Conversion})
class cosmolkit.ResidueAddress

Source residue address comprising numbering, insertion code, segment and residue name.

Members (7)
insertion_code: int | None

Optional source insertion-code byte.

matches(other) → bool

Compare residue addresses using the native matching rules, including the segment.

matches_without_segment(other) → bool

Compare residue addresses using native matching rules while ignoring the segment.

name: str

Name or identifier retained in this source record.

static new(sequence_number, insertion_code, segment, name) → ResidueAddress | None

Create a source residue address; return None if its residue name or address fields are invalid.

segment: str

Source segment identifier.

sequence_number: int | None

Author residue sequence number, or None when unspecified.

class cosmolkit.ResidueCode(value)

Typed ResidueCode values corresponding to the Rust enum.

Members: ALA, ARG, ASN, ABA, ASP, ASX, CYS, CSH, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, MSE, ORN, PHE, PRO, SER, THR, TRP, TYR, UNK, VAL, SEC, PYL, SEP, TPO, PCA, CSO, PTR, KCX, CSD, LLP, CME, MLY, DAL, TYS, OCS, M3L, FME, ALY, HYP, CAS, CRO, CSX, DPR, DGL, DVA, CSS, DPN, DSN, DLE, HIC, NLE, MVA, MLZ, CR2, SAR, DAR, DLY, YCM, NRQ, CGU, R0TD, MLE, DAS, DTR, CXM, TPQ, DCY, DSG, DTY, DHI, MEN, DTH, SAC, DGN, AIB, SMC, IAS, CIR, BMT, DIL, FGA, PHI, CRQ, SME, GHP, MHO, NEP, TRQ, TOX, ALC, R3FG, SCH, MDO, MAA, GYS, MK8, CR8, KPI, SCY, DHA, OMY, CAF, R0AF, SNN, MHS, MLU, SNC, PHD, B3E, MEA, MED, OAS, GL3, FVA, PHL, CRF, OMZ, BFD, MEQ, DAB, AGM, PSU, R5MU, R7MG, OMG, UR3, OMC, R2MG, H2U, R4SU, OMU, R4OC, MA6, M2G, R1MA, R6MZ, CCC, R2MA, R1MG, R5BU, MIA, DOC, R8OG, R5CM, R3DR, BRU, CBR, HOH, DOD, HEM, SO4, GOL, EDO, NAG, PO4, ACT, PEG, MAN, FAD, BMA, ADP, DMS, ACE, NH2, MPD, MES, NAD, NAP, TRS, ATP, PG4, GDP, FUC, FMT, GAL, PGE, FMN, PLP, EPE, SF4, BME, CIT, BE7, MRD, MHA, BU3, PGO, BU2, PDO, BU1, PG6, R1BO, PE7, PG5, TFP, DHD, PEU, TAU, SBT, SAL, IOH, IPA, PIG, B3P, BTB, NHE, C8E, OTE, PE4, XPE, PE8, P33, N8E, R2OS, R1PS, CPS, DMX, MPO, GCD, DXG, CM5, ACA, ACN, CCN, GLC, DR6, NH4, AZI, BNG, BOG, BGC, BCN, BRO, CAC, CBX, ACY, CBM, CLO, R3CO, NCO, CU1, CYN, MA4, TAR, GLO, MTL, SOR, DMU, DDQ, DMF, DIO, DOX, R12P, SDS, LMT, EOH, EEE, EGL, FLO, TRT, FCY, FRU, GBL, GPX, HTO, HTG, B7G, C10, R16D, HEZ, IOD, IDO, ICI, ICT, TLA, LAT, LBT, LDA, MN3, MRY, MOH, BEQ, C15, MG8, POL, NO3, JEF, P4C, CE1, DIA, CXE, IPH, PIN, R15P, CRY, PGR, PGQ, SPD, SPK, SPM, SUC, TBU, TMA, TEP, SCN, TRE, ETF, R144, UMQ, URE, YT3, ZN2, FE2, R3NI, SIA, XYP, A2G, GLA, NDG, NGA, A, C, G, I, U, N, F, K, DA, DC, DG, DI, DT, DU, DN, AG, AL, BA, BR, CA, CD, CL, CM, CN, CO, CS, CU, FE, HG, LI, MG, MN, NA, NI, NO, PB, RB, SR, Y1, ZN, UNKNOWN, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (372)
A = ResidueCode.A
A2G = ResidueCode.A2G
ABA = ResidueCode.ABA
ACA = ResidueCode.ACA
ACE = ResidueCode.ACE
ACN = ResidueCode.ACN
ACT = ResidueCode.ACT
ACY = ResidueCode.ACY
ADP = ResidueCode.ADP
AG = ResidueCode.AG
AGM = ResidueCode.AGM
AIB = ResidueCode.AIB
AL = ResidueCode.AL
ALA = ResidueCode.ALA
ALC = ResidueCode.ALC
ALY = ResidueCode.ALY
ARG = ResidueCode.ARG
ASN = ResidueCode.ASN
ASP = ResidueCode.ASP
ASX = ResidueCode.ASX
ATP = ResidueCode.ATP
AZI = ResidueCode.AZI
B3E = ResidueCode.B3E
B3P = ResidueCode.B3P
B7G = ResidueCode.B7G
BA = ResidueCode.BA
BCN = ResidueCode.BCN
BE7 = ResidueCode.BE7
BEQ = ResidueCode.BEQ
BFD = ResidueCode.BFD
BGC = ResidueCode.BGC
BMA = ResidueCode.BMA
BME = ResidueCode.BME
BMT = ResidueCode.BMT
BNG = ResidueCode.BNG
BOG = ResidueCode.BOG
BR = ResidueCode.BR
BRO = ResidueCode.BRO
BRU = ResidueCode.BRU
BTB = ResidueCode.BTB
BU1 = ResidueCode.BU1
BU2 = ResidueCode.BU2
BU3 = ResidueCode.BU3
C = ResidueCode.C
C10 = ResidueCode.C10
C15 = ResidueCode.C15
C8E = ResidueCode.C8E
CA = ResidueCode.CA
CAC = ResidueCode.CAC
CAF = ResidueCode.CAF
CAS = ResidueCode.CAS
CBM = ResidueCode.CBM
CBR = ResidueCode.CBR
CBX = ResidueCode.CBX
CCC = ResidueCode.CCC
CCN = ResidueCode.CCN
CD = ResidueCode.CD
CE1 = ResidueCode.CE1
CGU = ResidueCode.CGU
CIR = ResidueCode.CIR
CIT = ResidueCode.CIT
CL = ResidueCode.CL
CLO = ResidueCode.CLO
CM = ResidueCode.CM
CM5 = ResidueCode.CM5
CME = ResidueCode.CME
CN = ResidueCode.CN
CO = ResidueCode.CO
CPS = ResidueCode.CPS
CR2 = ResidueCode.CR2
CR8 = ResidueCode.CR8
CRF = ResidueCode.CRF
CRO = ResidueCode.CRO
CRQ = ResidueCode.CRQ
CRY = ResidueCode.CRY
CS = ResidueCode.CS
CSD = ResidueCode.CSD
CSH = ResidueCode.CSH
CSO = ResidueCode.CSO
CSS = ResidueCode.CSS
CSX = ResidueCode.CSX
CU = ResidueCode.CU
CU1 = ResidueCode.CU1
CXE = ResidueCode.CXE
CXM = ResidueCode.CXM
CYN = ResidueCode.CYN
CYS = ResidueCode.CYS
DA = ResidueCode.DA
DAB = ResidueCode.DAB
DAL = ResidueCode.DAL
DAR = ResidueCode.DAR
DAS = ResidueCode.DAS
DC = ResidueCode.DC
DCY = ResidueCode.DCY
DDQ = ResidueCode.DDQ
DG = ResidueCode.DG
DGL = ResidueCode.DGL
DGN = ResidueCode.DGN
DHA = ResidueCode.DHA
DHD = ResidueCode.DHD
DHI = ResidueCode.DHI
DI = ResidueCode.DI
DIA = ResidueCode.DIA
DIL = ResidueCode.DIL
DIO = ResidueCode.DIO
DLE = ResidueCode.DLE
DLY = ResidueCode.DLY
DMF = ResidueCode.DMF
DMS = ResidueCode.DMS
DMU = ResidueCode.DMU
DMX = ResidueCode.DMX
DN = ResidueCode.DN
DOC = ResidueCode.DOC
DOD = ResidueCode.DOD
DOX = ResidueCode.DOX
DPN = ResidueCode.DPN
DPR = ResidueCode.DPR
DR6 = ResidueCode.DR6
DSG = ResidueCode.DSG
DSN = ResidueCode.DSN
DT = ResidueCode.DT
DTH = ResidueCode.DTH
DTR = ResidueCode.DTR
DTY = ResidueCode.DTY
DU = ResidueCode.DU
DVA = ResidueCode.DVA
DXG = ResidueCode.DXG
EDO = ResidueCode.EDO
EEE = ResidueCode.EEE
EGL = ResidueCode.EGL
EOH = ResidueCode.EOH
EPE = ResidueCode.EPE
ETF = ResidueCode.ETF
F = ResidueCode.F
FAD = ResidueCode.FAD
FCY = ResidueCode.FCY
FE = ResidueCode.FE
FE2 = ResidueCode.FE2
FGA = ResidueCode.FGA
FLO = ResidueCode.FLO
FME = ResidueCode.FME
FMN = ResidueCode.FMN
FMT = ResidueCode.FMT
FRU = ResidueCode.FRU
FUC = ResidueCode.FUC
FVA = ResidueCode.FVA
G = ResidueCode.G
GAL = ResidueCode.GAL
GBL = ResidueCode.GBL
GCD = ResidueCode.GCD
GDP = ResidueCode.GDP
GHP = ResidueCode.GHP
GL3 = ResidueCode.GL3
GLA = ResidueCode.GLA
GLC = ResidueCode.GLC
GLN = ResidueCode.GLN
GLO = ResidueCode.GLO
GLU = ResidueCode.GLU
GLX = ResidueCode.GLX
GLY = ResidueCode.GLY
GOL = ResidueCode.GOL
GPX = ResidueCode.GPX
GYS = ResidueCode.GYS
H2U = ResidueCode.H2U
HEM = ResidueCode.HEM
HEZ = ResidueCode.HEZ
HG = ResidueCode.HG
HIC = ResidueCode.HIC
HIS = ResidueCode.HIS
HOH = ResidueCode.HOH
HTG = ResidueCode.HTG
HTO = ResidueCode.HTO
HYP = ResidueCode.HYP
I = ResidueCode.I
IAS = ResidueCode.IAS
ICI = ResidueCode.ICI
ICT = ResidueCode.ICT
IDO = ResidueCode.IDO
ILE = ResidueCode.ILE
IOD = ResidueCode.IOD
IOH = ResidueCode.IOH
IPA = ResidueCode.IPA
IPH = ResidueCode.IPH
JEF = ResidueCode.JEF
K = ResidueCode.K
KCX = ResidueCode.KCX
KPI = ResidueCode.KPI
LAT = ResidueCode.LAT
LBT = ResidueCode.LBT
LDA = ResidueCode.LDA
LEU = ResidueCode.LEU
LI = ResidueCode.LI
LLP = ResidueCode.LLP
LMT = ResidueCode.LMT
LYS = ResidueCode.LYS
M2G = ResidueCode.M2G
M3L = ResidueCode.M3L
MA4 = ResidueCode.MA4
MA6 = ResidueCode.MA6
MAA = ResidueCode.MAA
MAN = ResidueCode.MAN
MDO = ResidueCode.MDO
MEA = ResidueCode.MEA
MED = ResidueCode.MED
MEN = ResidueCode.MEN
MEQ = ResidueCode.MEQ
MES = ResidueCode.MES
MET = ResidueCode.MET
MG = ResidueCode.MG
MG8 = ResidueCode.MG8
MHA = ResidueCode.MHA
MHO = ResidueCode.MHO
MHS = ResidueCode.MHS
MIA = ResidueCode.MIA
MK8 = ResidueCode.MK8
MLE = ResidueCode.MLE
MLU = ResidueCode.MLU
MLY = ResidueCode.MLY
MLZ = ResidueCode.MLZ
MN = ResidueCode.MN
MN3 = ResidueCode.MN3
MOH = ResidueCode.MOH
MPD = ResidueCode.MPD
MPO = ResidueCode.MPO
MRD = ResidueCode.MRD
MRY = ResidueCode.MRY
MSE = ResidueCode.MSE
MTL = ResidueCode.MTL
MVA = ResidueCode.MVA
N = ResidueCode.N
N8E = ResidueCode.N8E
NA = ResidueCode.NA
NAD = ResidueCode.NAD
NAG = ResidueCode.NAG
NAP = ResidueCode.NAP
NCO = ResidueCode.NCO
NDG = ResidueCode.NDG
NEP = ResidueCode.NEP
NGA = ResidueCode.NGA
NH2 = ResidueCode.NH2
NH4 = ResidueCode.NH4
NHE = ResidueCode.NHE
NI = ResidueCode.NI
NLE = ResidueCode.NLE
NO = ResidueCode.NO
NO3 = ResidueCode.NO3
NRQ = ResidueCode.NRQ
OAS = ResidueCode.OAS
OCS = ResidueCode.OCS
OMC = ResidueCode.OMC
OMG = ResidueCode.OMG
OMU = ResidueCode.OMU
OMY = ResidueCode.OMY
OMZ = ResidueCode.OMZ
ORN = ResidueCode.ORN
OTE = ResidueCode.OTE
P33 = ResidueCode.P33
P4C = ResidueCode.P4C
PB = ResidueCode.PB
PCA = ResidueCode.PCA
PDO = ResidueCode.PDO
PE4 = ResidueCode.PE4
PE7 = ResidueCode.PE7
PE8 = ResidueCode.PE8
PEG = ResidueCode.PEG
PEU = ResidueCode.PEU
PG4 = ResidueCode.PG4
PG5 = ResidueCode.PG5
PG6 = ResidueCode.PG6
PGE = ResidueCode.PGE
PGO = ResidueCode.PGO
PGQ = ResidueCode.PGQ
PGR = ResidueCode.PGR
PHD = ResidueCode.PHD
PHE = ResidueCode.PHE
PHI = ResidueCode.PHI
PHL = ResidueCode.PHL
PIG = ResidueCode.PIG
PIN = ResidueCode.PIN
PLP = ResidueCode.PLP
PO4 = ResidueCode.PO4
POL = ResidueCode.POL
PRO = ResidueCode.PRO
PSU = ResidueCode.PSU
PTR = ResidueCode.PTR
PYL = ResidueCode.PYL
R0AF = ResidueCode.R0AF
R0TD = ResidueCode.R0TD
R12P = ResidueCode.R12P
R144 = ResidueCode.R144
R15P = ResidueCode.R15P
R16D = ResidueCode.R16D
R1BO = ResidueCode.R1BO
R1MA = ResidueCode.R1MA
R1MG = ResidueCode.R1MG
R1PS = ResidueCode.R1PS
R2MA = ResidueCode.R2MA
R2MG = ResidueCode.R2MG
R2OS = ResidueCode.R2OS
R3CO = ResidueCode.R3CO
R3DR = ResidueCode.R3DR
R3FG = ResidueCode.R3FG
R3NI = ResidueCode.R3NI
R4OC = ResidueCode.R4OC
R4SU = ResidueCode.R4SU
R5BU = ResidueCode.R5BU
R5CM = ResidueCode.R5CM
R5MU = ResidueCode.R5MU
R6MZ = ResidueCode.R6MZ
R7MG = ResidueCode.R7MG
R8OG = ResidueCode.R8OG
RB = ResidueCode.RB
SAC = ResidueCode.SAC
SAL = ResidueCode.SAL
SAR = ResidueCode.SAR
SBT = ResidueCode.SBT
SCH = ResidueCode.SCH
SCN = ResidueCode.SCN
SCY = ResidueCode.SCY
SDS = ResidueCode.SDS
SEC = ResidueCode.SEC
SEP = ResidueCode.SEP
SER = ResidueCode.SER
SF4 = ResidueCode.SF4
SIA = ResidueCode.SIA
SMC = ResidueCode.SMC
SME = ResidueCode.SME
SNC = ResidueCode.SNC
SNN = ResidueCode.SNN
SO4 = ResidueCode.SO4
SOR = ResidueCode.SOR
SPD = ResidueCode.SPD
SPK = ResidueCode.SPK
SPM = ResidueCode.SPM
SR = ResidueCode.SR
SUC = ResidueCode.SUC
TAR = ResidueCode.TAR
TAU = ResidueCode.TAU
TBU = ResidueCode.TBU
TEP = ResidueCode.TEP
TFP = ResidueCode.TFP
THR = ResidueCode.THR
TLA = ResidueCode.TLA
TMA = ResidueCode.TMA
TOX = ResidueCode.TOX
TPO = ResidueCode.TPO
TPQ = ResidueCode.TPQ
TRE = ResidueCode.TRE
TRP = ResidueCode.TRP
TRQ = ResidueCode.TRQ
TRS = ResidueCode.TRS
TRT = ResidueCode.TRT
TYR = ResidueCode.TYR
TYS = ResidueCode.TYS
U = ResidueCode.U
UMQ = ResidueCode.UMQ
UNK = ResidueCode.UNK
UNKNOWN = ResidueCode.UNKNOWN
UR3 = ResidueCode.UR3
URE = ResidueCode.URE
VAL = ResidueCode.VAL
XPE = ResidueCode.XPE
XYP = ResidueCode.XYP
Y1 = ResidueCode.Y1
YCM = ResidueCode.YCM
YT3 = ResidueCode.YT3
ZN = ResidueCode.ZN
ZN2 = ResidueCode.ZN2
as_u16() → int

Native numeric residue-table code.

name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ALA': ResidueCode.ALA, 'ARG': ResidueCode.ARG, 'ASN': ResidueCode.ASN, 'ABA': ResidueCode.ABA, 'ASP': ResidueCode.ASP, 'ASX': ResidueCode.ASX, 'CYS': ResidueCode.CYS, 'CSH': ResidueCode.CSH, 'GLN': ResidueCode.GLN, 'GLU': ResidueCode.GLU, 'GLX': ResidueCode.GLX, 'GLY': ResidueCode.GLY, 'HIS': ResidueCode.HIS, 'ILE': ResidueCode.ILE, 'LEU': ResidueCode.LEU, 'LYS': ResidueCode.LYS, 'MET': ResidueCode.MET, 'MSE': ResidueCode.MSE, 'ORN': ResidueCode.ORN, 'PHE': ResidueCode.PHE, 'PRO': ResidueCode.PRO, 'SER': ResidueCode.SER, 'THR': ResidueCode.THR, 'TRP': ResidueCode.TRP, 'TYR': ResidueCode.TYR, 'UNK': ResidueCode.UNK, 'VAL': ResidueCode.VAL, 'SEC': ResidueCode.SEC, 'PYL': ResidueCode.PYL, 'SEP': ResidueCode.SEP, 'TPO': ResidueCode.TPO, 'PCA': ResidueCode.PCA, 'CSO': ResidueCode.CSO, 'PTR': ResidueCode.PTR, 'KCX': ResidueCode.KCX, 'CSD': ResidueCode.CSD, 'LLP': ResidueCode.LLP, 'CME': ResidueCode.CME, 'MLY': ResidueCode.MLY, 'DAL': ResidueCode.DAL, 'TYS': ResidueCode.TYS, 'OCS': ResidueCode.OCS, 'M3L': ResidueCode.M3L, 'FME': ResidueCode.FME, 'ALY': ResidueCode.ALY, 'HYP': ResidueCode.HYP, 'CAS': ResidueCode.CAS, 'CRO': ResidueCode.CRO, 'CSX': ResidueCode.CSX, 'DPR': ResidueCode.DPR, 'DGL': ResidueCode.DGL, 'DVA': ResidueCode.DVA, 'CSS': ResidueCode.CSS, 'DPN': ResidueCode.DPN, 'DSN': ResidueCode.DSN, 'DLE': ResidueCode.DLE, 'HIC': ResidueCode.HIC, 'NLE': ResidueCode.NLE, 'MVA': ResidueCode.MVA, 'MLZ': ResidueCode.MLZ, 'CR2': ResidueCode.CR2, 'SAR': ResidueCode.SAR, 'DAR': ResidueCode.DAR, 'DLY': ResidueCode.DLY, 'YCM': ResidueCode.YCM, 'NRQ': ResidueCode.NRQ, 'CGU': ResidueCode.CGU, 'R0TD': ResidueCode.R0TD, 'MLE': ResidueCode.MLE, 'DAS': ResidueCode.DAS, 'DTR': ResidueCode.DTR, 'CXM': ResidueCode.CXM, 'TPQ': ResidueCode.TPQ, 'DCY': ResidueCode.DCY, 'DSG': ResidueCode.DSG, 'DTY': ResidueCode.DTY, 'DHI': ResidueCode.DHI, 'MEN': ResidueCode.MEN, 'DTH': ResidueCode.DTH, 'SAC': ResidueCode.SAC, 'DGN': ResidueCode.DGN, 'AIB': ResidueCode.AIB, 'SMC': ResidueCode.SMC, 'IAS': ResidueCode.IAS, 'CIR': ResidueCode.CIR, 'BMT': ResidueCode.BMT, 'DIL': ResidueCode.DIL, 'FGA': ResidueCode.FGA, 'PHI': ResidueCode.PHI, 'CRQ': ResidueCode.CRQ, 'SME': ResidueCode.SME, 'GHP': ResidueCode.GHP, 'MHO': ResidueCode.MHO, 'NEP': ResidueCode.NEP, 'TRQ': ResidueCode.TRQ, 'TOX': ResidueCode.TOX, 'ALC': ResidueCode.ALC, 'R3FG': ResidueCode.R3FG, 'SCH': ResidueCode.SCH, 'MDO': ResidueCode.MDO, 'MAA': ResidueCode.MAA, 'GYS': ResidueCode.GYS, 'MK8': ResidueCode.MK8, 'CR8': ResidueCode.CR8, 'KPI': ResidueCode.KPI, 'SCY': ResidueCode.SCY, 'DHA': ResidueCode.DHA, 'OMY': ResidueCode.OMY, 'CAF': ResidueCode.CAF, 'R0AF': ResidueCode.R0AF, 'SNN': ResidueCode.SNN, 'MHS': ResidueCode.MHS, 'MLU': ResidueCode.MLU, 'SNC': ResidueCode.SNC, 'PHD': ResidueCode.PHD, 'B3E': ResidueCode.B3E, 'MEA': ResidueCode.MEA, 'MED': ResidueCode.MED, 'OAS': ResidueCode.OAS, 'GL3': ResidueCode.GL3, 'FVA': ResidueCode.FVA, 'PHL': ResidueCode.PHL, 'CRF': ResidueCode.CRF, 'OMZ': ResidueCode.OMZ, 'BFD': ResidueCode.BFD, 'MEQ': ResidueCode.MEQ, 'DAB': ResidueCode.DAB, 'AGM': ResidueCode.AGM, 'PSU': ResidueCode.PSU, 'R5MU': ResidueCode.R5MU, 'R7MG': ResidueCode.R7MG, 'OMG': ResidueCode.OMG, 'UR3': ResidueCode.UR3, 'OMC': ResidueCode.OMC, 'R2MG': ResidueCode.R2MG, 'H2U': ResidueCode.H2U, 'R4SU': ResidueCode.R4SU, 'OMU': ResidueCode.OMU, 'R4OC': ResidueCode.R4OC, 'MA6': ResidueCode.MA6, 'M2G': ResidueCode.M2G, 'R1MA': ResidueCode.R1MA, 'R6MZ': ResidueCode.R6MZ, 'CCC': ResidueCode.CCC, 'R2MA': ResidueCode.R2MA, 'R1MG': ResidueCode.R1MG, 'R5BU': ResidueCode.R5BU, 'MIA': ResidueCode.MIA, 'DOC': ResidueCode.DOC, 'R8OG': ResidueCode.R8OG, 'R5CM': ResidueCode.R5CM, 'R3DR': ResidueCode.R3DR, 'BRU': ResidueCode.BRU, 'CBR': ResidueCode.CBR, 'HOH': ResidueCode.HOH, 'DOD': ResidueCode.DOD, 'HEM': ResidueCode.HEM, 'SO4': ResidueCode.SO4, 'GOL': ResidueCode.GOL, 'EDO': ResidueCode.EDO, 'NAG': ResidueCode.NAG, 'PO4': ResidueCode.PO4, 'ACT': ResidueCode.ACT, 'PEG': ResidueCode.PEG, 'MAN': ResidueCode.MAN, 'FAD': ResidueCode.FAD, 'BMA': ResidueCode.BMA, 'ADP': ResidueCode.ADP, 'DMS': ResidueCode.DMS, 'ACE': ResidueCode.ACE, 'NH2': ResidueCode.NH2, 'MPD': ResidueCode.MPD, 'MES': ResidueCode.MES, 'NAD': ResidueCode.NAD, 'NAP': ResidueCode.NAP, 'TRS': ResidueCode.TRS, 'ATP': ResidueCode.ATP, 'PG4': ResidueCode.PG4, 'GDP': ResidueCode.GDP, 'FUC': ResidueCode.FUC, 'FMT': ResidueCode.FMT, 'GAL': ResidueCode.GAL, 'PGE': ResidueCode.PGE, 'FMN': ResidueCode.FMN, 'PLP': ResidueCode.PLP, 'EPE': ResidueCode.EPE, 'SF4': ResidueCode.SF4, 'BME': ResidueCode.BME, 'CIT': ResidueCode.CIT, 'BE7': ResidueCode.BE7, 'MRD': ResidueCode.MRD, 'MHA': ResidueCode.MHA, 'BU3': ResidueCode.BU3, 'PGO': ResidueCode.PGO, 'BU2': ResidueCode.BU2, 'PDO': ResidueCode.PDO, 'BU1': ResidueCode.BU1, 'PG6': ResidueCode.PG6, 'R1BO': ResidueCode.R1BO, 'PE7': ResidueCode.PE7, 'PG5': ResidueCode.PG5, 'TFP': ResidueCode.TFP, 'DHD': ResidueCode.DHD, 'PEU': ResidueCode.PEU, 'TAU': ResidueCode.TAU, 'SBT': ResidueCode.SBT, 'SAL': ResidueCode.SAL, 'IOH': ResidueCode.IOH, 'IPA': ResidueCode.IPA, 'PIG': ResidueCode.PIG, 'B3P': ResidueCode.B3P, 'BTB': ResidueCode.BTB, 'NHE': ResidueCode.NHE, 'C8E': ResidueCode.C8E, 'OTE': ResidueCode.OTE, 'PE4': ResidueCode.PE4, 'XPE': ResidueCode.XPE, 'PE8': ResidueCode.PE8, 'P33': ResidueCode.P33, 'N8E': ResidueCode.N8E, 'R2OS': ResidueCode.R2OS, 'R1PS': ResidueCode.R1PS, 'CPS': ResidueCode.CPS, 'DMX': ResidueCode.DMX, 'MPO': ResidueCode.MPO, 'GCD': ResidueCode.GCD, 'DXG': ResidueCode.DXG, 'CM5': ResidueCode.CM5, 'ACA': ResidueCode.ACA, 'ACN': ResidueCode.ACN, 'CCN': ResidueCode.CCN, 'GLC': ResidueCode.GLC, 'DR6': ResidueCode.DR6, 'NH4': ResidueCode.NH4, 'AZI': ResidueCode.AZI, 'BNG': ResidueCode.BNG, 'BOG': ResidueCode.BOG, 'BGC': ResidueCode.BGC, 'BCN': ResidueCode.BCN, 'BRO': ResidueCode.BRO, 'CAC': ResidueCode.CAC, 'CBX': ResidueCode.CBX, 'ACY': ResidueCode.ACY, 'CBM': ResidueCode.CBM, 'CLO': ResidueCode.CLO, 'R3CO': ResidueCode.R3CO, 'NCO': ResidueCode.NCO, 'CU1': ResidueCode.CU1, 'CYN': ResidueCode.CYN, 'MA4': ResidueCode.MA4, 'TAR': ResidueCode.TAR, 'GLO': ResidueCode.GLO, 'MTL': ResidueCode.MTL, 'SOR': ResidueCode.SOR, 'DMU': ResidueCode.DMU, 'DDQ': ResidueCode.DDQ, 'DMF': ResidueCode.DMF, 'DIO': ResidueCode.DIO, 'DOX': ResidueCode.DOX, 'R12P': ResidueCode.R12P, 'SDS': ResidueCode.SDS, 'LMT': ResidueCode.LMT, 'EOH': ResidueCode.EOH, 'EEE': ResidueCode.EEE, 'EGL': ResidueCode.EGL, 'FLO': ResidueCode.FLO, 'TRT': ResidueCode.TRT, 'FCY': ResidueCode.FCY, 'FRU': ResidueCode.FRU, 'GBL': ResidueCode.GBL, 'GPX': ResidueCode.GPX, 'HTO': ResidueCode.HTO, 'HTG': ResidueCode.HTG, 'B7G': ResidueCode.B7G, 'C10': ResidueCode.C10, 'R16D': ResidueCode.R16D, 'HEZ': ResidueCode.HEZ, 'IOD': ResidueCode.IOD, 'IDO': ResidueCode.IDO, 'ICI': ResidueCode.ICI, 'ICT': ResidueCode.ICT, 'TLA': ResidueCode.TLA, 'LAT': ResidueCode.LAT, 'LBT': ResidueCode.LBT, 'LDA': ResidueCode.LDA, 'MN3': ResidueCode.MN3, 'MRY': ResidueCode.MRY, 'MOH': ResidueCode.MOH, 'BEQ': ResidueCode.BEQ, 'C15': ResidueCode.C15, 'MG8': ResidueCode.MG8, 'POL': ResidueCode.POL, 'NO3': ResidueCode.NO3, 'JEF': ResidueCode.JEF, 'P4C': ResidueCode.P4C, 'CE1': ResidueCode.CE1, 'DIA': ResidueCode.DIA, 'CXE': ResidueCode.CXE, 'IPH': ResidueCode.IPH, 'PIN': ResidueCode.PIN, 'R15P': ResidueCode.R15P, 'CRY': ResidueCode.CRY, 'PGR': ResidueCode.PGR, 'PGQ': ResidueCode.PGQ, 'SPD': ResidueCode.SPD, 'SPK': ResidueCode.SPK, 'SPM': ResidueCode.SPM, 'SUC': ResidueCode.SUC, 'TBU': ResidueCode.TBU, 'TMA': ResidueCode.TMA, 'TEP': ResidueCode.TEP, 'SCN': ResidueCode.SCN, 'TRE': ResidueCode.TRE, 'ETF': ResidueCode.ETF, 'R144': ResidueCode.R144, 'UMQ': ResidueCode.UMQ, 'URE': ResidueCode.URE, 'YT3': ResidueCode.YT3, 'ZN2': ResidueCode.ZN2, 'FE2': ResidueCode.FE2, 'R3NI': ResidueCode.R3NI, 'SIA': ResidueCode.SIA, 'XYP': ResidueCode.XYP, 'A2G': ResidueCode.A2G, 'GLA': ResidueCode.GLA, 'NDG': ResidueCode.NDG, 'NGA': ResidueCode.NGA, 'A': ResidueCode.A, 'C': ResidueCode.C, 'G': ResidueCode.G, 'I': ResidueCode.I, 'U': ResidueCode.U, 'N': ResidueCode.N, 'F': ResidueCode.F, 'K': ResidueCode.K, 'DA': ResidueCode.DA, 'DC': ResidueCode.DC, 'DG': ResidueCode.DG, 'DI': ResidueCode.DI, 'DT': ResidueCode.DT, 'DU': ResidueCode.DU, 'DN': ResidueCode.DN, 'AG': ResidueCode.AG, 'AL': ResidueCode.AL, 'BA': ResidueCode.BA, 'BR': ResidueCode.BR, 'CA': ResidueCode.CA, 'CD': ResidueCode.CD, 'CL': ResidueCode.CL, 'CM': ResidueCode.CM, 'CN': ResidueCode.CN, 'CO': ResidueCode.CO, 'CS': ResidueCode.CS, 'CU': ResidueCode.CU, 'FE': ResidueCode.FE, 'HG': ResidueCode.HG, 'LI': ResidueCode.LI, 'MG': ResidueCode.MG, 'MN': ResidueCode.MN, 'NA': ResidueCode.NA, 'NI': ResidueCode.NI, 'NO': ResidueCode.NO, 'PB': ResidueCode.PB, 'RB': ResidueCode.RB, 'SR': ResidueCode.SR, 'Y1': ResidueCode.Y1, 'ZN': ResidueCode.ZN, 'UNKNOWN': ResidueCode.UNKNOWN})
values = mappingproxy({0: ResidueCode.ALA, 1: ResidueCode.ARG, 2: ResidueCode.ASN, 3: ResidueCode.ABA, 4: ResidueCode.ASP, 5: ResidueCode.ASX, 6: ResidueCode.CYS, 7: ResidueCode.CSH, 8: ResidueCode.GLN, 9: ResidueCode.GLU, 10: ResidueCode.GLX, 11: ResidueCode.GLY, 12: ResidueCode.HIS, 13: ResidueCode.ILE, 14: ResidueCode.LEU, 15: ResidueCode.LYS, 16: ResidueCode.MET, 17: ResidueCode.MSE, 18: ResidueCode.ORN, 19: ResidueCode.PHE, 20: ResidueCode.PRO, 21: ResidueCode.SER, 22: ResidueCode.THR, 23: ResidueCode.TRP, 24: ResidueCode.TYR, 25: ResidueCode.UNK, 26: ResidueCode.VAL, 27: ResidueCode.SEC, 28: ResidueCode.PYL, 29: ResidueCode.SEP, 30: ResidueCode.TPO, 31: ResidueCode.PCA, 32: ResidueCode.CSO, 33: ResidueCode.PTR, 34: ResidueCode.KCX, 35: ResidueCode.CSD, 36: ResidueCode.LLP, 37: ResidueCode.CME, 38: ResidueCode.MLY, 39: ResidueCode.DAL, 40: ResidueCode.TYS, 41: ResidueCode.OCS, 42: ResidueCode.M3L, 43: ResidueCode.FME, 44: ResidueCode.ALY, 45: ResidueCode.HYP, 46: ResidueCode.CAS, 47: ResidueCode.CRO, 48: ResidueCode.CSX, 49: ResidueCode.DPR, 50: ResidueCode.DGL, 51: ResidueCode.DVA, 52: ResidueCode.CSS, 53: ResidueCode.DPN, 54: ResidueCode.DSN, 55: ResidueCode.DLE, 56: ResidueCode.HIC, 57: ResidueCode.NLE, 58: ResidueCode.MVA, 59: ResidueCode.MLZ, 60: ResidueCode.CR2, 61: ResidueCode.SAR, 62: ResidueCode.DAR, 63: ResidueCode.DLY, 64: ResidueCode.YCM, 65: ResidueCode.NRQ, 66: ResidueCode.CGU, 67: ResidueCode.R0TD, 68: ResidueCode.MLE, 69: ResidueCode.DAS, 70: ResidueCode.DTR, 71: ResidueCode.CXM, 72: ResidueCode.TPQ, 73: ResidueCode.DCY, 74: ResidueCode.DSG, 75: ResidueCode.DTY, 76: ResidueCode.DHI, 77: ResidueCode.MEN, 78: ResidueCode.DTH, 79: ResidueCode.SAC, 80: ResidueCode.DGN, 81: ResidueCode.AIB, 82: ResidueCode.SMC, 83: ResidueCode.IAS, 84: ResidueCode.CIR, 85: ResidueCode.BMT, 86: ResidueCode.DIL, 87: ResidueCode.FGA, 88: ResidueCode.PHI, 89: ResidueCode.CRQ, 90: ResidueCode.SME, 91: ResidueCode.GHP, 92: ResidueCode.MHO, 93: ResidueCode.NEP, 94: ResidueCode.TRQ, 95: ResidueCode.TOX, 96: ResidueCode.ALC, 97: ResidueCode.R3FG, 98: ResidueCode.SCH, 99: ResidueCode.MDO, 100: ResidueCode.MAA, 101: ResidueCode.GYS, 102: ResidueCode.MK8, 103: ResidueCode.CR8, 104: ResidueCode.KPI, 105: ResidueCode.SCY, 106: ResidueCode.DHA, 107: ResidueCode.OMY, 108: ResidueCode.CAF, 109: ResidueCode.R0AF, 110: ResidueCode.SNN, 111: ResidueCode.MHS, 112: ResidueCode.MLU, 113: ResidueCode.SNC, 114: ResidueCode.PHD, 115: ResidueCode.B3E, 116: ResidueCode.MEA, 117: ResidueCode.MED, 118: ResidueCode.OAS, 119: ResidueCode.GL3, 120: ResidueCode.FVA, 121: ResidueCode.PHL, 122: ResidueCode.CRF, 123: ResidueCode.OMZ, 124: ResidueCode.BFD, 125: ResidueCode.MEQ, 126: ResidueCode.DAB, 127: ResidueCode.AGM, 128: ResidueCode.PSU, 129: ResidueCode.R5MU, 130: ResidueCode.R7MG, 131: ResidueCode.OMG, 132: ResidueCode.UR3, 133: ResidueCode.OMC, 134: ResidueCode.R2MG, 135: ResidueCode.H2U, 136: ResidueCode.R4SU, 137: ResidueCode.OMU, 138: ResidueCode.R4OC, 139: ResidueCode.MA6, 140: ResidueCode.M2G, 141: ResidueCode.R1MA, 142: ResidueCode.R6MZ, 143: ResidueCode.CCC, 144: ResidueCode.R2MA, 145: ResidueCode.R1MG, 146: ResidueCode.R5BU, 147: ResidueCode.MIA, 148: ResidueCode.DOC, 149: ResidueCode.R8OG, 150: ResidueCode.R5CM, 151: ResidueCode.R3DR, 152: ResidueCode.BRU, 153: ResidueCode.CBR, 154: ResidueCode.HOH, 155: ResidueCode.DOD, 156: ResidueCode.HEM, 157: ResidueCode.SO4, 158: ResidueCode.GOL, 159: ResidueCode.EDO, 160: ResidueCode.NAG, 161: ResidueCode.PO4, 162: ResidueCode.ACT, 163: ResidueCode.PEG, 164: ResidueCode.MAN, 165: ResidueCode.FAD, 166: ResidueCode.BMA, 167: ResidueCode.ADP, 168: ResidueCode.DMS, 169: ResidueCode.ACE, 170: ResidueCode.NH2, 171: ResidueCode.MPD, 172: ResidueCode.MES, 173: ResidueCode.NAD, 174: ResidueCode.NAP, 175: ResidueCode.TRS, 176: ResidueCode.ATP, 177: ResidueCode.PG4, 178: ResidueCode.GDP, 179: ResidueCode.FUC, 180: ResidueCode.FMT, 181: ResidueCode.GAL, 182: ResidueCode.PGE, 183: ResidueCode.FMN, 184: ResidueCode.PLP, 185: ResidueCode.EPE, 186: ResidueCode.SF4, 187: ResidueCode.BME, 188: ResidueCode.CIT, 189: ResidueCode.BE7, 190: ResidueCode.MRD, 191: ResidueCode.MHA, 192: ResidueCode.BU3, 193: ResidueCode.PGO, 194: ResidueCode.BU2, 195: ResidueCode.PDO, 196: ResidueCode.BU1, 197: ResidueCode.PG6, 198: ResidueCode.R1BO, 199: ResidueCode.PE7, 200: ResidueCode.PG5, 201: ResidueCode.TFP, 202: ResidueCode.DHD, 203: ResidueCode.PEU, 204: ResidueCode.TAU, 205: ResidueCode.SBT, 206: ResidueCode.SAL, 207: ResidueCode.IOH, 208: ResidueCode.IPA, 209: ResidueCode.PIG, 210: ResidueCode.B3P, 211: ResidueCode.BTB, 212: ResidueCode.NHE, 213: ResidueCode.C8E, 214: ResidueCode.OTE, 215: ResidueCode.PE4, 216: ResidueCode.XPE, 217: ResidueCode.PE8, 218: ResidueCode.P33, 219: ResidueCode.N8E, 220: ResidueCode.R2OS, 221: ResidueCode.R1PS, 222: ResidueCode.CPS, 223: ResidueCode.DMX, 224: ResidueCode.MPO, 225: ResidueCode.GCD, 226: ResidueCode.DXG, 227: ResidueCode.CM5, 228: ResidueCode.ACA, 229: ResidueCode.ACN, 230: ResidueCode.CCN, 231: ResidueCode.GLC, 232: ResidueCode.DR6, 233: ResidueCode.NH4, 234: ResidueCode.AZI, 235: ResidueCode.BNG, 236: ResidueCode.BOG, 237: ResidueCode.BGC, 238: ResidueCode.BCN, 239: ResidueCode.BRO, 240: ResidueCode.CAC, 241: ResidueCode.CBX, 242: ResidueCode.ACY, 243: ResidueCode.CBM, 244: ResidueCode.CLO, 245: ResidueCode.R3CO, 246: ResidueCode.NCO, 247: ResidueCode.CU1, 248: ResidueCode.CYN, 249: ResidueCode.MA4, 250: ResidueCode.TAR, 251: ResidueCode.GLO, 252: ResidueCode.MTL, 253: ResidueCode.SOR, 254: ResidueCode.DMU, 255: ResidueCode.DDQ, 256: ResidueCode.DMF, 257: ResidueCode.DIO, 258: ResidueCode.DOX, 259: ResidueCode.R12P, 260: ResidueCode.SDS, 261: ResidueCode.LMT, 262: ResidueCode.EOH, 263: ResidueCode.EEE, 264: ResidueCode.EGL, 265: ResidueCode.FLO, 266: ResidueCode.TRT, 267: ResidueCode.FCY, 268: ResidueCode.FRU, 269: ResidueCode.GBL, 270: ResidueCode.GPX, 271: ResidueCode.HTO, 272: ResidueCode.HTG, 273: ResidueCode.B7G, 274: ResidueCode.C10, 275: ResidueCode.R16D, 276: ResidueCode.HEZ, 277: ResidueCode.IOD, 278: ResidueCode.IDO, 279: ResidueCode.ICI, 280: ResidueCode.ICT, 281: ResidueCode.TLA, 282: ResidueCode.LAT, 283: ResidueCode.LBT, 284: ResidueCode.LDA, 285: ResidueCode.MN3, 286: ResidueCode.MRY, 287: ResidueCode.MOH, 288: ResidueCode.BEQ, 289: ResidueCode.C15, 290: ResidueCode.MG8, 291: ResidueCode.POL, 292: ResidueCode.NO3, 293: ResidueCode.JEF, 294: ResidueCode.P4C, 295: ResidueCode.CE1, 296: ResidueCode.DIA, 297: ResidueCode.CXE, 298: ResidueCode.IPH, 299: ResidueCode.PIN, 300: ResidueCode.R15P, 301: ResidueCode.CRY, 302: ResidueCode.PGR, 303: ResidueCode.PGQ, 304: ResidueCode.SPD, 305: ResidueCode.SPK, 306: ResidueCode.SPM, 307: ResidueCode.SUC, 308: ResidueCode.TBU, 309: ResidueCode.TMA, 310: ResidueCode.TEP, 311: ResidueCode.SCN, 312: ResidueCode.TRE, 313: ResidueCode.ETF, 314: ResidueCode.R144, 315: ResidueCode.UMQ, 316: ResidueCode.URE, 317: ResidueCode.YT3, 318: ResidueCode.ZN2, 319: ResidueCode.FE2, 320: ResidueCode.R3NI, 321: ResidueCode.SIA, 322: ResidueCode.XYP, 323: ResidueCode.A2G, 324: ResidueCode.GLA, 325: ResidueCode.NDG, 326: ResidueCode.NGA, 327: ResidueCode.A, 328: ResidueCode.C, 329: ResidueCode.G, 330: ResidueCode.I, 331: ResidueCode.U, 332: ResidueCode.N, 333: ResidueCode.F, 334: ResidueCode.K, 335: ResidueCode.DA, 336: ResidueCode.DC, 337: ResidueCode.DG, 338: ResidueCode.DI, 339: ResidueCode.DT, 340: ResidueCode.DU, 341: ResidueCode.DN, 342: ResidueCode.AG, 343: ResidueCode.AL, 344: ResidueCode.BA, 345: ResidueCode.BR, 346: ResidueCode.CA, 347: ResidueCode.CD, 348: ResidueCode.CL, 349: ResidueCode.CM, 350: ResidueCode.CN, 351: ResidueCode.CO, 352: ResidueCode.CS, 353: ResidueCode.CU, 354: ResidueCode.FE, 355: ResidueCode.HG, 356: ResidueCode.LI, 357: ResidueCode.MG, 358: ResidueCode.MN, 359: ResidueCode.NA, 360: ResidueCode.NI, 361: ResidueCode.NO, 362: ResidueCode.PB, 363: ResidueCode.RB, 364: ResidueCode.SR, 365: ResidueCode.Y1, 366: ResidueCode.ZN, 367: ResidueCode.UNKNOWN})
exception cosmolkit.ResidueCodeParseError(*args, **kwargs)

ResidueCodeParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property input: str

Original residue-code text rejected by the parser.

class cosmolkit.ResidueIdentity(name)

Residue name preserved together with its canonical table lookup, including unrecognized names.

Members (5)
code: ResidueCode

Canonical residue code associated with this table entry or identity.

info: ResidueInfo

Native table information for this residue identity.

is_tabulated: bool

Whether the identity matches a known native residue-table entry.

name: str

Stored residue name.

static new(name) → ResidueIdentity

Create a residue identity preserving the supplied name and its native table lookup.

class cosmolkit.ResidueInfo

Readonly residue-table entry containing chemical classification, sequence codes and tabulated composition information.

Members (16)
canonical_one_letter_code: str | None

Canonical parent one-letter code, or None when no canonical code is known.

code: ResidueCode

Canonical residue code associated with this table entry or identity.

fasta_code: str

Native FASTA code, using X for a nonstandard residue.

found: bool

Whether this is a recognized entry rather than the unknown-residue sentinel.

hydrogen_count: int

Hydrogen count recorded in the residue table.

is_amino_acid: bool

Whether the native residue table classifies this entry as an amino acid.

is_dna: bool

Whether this entry is classified as a DNA residue.

is_modified_amino_acid: bool

Whether the native table classifies this as a modified amino acid.

is_rna: bool

Whether this entry is classified as an RNA residue.

is_water: bool

Whether this entry is classified as water.

kind: ResidueInfoKind

Chemical category of the residue-table entry.

linking_type: int

Native linking-type code for this residue.

name: str

Stored residue name.

one_letter_code: str

One-letter code stored in the native residue table.

parent_standard_code: ResidueCode | None

Standard parent residue code for this entry, or None when unavailable.

weight: float

Residue molecular weight recorded in the native table.

class cosmolkit.ResidueInfoKind(value)

Typed ResidueInfoKind values corresponding to the Rust enum.

Members: UNKNOWN, AA, AAD, PAA, MAA, RNA, DNA, BUF, HOH, PYR, KET, ELS, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (15)
AA = ResidueInfoKind.AA
AAD = ResidueInfoKind.AAD
BUF = ResidueInfoKind.BUF
DNA = ResidueInfoKind.DNA
ELS = ResidueInfoKind.ELS
HOH = ResidueInfoKind.HOH
KET = ResidueInfoKind.KET
MAA = ResidueInfoKind.MAA
PAA = ResidueInfoKind.PAA
PYR = ResidueInfoKind.PYR
RNA = ResidueInfoKind.RNA
UNKNOWN = ResidueInfoKind.UNKNOWN
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UNKNOWN': ResidueInfoKind.UNKNOWN, 'AA': ResidueInfoKind.AA, 'AAD': ResidueInfoKind.AAD, 'PAA': ResidueInfoKind.PAA, 'MAA': ResidueInfoKind.MAA, 'RNA': ResidueInfoKind.RNA, 'DNA': ResidueInfoKind.DNA, 'BUF': ResidueInfoKind.BUF, 'HOH': ResidueInfoKind.HOH, 'PYR': ResidueInfoKind.PYR, 'KET': ResidueInfoKind.KET, 'ELS': ResidueInfoKind.ELS})
values = mappingproxy({0: ResidueInfoKind.UNKNOWN, 1: ResidueInfoKind.AA, 2: ResidueInfoKind.AAD, 3: ResidueInfoKind.PAA, 4: ResidueInfoKind.MAA, 5: ResidueInfoKind.RNA, 6: ResidueInfoKind.DNA, 7: ResidueInfoKind.BUF, 8: ResidueInfoKind.HOH, 9: ResidueInfoKind.PYR, 10: ResidueInfoKind.KET, 11: ResidueInfoKind.ELS})
class cosmolkit.ResidueKind(value)

Typed ResidueKind values corresponding to the Rust enum.

Members: AminoAcid, Dna, Rna, Saccharide, Water, Buffer, Ligand, Unknown, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (11)
AminoAcid = ResidueKind.AminoAcid
Buffer = ResidueKind.Buffer
Dna = ResidueKind.Dna
Ligand = ResidueKind.Ligand
Rna = ResidueKind.Rna
Saccharide = ResidueKind.Saccharide
Unknown = ResidueKind.Unknown
Water = ResidueKind.Water
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'AminoAcid': ResidueKind.AminoAcid, 'Dna': ResidueKind.Dna, 'Rna': ResidueKind.Rna, 'Saccharide': ResidueKind.Saccharide, 'Water': ResidueKind.Water, 'Buffer': ResidueKind.Buffer, 'Ligand': ResidueKind.Ligand, 'Unknown': ResidueKind.Unknown})
values = mappingproxy({0: ResidueKind.AminoAcid, 1: ResidueKind.Dna, 2: ResidueKind.Rna, 3: ResidueKind.Saccharide, 4: ResidueKind.Water, 5: ResidueKind.Buffer, 6: ResidueKind.Ligand, 7: ResidueKind.Unknown})
exception cosmolkit.ResidueSequenceError(*args, **kwargs)

Failure in the bio domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ResidueSequenceError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property kind: str | None

Readonly kind payload of the UnexpectedLetter error variant; None for other variants.

property letter: str | None

Readonly letter payload of the UnexpectedLetter error variant; None for other variants.

property source_code: int | None

Readonly source_code payload of the UnexpectedLetter error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: ResidueSequenceErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ResidueSequenceErrorKind(value)

Discriminants of ResidueSequenceErrorKind.

Members: UnmatchedParenthesis, UnexpectedLetter, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
UnexpectedLetter = ResidueSequenceErrorKind.UnexpectedLetter
UnmatchedParenthesis = ResidueSequenceErrorKind.UnmatchedParenthesis
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UnmatchedParenthesis': ResidueSequenceErrorKind.UnmatchedParenthesis, 'UnexpectedLetter': ResidueSequenceErrorKind.UnexpectedLetter})
values = mappingproxy({0: ResidueSequenceErrorKind.UnmatchedParenthesis, 1: ResidueSequenceErrorKind.UnexpectedLetter})
class cosmolkit.ResidueSourceIds

Source residue numbering, subchain, segment and entity identifiers.

Members (6)
label_entity_id: str | None

mmCIF label entity identifier, or None if absent.

label_seq_id: int | None

mmCIF label sequence identifier, or None if absent.

static new(seq_id=None, label_seq_id=None, segment_id=None, subchain_id=None, label_entity_id=None) → ResidueSourceIds | None

Create residue source identifiers, returning None when the native identifier validation rejects them.

segment_id: bytes | None

Raw source segment identifier bytes, or None if absent.

seq_id: PdbSeqId | None

Author residue sequence identifier, or None if absent.

subchain_id: str | None

Source subchain identifier, or None if absent.

exception cosmolkit.RingDecomposerError(*args, **kwargs)

Failure in the rings domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

RingDecomposerError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (9)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property from_: int | None

Rust from is escaped only because it is a Python keyword.

property node: int | None

Graph node involved in the decomposition failure. Present for RingDecomposerError.NodeOutOfRange, RingDecomposerError.SelfLoop; None when unavailable.

property node_count: int | None

Readonly node_count payload of the NodeOutOfRange error variant; None for other variants.

property root: int | None

Readonly root payload of the InvalidShortestPathDag error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property target: int | None

Readonly target payload of the InvalidShortestPathDag error variant; None for other variants.

property to: int | None

Destination graph node involved in the failure. Present for RingDecomposerError.DuplicateEdge, RingDecomposerError.EdgeNotFound; None when unavailable.

property variant: RingDecomposerErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.RingDecomposerErrorKind(value)

Discriminants of RingDecomposerErrorKind.

Members: NodeOutOfRange, SelfLoop, DuplicateEdge, EmptyGraph, EdgeNotFound, RelevantCycleCountOverflow, InvalidShortestPathDag, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (10)
DuplicateEdge = RingDecomposerErrorKind.DuplicateEdge
EdgeNotFound = RingDecomposerErrorKind.EdgeNotFound
EmptyGraph = RingDecomposerErrorKind.EmptyGraph
InvalidShortestPathDag = RingDecomposerErrorKind.InvalidShortestPathDag
NodeOutOfRange = RingDecomposerErrorKind.NodeOutOfRange
RelevantCycleCountOverflow = RingDecomposerErrorKind.RelevantCycleCountOverflow
SelfLoop = RingDecomposerErrorKind.SelfLoop
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NodeOutOfRange': RingDecomposerErrorKind.NodeOutOfRange, 'SelfLoop': RingDecomposerErrorKind.SelfLoop, 'DuplicateEdge': RingDecomposerErrorKind.DuplicateEdge, 'EmptyGraph': RingDecomposerErrorKind.EmptyGraph, 'EdgeNotFound': RingDecomposerErrorKind.EdgeNotFound, 'RelevantCycleCountOverflow': RingDecomposerErrorKind.RelevantCycleCountOverflow, 'InvalidShortestPathDag': RingDecomposerErrorKind.InvalidShortestPathDag})
values = mappingproxy({0: RingDecomposerErrorKind.NodeOutOfRange, 1: RingDecomposerErrorKind.SelfLoop, 2: RingDecomposerErrorKind.DuplicateEdge, 3: RingDecomposerErrorKind.EmptyGraph, 4: RingDecomposerErrorKind.EdgeNotFound, 5: RingDecomposerErrorKind.RelevantCycleCountOverflow, 6: RingDecomposerErrorKind.InvalidShortestPathDag})
exception cosmolkit.RingFindingError(*args, **kwargs)

Failure in the rings domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

RingFindingError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (17)
property adjacency: AdjacencyError | None

“error_payload”} Structured AdjacencyError payload of RingFindingError.Adjacency; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property atom: int | None

Readonly atom payload of the RingAtomOutOfRange error variant; None for other variants.

property atom_count: int | None

Readonly atom_count payload of the RingAtomOutOfRange error variant; None for other variants.

property begin: int | None

Readonly begin payload of the ExpectedBondNotFound error variant; None for other variants.

property bond: int | None

Readonly bond payload of the RingBondOutOfRange error variant; None for other variants.

property bond_count: int | None

Readonly bond_count payload of the RingBondOutOfRange error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property edge: int | None

Readonly edge payload of the RingFamilyEdgeMappingMissing error variant; None for other variants.

property end: int | None

Readonly end payload of the ExpectedBondNotFound error variant; None for other variants.

property message: str | None

Readonly message payload of the Value error variant; None for other variants.

property reason: str | None

Readonly reason payload of the UnsupportedBranch error variant; None for other variants.

property ring_decomposer: RingDecomposerError | None

“error_payload”} Structured RingDecomposerError payload of RingFindingError.RingDecomposer; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: MoleculePropertyError | StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property tag: int | None

Readonly tag payload of the SourceRingFindType error variant; None for other variants.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of RingFindingError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: RingFindingErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.RingFindingErrorKind(value)

Discriminants of RingFindingErrorKind.

Members: SourceRingFindType, MoleculeProperty, Value, ExpectedBondNotFound, RingAtomOutOfRange, RingBondOutOfRange, RingFamilyEdgeMappingMissing, RelevantCycleCountOutOfRange, UnsupportedBranch, Adjacency, InvalidTopology, RingDecomposer, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (15)
Adjacency = RingFindingErrorKind.Adjacency
ExpectedBondNotFound = RingFindingErrorKind.ExpectedBondNotFound
InvalidTopology = RingFindingErrorKind.InvalidTopology
MoleculeProperty = RingFindingErrorKind.MoleculeProperty
RelevantCycleCountOutOfRange = RingFindingErrorKind.RelevantCycleCountOutOfRange
RingAtomOutOfRange = RingFindingErrorKind.RingAtomOutOfRange
RingBondOutOfRange = RingFindingErrorKind.RingBondOutOfRange
RingDecomposer = RingFindingErrorKind.RingDecomposer
RingFamilyEdgeMappingMissing = RingFindingErrorKind.RingFamilyEdgeMappingMissing
SourceRingFindType = RingFindingErrorKind.SourceRingFindType
UnsupportedBranch = RingFindingErrorKind.UnsupportedBranch
Value = RingFindingErrorKind.Value
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SourceRingFindType': RingFindingErrorKind.SourceRingFindType, 'MoleculeProperty': RingFindingErrorKind.MoleculeProperty, 'Value': RingFindingErrorKind.Value, 'ExpectedBondNotFound': RingFindingErrorKind.ExpectedBondNotFound, 'RingAtomOutOfRange': RingFindingErrorKind.RingAtomOutOfRange, 'RingBondOutOfRange': RingFindingErrorKind.RingBondOutOfRange, 'RingFamilyEdgeMappingMissing': RingFindingErrorKind.RingFamilyEdgeMappingMissing, 'RelevantCycleCountOutOfRange': RingFindingErrorKind.RelevantCycleCountOutOfRange, 'UnsupportedBranch': RingFindingErrorKind.UnsupportedBranch, 'Adjacency': RingFindingErrorKind.Adjacency, 'InvalidTopology': RingFindingErrorKind.InvalidTopology, 'RingDecomposer': RingFindingErrorKind.RingDecomposer})
values = mappingproxy({0: RingFindingErrorKind.SourceRingFindType, 1: RingFindingErrorKind.MoleculeProperty, 2: RingFindingErrorKind.Value, 3: RingFindingErrorKind.ExpectedBondNotFound, 4: RingFindingErrorKind.RingAtomOutOfRange, 5: RingFindingErrorKind.RingBondOutOfRange, 6: RingFindingErrorKind.RingFamilyEdgeMappingMissing, 7: RingFindingErrorKind.RelevantCycleCountOutOfRange, 8: RingFindingErrorKind.UnsupportedBranch, 9: RingFindingErrorKind.Adjacency, 10: RingFindingErrorKind.InvalidTopology, 11: RingFindingErrorKind.RingDecomposer})
class cosmolkit.RingSearchParams(*, include_dative_bonds=Ellipsis, include_hydrogen_bonds=Ellipsis)

Bond-type inclusion policy for molecular ring search.

Members (2)
include_dative_bonds: bool

Include dative bonds when finding rings.

include_hydrogen_bonds: bool

Include hydrogen bonds when finding rings.

class cosmolkit.RingSearchResult

Owned symmetrized SSSR rows; indices refer to the queried molecular version.

Members (3)
atom_rings: list[list[int]]

Ordered atom-index cycles for the symmetrized SSSR, returned as independent lists.

bond_rings: list[list[int]]

Ordered bond-index cycles corresponding to atom_rings, returned as independent lists.

num_rings: int

Number of rings in this symmetrized SSSR result.

class cosmolkit.RingStereoRelation(atom, other, same_orientation)

Relative stereochemical orientation of a pair of ring atoms.

Members (3)
atom: int

First atom participating in the ring stereochemistry relationship.

other: int

Second atom participating in the ring stereochemistry relationship.

same_orientation: bool

Whether the two related ring atoms have the same orientation.

class cosmolkit.RotatableBondsOptions(value)

Typed RotatableBondsOptions values corresponding to the Rust enum.

Members: Default, NonStrict, Strict, StrictLinkages, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
Default = RotatableBondsOptions.Default
NonStrict = RotatableBondsOptions.NonStrict
Strict = RotatableBondsOptions.Strict
StrictLinkages = RotatableBondsOptions.StrictLinkages
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Default': RotatableBondsOptions.Default, 'NonStrict': RotatableBondsOptions.NonStrict, 'Strict': RotatableBondsOptions.Strict, 'StrictLinkages': RotatableBondsOptions.StrictLinkages})
values = mappingproxy({0: RotatableBondsOptions.Default, 1: RotatableBondsOptions.NonStrict, 2: RotatableBondsOptions.Strict, 3: RotatableBondsOptions.StrictLinkages})
exception cosmolkit.SanitizeError(*args, **kwargs)

Failure in the sanitize domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SanitizeError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property bits: int | None

Readonly bits payload of the InvalidOperations error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: MoleculePropertyError | BondValueError | AtomPropertyError | TopologyValidationError | QueryStateError | CleanupError | PropertyCacheError | RingFindingError | KekulizeError | RadicalError | AromaticityError | ConjugationError | HybridizationError | AtropisomerError | StereoError | AdjustHsError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stage: SanitizeStage | None

“error_payload”} Native processing stage that failed. Present for SanitizeError.InvalidTopology, SanitizeError.InvalidQueryState, SanitizeError.Cleanup, SanitizeError.Properties, SanitizeError.Rings, SanitizeError.Kekulize, SanitizeError.Radicals, SanitizeError.Aromaticity, SanitizeError.Conjugation, SanitizeError.Hybridization, SanitizeError.Atropisomers, SanitizeError.Chirality, SanitizeError.AdjustHs; None when unavailable.

Type:

{“role”

property unknown_bits: int | None

Readonly unknown_bits payload of the InvalidOperations error variant; None for other variants.

property variant: SanitizeErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SanitizeErrorKind(value)

Discriminants of SanitizeErrorKind.

Members: MoleculeProperty, BondProperty, AtomProperty, InvalidOperations, InvalidTopology, InvalidQueryState, Cleanup, Properties, Rings, Kekulize, Radicals, Aromaticity, Conjugation, Hybridization, Atropisomers, Chirality, AdjustHs, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (20)
AdjustHs = SanitizeErrorKind.AdjustHs
Aromaticity = SanitizeErrorKind.Aromaticity
AtomProperty = SanitizeErrorKind.AtomProperty
Atropisomers = SanitizeErrorKind.Atropisomers
BondProperty = SanitizeErrorKind.BondProperty
Chirality = SanitizeErrorKind.Chirality
Cleanup = SanitizeErrorKind.Cleanup
Conjugation = SanitizeErrorKind.Conjugation
Hybridization = SanitizeErrorKind.Hybridization
InvalidOperations = SanitizeErrorKind.InvalidOperations
InvalidQueryState = SanitizeErrorKind.InvalidQueryState
InvalidTopology = SanitizeErrorKind.InvalidTopology
Kekulize = SanitizeErrorKind.Kekulize
MoleculeProperty = SanitizeErrorKind.MoleculeProperty
Properties = SanitizeErrorKind.Properties
Radicals = SanitizeErrorKind.Radicals
Rings = SanitizeErrorKind.Rings
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MoleculeProperty': SanitizeErrorKind.MoleculeProperty, 'BondProperty': SanitizeErrorKind.BondProperty, 'AtomProperty': SanitizeErrorKind.AtomProperty, 'InvalidOperations': SanitizeErrorKind.InvalidOperations, 'InvalidTopology': SanitizeErrorKind.InvalidTopology, 'InvalidQueryState': SanitizeErrorKind.InvalidQueryState, 'Cleanup': SanitizeErrorKind.Cleanup, 'Properties': SanitizeErrorKind.Properties, 'Rings': SanitizeErrorKind.Rings, 'Kekulize': SanitizeErrorKind.Kekulize, 'Radicals': SanitizeErrorKind.Radicals, 'Aromaticity': SanitizeErrorKind.Aromaticity, 'Conjugation': SanitizeErrorKind.Conjugation, 'Hybridization': SanitizeErrorKind.Hybridization, 'Atropisomers': SanitizeErrorKind.Atropisomers, 'Chirality': SanitizeErrorKind.Chirality, 'AdjustHs': SanitizeErrorKind.AdjustHs})
values = mappingproxy({0: SanitizeErrorKind.MoleculeProperty, 1: SanitizeErrorKind.BondProperty, 2: SanitizeErrorKind.AtomProperty, 3: SanitizeErrorKind.InvalidOperations, 4: SanitizeErrorKind.InvalidTopology, 5: SanitizeErrorKind.InvalidQueryState, 6: SanitizeErrorKind.Cleanup, 7: SanitizeErrorKind.Properties, 8: SanitizeErrorKind.Rings, 9: SanitizeErrorKind.Kekulize, 10: SanitizeErrorKind.Radicals, 11: SanitizeErrorKind.Aromaticity, 12: SanitizeErrorKind.Conjugation, 13: SanitizeErrorKind.Hybridization, 14: SanitizeErrorKind.Atropisomers, 15: SanitizeErrorKind.Chirality, 16: SanitizeErrorKind.AdjustHs})
class cosmolkit.SanitizeOperations

Bit mask selecting sanitization stages; combine constants with the bitwise OR operator.

Members (18)
ADJUST_HS = <cosmolkit.SanitizeOperations object>
ALL = <cosmolkit.SanitizeOperations object>
CLEANUP = <cosmolkit.SanitizeOperations object>
CLEANUP_ATROPISOMERS = <cosmolkit.SanitizeOperations object>
CLEANUP_CHIRALITY = <cosmolkit.SanitizeOperations object>
CLEANUP_ORGANOMETALLICS = <cosmolkit.SanitizeOperations object>
FIND_RADICALS = <cosmolkit.SanitizeOperations object>
KEKULIZE = <cosmolkit.SanitizeOperations object>
NONE = <cosmolkit.SanitizeOperations object>
PROPERTIES = <cosmolkit.SanitizeOperations object>
SET_AROMATICITY = <cosmolkit.SanitizeOperations object>
SET_CONJUGATION = <cosmolkit.SanitizeOperations object>
SET_HYBRIDIZATION = <cosmolkit.SanitizeOperations object>
SYMM_RINGS = <cosmolkit.SanitizeOperations object>
bits: int

Integer representation of this option mask.

contains(operation) → bool

Whether every bit in the supplied mask is present.

static from_bits(bits) → SanitizeOperations

Construct a sanitization mask, rejecting bits not recognized by the native API.

is_empty: bool

Whether the mask contains no enabled options.

class cosmolkit.SanitizeParams(*, operations=Ellipsis)

Parameters for the detached sanitization pipeline.

Members (1)
operations: SanitizeOperations

Sanitization stages to execute.

class cosmolkit.SanitizeStage(value)

Typed SanitizeStage values corresponding to the Rust enum.

Members: None, Cleanup, Properties, SymmRings, Kekulize, FindRadicals, SetAromaticity, SetConjugation, SetHybridization, CleanupChirality, AdjustHs, CleanupOrganometallics, CleanupAtropisomers, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (16)
AdjustHs = SanitizeStage.AdjustHs
Cleanup = SanitizeStage.Cleanup
CleanupAtropisomers = SanitizeStage.CleanupAtropisomers
CleanupChirality = SanitizeStage.CleanupChirality
CleanupOrganometallics = SanitizeStage.CleanupOrganometallics
FindRadicals = SanitizeStage.FindRadicals
Kekulize = SanitizeStage.Kekulize
None_ = SanitizeStage.None_
Properties = SanitizeStage.Properties
SetAromaticity = SanitizeStage.SetAromaticity
SetConjugation = SanitizeStage.SetConjugation
SetHybridization = SanitizeStage.SetHybridization
SymmRings = SanitizeStage.SymmRings
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'None_': SanitizeStage.None_, 'Cleanup': SanitizeStage.Cleanup, 'Properties': SanitizeStage.Properties, 'SymmRings': SanitizeStage.SymmRings, 'Kekulize': SanitizeStage.Kekulize, 'FindRadicals': SanitizeStage.FindRadicals, 'SetAromaticity': SanitizeStage.SetAromaticity, 'SetConjugation': SanitizeStage.SetConjugation, 'SetHybridization': SanitizeStage.SetHybridization, 'CleanupChirality': SanitizeStage.CleanupChirality, 'AdjustHs': SanitizeStage.AdjustHs, 'CleanupOrganometallics': SanitizeStage.CleanupOrganometallics, 'CleanupAtropisomers': SanitizeStage.CleanupAtropisomers})
values = mappingproxy({0: SanitizeStage.None_, 1: SanitizeStage.Cleanup, 2: SanitizeStage.Properties, 4: SanitizeStage.SymmRings, 8: SanitizeStage.Kekulize, 16: SanitizeStage.FindRadicals, 32: SanitizeStage.SetAromaticity, 64: SanitizeStage.SetConjugation, 128: SanitizeStage.SetHybridization, 256: SanitizeStage.CleanupChirality, 512: SanitizeStage.AdjustHs, 1024: SanitizeStage.CleanupOrganometallics, 2048: SanitizeStage.CleanupAtropisomers})
exception cosmolkit.ScaffoldError(*args, **kwargs)

Failure in the scaffold domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ScaffoldError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (21)
property actual: int | None

Readonly actual payload of the ValenceRowCount error variant; None for other variants.

property atom: int | None

Readonly atom payload of the MissingImplicitHydrogens error variant; None for other variants.

property atom_property: AtomPropertyError | None

“error_payload”} Structured AtomPropertyError payload of ScaffoldError.AtomProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property atoms: int | None

Readonly atoms payload of the MatrixSize error variant; None for other variants.

property bond_property: BondValueError | None

“error_payload”} Structured BondValueError payload of ScaffoldError.BondProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property edit: TopologyEditError | None

“error_payload”} Structured TopologyEditError payload of ScaffoldError.Edit; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property expected: int | None

Readonly expected payload of the ValenceRowCount error variant; None for other variants.

property field: str | None

Readonly field payload of the ValenceRowCount error variant; None for other variants.

property matrix: MatrixError | None

“error_payload”} Structured MatrixError payload of ScaffoldError.Matrix; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property property_error: MoleculePropertyError | None

“error_payload”} Structured MoleculePropertyError payload of ScaffoldError.Property; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property radicals: RadicalError | None

“error_payload”} Structured RadicalError payload of ScaffoldError.Radicals; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property rings: RingFindingError | None

“error_payload”} Structured RingFindingError payload of ScaffoldError.Rings; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | StereoOrderError | AtomPropertyError | PropertyIntReadError | TemplateAttachmentOrderError | MappingValidationError | PropertyUIntReadError | CanonicalRankError | DoubleBondStereoError | MoleculePropertyError | UIntLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stereo: LegacyStereoError | None

“error_payload”} Structured LegacyStereoError payload of ScaffoldError.Stereo; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property text_property: PropertyStringError | None

“error_payload”} Structured PropertyStringError payload of ScaffoldError.TextProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of ScaffoldError.Topology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property uint_property: PropertyUIntReadError | None

“error_payload”} Structured PropertyUIntReadError payload of ScaffoldError.UIntProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of ScaffoldError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: ScaffoldErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ScaffoldErrorKind(value)

Discriminants of ScaffoldErrorKind.

Members: Topology, Edit, Valence, Rings, Radicals, Stereo, Property, AtomProperty, BondProperty, UIntProperty, TextProperty, Matrix, MissingImplicitHydrogens, ValenceRowCount, MissingRingInfo, MatrixSize, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (19)
AtomProperty = ScaffoldErrorKind.AtomProperty
BondProperty = ScaffoldErrorKind.BondProperty
Edit = ScaffoldErrorKind.Edit
Matrix = ScaffoldErrorKind.Matrix
MatrixSize = ScaffoldErrorKind.MatrixSize
MissingImplicitHydrogens = ScaffoldErrorKind.MissingImplicitHydrogens
MissingRingInfo = ScaffoldErrorKind.MissingRingInfo
Property = ScaffoldErrorKind.Property
Radicals = ScaffoldErrorKind.Radicals
Rings = ScaffoldErrorKind.Rings
Stereo = ScaffoldErrorKind.Stereo
TextProperty = ScaffoldErrorKind.TextProperty
Topology = ScaffoldErrorKind.Topology
UIntProperty = ScaffoldErrorKind.UIntProperty
Valence = ScaffoldErrorKind.Valence
ValenceRowCount = ScaffoldErrorKind.ValenceRowCount
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Topology': ScaffoldErrorKind.Topology, 'Edit': ScaffoldErrorKind.Edit, 'Valence': ScaffoldErrorKind.Valence, 'Rings': ScaffoldErrorKind.Rings, 'Radicals': ScaffoldErrorKind.Radicals, 'Stereo': ScaffoldErrorKind.Stereo, 'Property': ScaffoldErrorKind.Property, 'AtomProperty': ScaffoldErrorKind.AtomProperty, 'BondProperty': ScaffoldErrorKind.BondProperty, 'UIntProperty': ScaffoldErrorKind.UIntProperty, 'TextProperty': ScaffoldErrorKind.TextProperty, 'Matrix': ScaffoldErrorKind.Matrix, 'MissingImplicitHydrogens': ScaffoldErrorKind.MissingImplicitHydrogens, 'ValenceRowCount': ScaffoldErrorKind.ValenceRowCount, 'MissingRingInfo': ScaffoldErrorKind.MissingRingInfo, 'MatrixSize': ScaffoldErrorKind.MatrixSize})
values = mappingproxy({0: ScaffoldErrorKind.Topology, 1: ScaffoldErrorKind.Edit, 2: ScaffoldErrorKind.Valence, 3: ScaffoldErrorKind.Rings, 4: ScaffoldErrorKind.Radicals, 5: ScaffoldErrorKind.Stereo, 6: ScaffoldErrorKind.Property, 7: ScaffoldErrorKind.AtomProperty, 8: ScaffoldErrorKind.BondProperty, 9: ScaffoldErrorKind.UIntProperty, 10: ScaffoldErrorKind.TextProperty, 11: ScaffoldErrorKind.Matrix, 12: ScaffoldErrorKind.MissingImplicitHydrogens, 13: ScaffoldErrorKind.ValenceRowCount, 14: ScaffoldErrorKind.MissingRingInfo, 15: ScaffoldErrorKind.MatrixSize})
class cosmolkit.SdfBatchIterator

Forward iterator yielding MoleculeBatch values from a native SDF source.

Members (1)
next_batch() → MoleculeBatch | None

Consume the next molecule batch, or return None when the native iterator is exhausted.

class cosmolkit.SdfCoordinateMode(value)

Typed SdfCoordinateMode values corresponding to the Rust enum.

Members: Preserve, Require2D, Require3D, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
Preserve = SdfCoordinateMode.Preserve
Require2D = SdfCoordinateMode.Require2D
Require3D = SdfCoordinateMode.Require3D
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Preserve': SdfCoordinateMode.Preserve, 'Require2D': SdfCoordinateMode.Require2D, 'Require3D': SdfCoordinateMode.Require3D})
values = mappingproxy({0: SdfCoordinateMode.Preserve, 1: SdfCoordinateMode.Require2D, 2: SdfCoordinateMode.Require3D})
class cosmolkit.SdfDataset

Indexed SDF file for random record access. Integer indexing returns SdfRecord; slices and selections parse records into a MoleculeBatch.

Members (11)
batches(size, errors=None, n_jobs=None, progress_bar=False) → SdfBatchIterator

Create a batch iterator over this indexed dataset with the requested batch size and native execution settings.

is_empty: bool

Whether the indexed dataset contains zero records.

iter() → SdfDatasetIterator

Create an independent forward iterator over this indexed dataset.

len: int

Number of indexed SDF records.

metadata(index) → SdfRecordMetadata | None

Return byte-offset and source-location metadata for the indexed record, or None when out of range.

static open(path: str | os.PathLike[str], *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → SdfDataset
static open(path: str | os.PathLike[str], params: SdfReadParams | None = None) → SdfDataset

Open an SDF filesystem path using a parameter object or mutually exclusive reader keywords.

static open_with_params(path, params) → SdfDataset

Open an SDF filesystem path using explicit reader parameters.

path: pathlib.Path

Filesystem path associated with this SDF source.

record(index: SupportsIndex, *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → SdfRecord
record(index: SupportsIndex, params: SdfReadParams | None = None) → SdfRecord

Parse a zero-based record using a parameter object or mutually exclusive reader keywords; native record failures propagate.

record_text(index) → str

Read the indexed record’s source text; native IO and index errors propagate.

record_with_params(index, params) → SdfRecord

Parse a zero-based record using explicit SDF reader parameters.

class cosmolkit.SdfDatasetIterator

Forward iterator over the records of an indexed SDF dataset.

exception cosmolkit.SdfError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SdfError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property actual: str | None

Readonly actual payload of the WrongGraphKind error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: str | None

Readonly expected payload of the WrongGraphKind error variant; None for other variants.

property source: SdfReadError | MolPostError | OperationError | QueryGraphError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SdfErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SdfErrorKind(value)

Discriminants of SdfErrorKind.

Members: Read, Post, Construction, QueryGraph, QueryRecord, WrongGraphKind, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
Construction = SdfErrorKind.Construction
Post = SdfErrorKind.Post
QueryGraph = SdfErrorKind.QueryGraph
QueryRecord = SdfErrorKind.QueryRecord
Read = SdfErrorKind.Read
WrongGraphKind = SdfErrorKind.WrongGraphKind
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Read': SdfErrorKind.Read, 'Post': SdfErrorKind.Post, 'Construction': SdfErrorKind.Construction, 'QueryGraph': SdfErrorKind.QueryGraph, 'QueryRecord': SdfErrorKind.QueryRecord, 'WrongGraphKind': SdfErrorKind.WrongGraphKind})
values = mappingproxy({0: SdfErrorKind.Read, 1: SdfErrorKind.Post, 2: SdfErrorKind.Construction, 3: SdfErrorKind.QueryGraph, 4: SdfErrorKind.QueryRecord, 5: SdfErrorKind.WrongGraphKind})
class cosmolkit.SdfFormat(value)

Typed SdfFormat values corresponding to the Rust enum.

Members: V2000, V3000, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
V2000 = SdfFormat.V2000
V3000 = SdfFormat.V3000
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'V2000': SdfFormat.V2000, 'V3000': SdfFormat.V3000})
values = mappingproxy({0: SdfFormat.V2000, 1: SdfFormat.V3000})
class cosmolkit.SdfGraph

SDF graph holding either a concrete Molecule or a QueryGraph.

Members (2)
class Molecule(value)

Concrete molecular graph stored in this SDF record.

Members (1)
value: Molecule

Concrete molecular value held by this record variant.

class Query(value)

Query graph stored in this SDF record.

Members (1)
value: QueryGraph

Query graph held by this record variant.

class cosmolkit.SdfPropertyList(target, name, values)

Named, ordered per-atom or per-bond property values, with explicit missing entries.

Members (3)
name: str

Stored property-list name or molecular name; an absent molecular name is None.

target: SdfPropertyListTarget

Whether the list assigns values to atoms or bonds.

values: list[PropertyValue | None]

Independent property-value list in target-index order, preserving missing entries as None.

class cosmolkit.SdfPropertyListTarget(value)

Typed SdfPropertyListTarget values corresponding to the Rust enum.

Members: Atom, Bond, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Atom = SdfPropertyListTarget.Atom
Bond = SdfPropertyListTarget.Bond
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Atom': SdfPropertyListTarget.Atom, 'Bond': SdfPropertyListTarget.Bond})
values = mappingproxy({0: SdfPropertyListTarget.Atom, 1: SdfPropertyListTarget.Bond})
class cosmolkit.SdfReader

SDF source path and parsing configuration used to create native batch iterators.

Members (5)
batches(size, errors=None, n_jobs=None) → SdfReaderBatchIterator

Open this source as an iterator yielding molecule batches of at most size records.

static open(path: str | os.PathLike[str], *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → SdfReader
static open(path: str | os.PathLike[str], params: SdfReadParams | None = None) → SdfReader

Open an SDF filesystem path using a parameter object or mutually exclusive reader keywords.

static open_with_params(path, params) → SdfReader

Open an SDF filesystem path using explicit reader parameters.

params: SdfReadParams

Independent value copy of this reader’s SDF parsing configuration.

path: pathlib.Path

Filesystem path associated with this SDF source.

class cosmolkit.SdfReaderBatchIterator

Forward iterator yielding molecule batches from an SDF reader.

Members (1)
next_batch() → MoleculeBatch | None

Consume the next molecule batch, or return None when the native iterator is exhausted.

exception cosmolkit.SdfReadError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SdfReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (18)
property actual: int | None

Readonly actual payload of the PropertyListCount error variant; None for other variants.

property byte_offset: int | None

Readonly byte_offset payload of the Record error variant; None for other variants.

property capability: str | None

Capability required by this input. Present for SdfReadError.MissingCapability; None when unavailable.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the PropertyListCount error variant; None for other variants.

property format: str | None

Format associated with the failure. Present for SdfReadError.Unsupported; None when unavailable.

property index: int | None

Index associated with the failure. Present for SdfReadError.RecordIndexOutOfRange, SdfReadError.Record; None when unavailable.

property kind: str | None

Readonly kind payload of the Field error variant; None for other variants.

property line: int | None

Readonly line payload of the Field error variant; None for other variants.

property line_offset: int | None

Readonly line_offset payload of the Record error variant; None for other variants.

property message: str | None

Native diagnostic message. Present for SdfReadError.Parse; None when unavailable.

property name: str | None

Readonly name payload of the PropertyListCount error variant; None for other variants.

property record_count: int | None

Readonly record_count payload of the RecordIndexOutOfRange error variant; None for other variants.

property source: StereoGroupError | MolPostError | TopologyValidationError | CoordinateValidationError | QueryGraphError | AtomPropertyError | BondValueError | MoleculePropertyError | SdfReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property target: str | None

Readonly target payload of the PropertyListCount error variant; None for other variants.

property value: str | None

Readonly value payload of the Field error variant; None for other variants.

property variant: SdfReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SdfReadErrorKind(value)

Discriminants of SdfReadErrorKind.

Members: StereoGroup, MissingCapability, MolPost, QueryRecord, Empty, Counts, Field, Unsupported, Parse, Topology, Coordinates, QueryGraph, AtomProperty, BondValue, MoleculeProperty, PropertyListCount, RecordIndexOutOfRange, Record, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (21)
AtomProperty = SdfReadErrorKind.AtomProperty
BondValue = SdfReadErrorKind.BondValue
Coordinates = SdfReadErrorKind.Coordinates
Counts = SdfReadErrorKind.Counts
Empty = SdfReadErrorKind.Empty
Field = SdfReadErrorKind.Field
MissingCapability = SdfReadErrorKind.MissingCapability
MolPost = SdfReadErrorKind.MolPost
MoleculeProperty = SdfReadErrorKind.MoleculeProperty
Parse = SdfReadErrorKind.Parse
PropertyListCount = SdfReadErrorKind.PropertyListCount
QueryGraph = SdfReadErrorKind.QueryGraph
QueryRecord = SdfReadErrorKind.QueryRecord
Record = SdfReadErrorKind.Record
RecordIndexOutOfRange = SdfReadErrorKind.RecordIndexOutOfRange
StereoGroup = SdfReadErrorKind.StereoGroup
Topology = SdfReadErrorKind.Topology
Unsupported = SdfReadErrorKind.Unsupported
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': SdfReadErrorKind.StereoGroup, 'MissingCapability': SdfReadErrorKind.MissingCapability, 'MolPost': SdfReadErrorKind.MolPost, 'QueryRecord': SdfReadErrorKind.QueryRecord, 'Empty': SdfReadErrorKind.Empty, 'Counts': SdfReadErrorKind.Counts, 'Field': SdfReadErrorKind.Field, 'Unsupported': SdfReadErrorKind.Unsupported, 'Parse': SdfReadErrorKind.Parse, 'Topology': SdfReadErrorKind.Topology, 'Coordinates': SdfReadErrorKind.Coordinates, 'QueryGraph': SdfReadErrorKind.QueryGraph, 'AtomProperty': SdfReadErrorKind.AtomProperty, 'BondValue': SdfReadErrorKind.BondValue, 'MoleculeProperty': SdfReadErrorKind.MoleculeProperty, 'PropertyListCount': SdfReadErrorKind.PropertyListCount, 'RecordIndexOutOfRange': SdfReadErrorKind.RecordIndexOutOfRange, 'Record': SdfReadErrorKind.Record})
values = mappingproxy({0: SdfReadErrorKind.StereoGroup, 1: SdfReadErrorKind.MissingCapability, 2: SdfReadErrorKind.MolPost, 3: SdfReadErrorKind.QueryRecord, 4: SdfReadErrorKind.Empty, 5: SdfReadErrorKind.Counts, 6: SdfReadErrorKind.Field, 7: SdfReadErrorKind.Unsupported, 8: SdfReadErrorKind.Parse, 9: SdfReadErrorKind.Topology, 10: SdfReadErrorKind.Coordinates, 11: SdfReadErrorKind.QueryGraph, 12: SdfReadErrorKind.AtomProperty, 13: SdfReadErrorKind.BondValue, 14: SdfReadErrorKind.MoleculeProperty, 15: SdfReadErrorKind.PropertyListCount, 16: SdfReadErrorKind.RecordIndexOutOfRange, 17: SdfReadErrorKind.Record})
class cosmolkit.SdfReadParams(*, sanitize=Ellipsis, remove_hs=Ellipsis, strict_parsing=Ellipsis, expand_attachment_points=Ellipsis, process_property_lists=Ellipsis, coordinate_mode=Ellipsis)

Public policy for reading one SDF record into its final Rust graph value.

Members (6)
coordinate_mode: SdfCoordinateMode

Preserve source coordinate dimensionality or require a specific dimension.

expand_attachment_points: bool

Expand encoded attachment points into explicit graph entries.

process_property_lists: bool

Interpret supported SDF atom/bond property lists.

remove_hs: bool

Remove removable explicit hydrogens during native post-processing.

sanitize: bool

Sanitize concrete molecules after parsing.

strict_parsing: bool

Use strict MolBlock parsing rather than the native permissive path.

class cosmolkit.SdfRecord

SDF record retaining a molecular or query graph, source metadata and ordered data fields.

Members (17)
data_field(name) → str | None

Look up a named SDF data field; return None when it is absent.

data_fields: list[tuple[str, str]]

Ordered SDF name/value pairs, retaining repeated field names.

static from_query_graph(query, properties) → SdfRecord

Create an SDF query record from the supplied query graph and molecular properties.

static from_sdf(input: str, *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → SdfRecord
static from_sdf(input: str, params: SdfReadParams | None = None) → SdfRecord

Parse one SDF record, preserving its molecular or query graph and data fields.

static from_sdf_with_params(input, params) → SdfRecord

Parse one SDF record with explicit parsing parameters; propagate native parsing errors.

graph: SdfGraph

Tagged molecular or query graph stored by this record.

index: int

Zero-based record index in its source.

molecule: Molecule

Molecular value stored by this record; raises SdfError if the record contains a query graph.

properties: MoleculeProperties

Independent copy of the molecular properties stored with this record.

query_graph: QueryGraph

Query graph stored by this record; raises SdfError if the record contains a molecular graph.

source_coordinate_dim: CoordinateDimension | None

Coordinate dimensionality recorded in the input, or None when unspecified.

substance_groups: list[SubstanceGroup]

Substance-group values stored in this record.

title: str | None

Record title, or None when the source supplies no title.

to_mol(*, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → str
to_mol(params: MolBlockWriteParams | None = None) → str

Write this record as a MolBlock, without SDF data fields. Supply a parameter object or keyword options, not both.

to_mol_with_params(params) → str

Write the record’s graph as a MolBlock using the supplied writer configuration.

to_sdf(*, format: SdfFormat | str | None = None, force_2d: bool | None = None, include_stereo: bool | None = None, kekulize: bool | None = None, precision: SupportsIndex | None = None, coordinate_selection: MolCoordinateSelection | str | None = None, include_coordinates: bool | None = None) → str
to_sdf(params: MolBlockWriteParams | None = None) → str

Write this record as SDF, including its data fields. Supply a parameter object or keyword options, not both.

to_sdf_with_params(params) → str

Write the complete SDF record using the supplied writer configuration.

class cosmolkit.SdfRecordMetadata(index, byte_offset, byte_len, line_offset, line_len, title)

Record index, source byte/line ranges and optional title for indexed SDF access.

Members (6)
byte_len: int

Length of the record in bytes.

byte_offset: int

Byte offset of the record in its source.

byte_range: tuple[int, int]

Half-open byte range (start, end) for this record.

index: int

Zero-based SDF record index.

line_range: tuple[int, int]

Half-open source-line range (start, end) for this record.

title: str | None

Record title, or None if absent.

class cosmolkit.SdfRecordStream

Single-pass SDF record reader. Calling batches transfers its cursor; subsequent use of this stream raises RuntimeError.

Members (9)
batches(size, errors=None, n_jobs=None) → SdfReaderBatchIterator

Transfer the current stream to a batch iterator. Invalid batch arguments leave the stream usable at its current position; success transfers ownership.

bytes_consumed: int

Number of source bytes consumed by the native stream; unavailable after transfer to batches.

is_end: bool

Whether the native stream has reached end of input; unavailable after ownership transfers to batches.

lines_consumed: int

Number of source lines consumed by the native stream; unavailable after transfer to batches.

next_record() → SdfRecord | None

Consume the next SDF record, or return None at end of input; parse errors propagate.

static open(path: str | os.PathLike[str], *, sanitize: bool | None = None, remove_hs: bool | None = None, strict_parsing: bool | None = None, expand_attachment_points: bool | None = None, process_property_lists: bool | None = None, coordinate_mode: SdfCoordinateMode | str | None = None) → SdfRecordStream
static open(path: str | os.PathLike[str], params: SdfReadParams | None = None) → SdfRecordStream

Open an SDF filesystem path using a parameter object or mutually exclusive reader keywords.

static open_with_params(path, params) → SdfRecordStream

Open an SDF filesystem path using explicit reader parameters.

records_consumed: int

Number of records consumed by the native stream; unavailable after transfer to batches.

static validate_batch_params(size, n_jobs) → None

Validate batch arguments without consuming or advancing a stream.

exception cosmolkit.SdfWriteError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SdfWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (14)
property atom: int | None

Atom identifier implicated in the failure. Applies to SdfWriteError.UnsignedPropertyOverflow. None when this payload is absent.

property atom_state: str | None

Atom state that prevented SDF writing; None for other variants.

property bond: int | None

Bond identifier implicated in the failure. Applies to SdfWriteError.UnsignedPropertyOverflow, SdfWriteError.SGroupBondMembership. None when this payload is absent.

property bond_order: BondOrder | None

“error_payload”} Bond order implicated in the failed chemistry check. Applies to SdfWriteError.BondOrder. None when this payload is absent.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property group: int | None

Group identifier involved in the failure. Applies to SdfWriteError.SGroupBondMembership. None when this payload is absent.

property integer_property: PropertyIntReadError | None

“error_payload”} Structured PropertyIntReadError payload of SdfWriteError.IntegerProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property property: str | None

Readonly property payload of the UnsignedPropertyOverflow error variant; None for other variants.

property property_value: PropertyValueError | None

“error_payload”} Structured PropertyValueError payload of SdfWriteError.PropertyValue; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: PropertyStringError | PropertyUIntReadError | TopologyValidationError | CoordinateValidationError | UIntLexicalReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property substance_group: str | None

Substance-group diagnostic that prevented SDF writing; None for other variants.

property value: int | None

Readonly value payload of the UnsignedPropertyOverflow error variant; None for other variants.

property variant: SdfWriteErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SdfWriteErrorKind(value)

Discriminants of SdfWriteErrorKind.

Members: Property, UnsignedProperty, UnsignedPropertyOverflow, CountLimit, Topology, Coordinates, IntegerProperty, PropertyValue, BondOrder, Atom, SGroupBondMembership, SubstanceGroup, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (15)
Atom = SdfWriteErrorKind.Atom
BondOrder = SdfWriteErrorKind.BondOrder
Coordinates = SdfWriteErrorKind.Coordinates
CountLimit = SdfWriteErrorKind.CountLimit
IntegerProperty = SdfWriteErrorKind.IntegerProperty
Property = SdfWriteErrorKind.Property
PropertyValue = SdfWriteErrorKind.PropertyValue
SGroupBondMembership = SdfWriteErrorKind.SGroupBondMembership
SubstanceGroup = SdfWriteErrorKind.SubstanceGroup
Topology = SdfWriteErrorKind.Topology
UnsignedProperty = SdfWriteErrorKind.UnsignedProperty
UnsignedPropertyOverflow = SdfWriteErrorKind.UnsignedPropertyOverflow
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Property': SdfWriteErrorKind.Property, 'UnsignedProperty': SdfWriteErrorKind.UnsignedProperty, 'UnsignedPropertyOverflow': SdfWriteErrorKind.UnsignedPropertyOverflow, 'CountLimit': SdfWriteErrorKind.CountLimit, 'Topology': SdfWriteErrorKind.Topology, 'Coordinates': SdfWriteErrorKind.Coordinates, 'IntegerProperty': SdfWriteErrorKind.IntegerProperty, 'PropertyValue': SdfWriteErrorKind.PropertyValue, 'BondOrder': SdfWriteErrorKind.BondOrder, 'Atom': SdfWriteErrorKind.Atom, 'SGroupBondMembership': SdfWriteErrorKind.SGroupBondMembership, 'SubstanceGroup': SdfWriteErrorKind.SubstanceGroup})
values = mappingproxy({0: SdfWriteErrorKind.Property, 1: SdfWriteErrorKind.UnsignedProperty, 2: SdfWriteErrorKind.UnsignedPropertyOverflow, 3: SdfWriteErrorKind.CountLimit, 4: SdfWriteErrorKind.Topology, 5: SdfWriteErrorKind.Coordinates, 6: SdfWriteErrorKind.IntegerProperty, 7: SdfWriteErrorKind.PropertyValue, 8: SdfWriteErrorKind.BondOrder, 9: SdfWriteErrorKind.Atom, 10: SdfWriteErrorKind.SGroupBondMembership, 11: SdfWriteErrorKind.SubstanceGroup})
exception cosmolkit.SearchMcsError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SearchMcsError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property added: int | None

Readonly added payload of the SeedRemainingAtomUnderflow error variant; None for other variants.

property atom: int | None

Atom identifier implicated in the failure. Applies to SearchMcsError.AtomOutOfRange, SearchMcsError.CoordinateOutOfRange, SearchMcsError.ValenceOutOfRange, SearchMcsError.SeedAtomMappingMissing, SearchMcsError.TargetAtomMappingMissing, SearchMcsError.SeedAtomNotBondEndpoint, SearchMcsError.SeedNewAtomMissing. None when this payload is absent.

property bond: int | None

Bond identifier implicated in the failure. Applies to SearchMcsError.BondOutOfRange, SearchMcsError.SeedExcludedBondOutOfRange, SearchMcsError.SeedBondAlreadyExcluded, SearchMcsError.SeedAtomNotBondEndpoint. None when this payload is absent.

property count: int | None

Count reported by the native failure. Applies to SearchMcsError.TooFewInputs, SearchMcsError.SeedExcludedBondOutOfRange. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property frontier: int | None

Readonly frontier payload of the SeedRemainingBondUnderflow error variant; None for other variants.

property remaining: int | None

Remaining input or entries reported by the native failure. Applies to SearchMcsError.SeedRemainingBondUnderflow, SearchMcsError.SeedRemainingAtomUnderflow. None when this payload is absent.

property side: str | None

Probe/reference or source/target side identified by the native check. Applies to SearchMcsError.AtomOutOfRange, SearchMcsError.MissingConformer, SearchMcsError.CoordinateOutOfRange, SearchMcsError.MissingRingInfo, SearchMcsError.MissingValence, SearchMcsError.ValenceOutOfRange, SearchMcsError.BondOutOfRange. None when this payload is absent.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SearchMcsErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SearchMcsErrorKind(value)

Discriminants of SearchMcsErrorKind.

Members: TooFewInputs, ThresholdAboveOne, AtomOutOfRange, MissingConformer, CoordinateOutOfRange, MissingRingInfo, MissingValence, ValenceOutOfRange, BondOutOfRange, SeedExcludedBondOutOfRange, SeedBondAlreadyExcluded, SeedAtomMappingMissing, TargetAtomMappingMissing, SeedAtomNotBondEndpoint, SeedNewAtomMissing, SeedRemainingBondUnderflow, SeedRemainingAtomUnderflow, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (20)
AtomOutOfRange = SearchMcsErrorKind.AtomOutOfRange
BondOutOfRange = SearchMcsErrorKind.BondOutOfRange
CoordinateOutOfRange = SearchMcsErrorKind.CoordinateOutOfRange
MissingConformer = SearchMcsErrorKind.MissingConformer
MissingRingInfo = SearchMcsErrorKind.MissingRingInfo
MissingValence = SearchMcsErrorKind.MissingValence
SeedAtomMappingMissing = SearchMcsErrorKind.SeedAtomMappingMissing
SeedAtomNotBondEndpoint = SearchMcsErrorKind.SeedAtomNotBondEndpoint
SeedBondAlreadyExcluded = SearchMcsErrorKind.SeedBondAlreadyExcluded
SeedExcludedBondOutOfRange = SearchMcsErrorKind.SeedExcludedBondOutOfRange
SeedNewAtomMissing = SearchMcsErrorKind.SeedNewAtomMissing
SeedRemainingAtomUnderflow = SearchMcsErrorKind.SeedRemainingAtomUnderflow
SeedRemainingBondUnderflow = SearchMcsErrorKind.SeedRemainingBondUnderflow
TargetAtomMappingMissing = SearchMcsErrorKind.TargetAtomMappingMissing
ThresholdAboveOne = SearchMcsErrorKind.ThresholdAboveOne
TooFewInputs = SearchMcsErrorKind.TooFewInputs
ValenceOutOfRange = SearchMcsErrorKind.ValenceOutOfRange
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TooFewInputs': SearchMcsErrorKind.TooFewInputs, 'ThresholdAboveOne': SearchMcsErrorKind.ThresholdAboveOne, 'AtomOutOfRange': SearchMcsErrorKind.AtomOutOfRange, 'MissingConformer': SearchMcsErrorKind.MissingConformer, 'CoordinateOutOfRange': SearchMcsErrorKind.CoordinateOutOfRange, 'MissingRingInfo': SearchMcsErrorKind.MissingRingInfo, 'MissingValence': SearchMcsErrorKind.MissingValence, 'ValenceOutOfRange': SearchMcsErrorKind.ValenceOutOfRange, 'BondOutOfRange': SearchMcsErrorKind.BondOutOfRange, 'SeedExcludedBondOutOfRange': SearchMcsErrorKind.SeedExcludedBondOutOfRange, 'SeedBondAlreadyExcluded': SearchMcsErrorKind.SeedBondAlreadyExcluded, 'SeedAtomMappingMissing': SearchMcsErrorKind.SeedAtomMappingMissing, 'TargetAtomMappingMissing': SearchMcsErrorKind.TargetAtomMappingMissing, 'SeedAtomNotBondEndpoint': SearchMcsErrorKind.SeedAtomNotBondEndpoint, 'SeedNewAtomMissing': SearchMcsErrorKind.SeedNewAtomMissing, 'SeedRemainingBondUnderflow': SearchMcsErrorKind.SeedRemainingBondUnderflow, 'SeedRemainingAtomUnderflow': SearchMcsErrorKind.SeedRemainingAtomUnderflow})
values = mappingproxy({0: SearchMcsErrorKind.TooFewInputs, 1: SearchMcsErrorKind.ThresholdAboveOne, 2: SearchMcsErrorKind.AtomOutOfRange, 3: SearchMcsErrorKind.MissingConformer, 4: SearchMcsErrorKind.CoordinateOutOfRange, 5: SearchMcsErrorKind.MissingRingInfo, 6: SearchMcsErrorKind.MissingValence, 7: SearchMcsErrorKind.ValenceOutOfRange, 8: SearchMcsErrorKind.BondOutOfRange, 9: SearchMcsErrorKind.SeedExcludedBondOutOfRange, 10: SearchMcsErrorKind.SeedBondAlreadyExcluded, 11: SearchMcsErrorKind.SeedAtomMappingMissing, 12: SearchMcsErrorKind.TargetAtomMappingMissing, 13: SearchMcsErrorKind.SeedAtomNotBondEndpoint, 14: SearchMcsErrorKind.SeedNewAtomMissing, 15: SearchMcsErrorKind.SeedRemainingBondUnderflow, 16: SearchMcsErrorKind.SeedRemainingAtomUnderflow})
exception cosmolkit.SelectedBondCopyError(*args, **kwargs)

Failure in the fragments domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SelectedBondCopyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property atom: int | None

Readonly atom payload of the MissingEndpointMapping error variant; None for other variants.

property bond: int | None

Readonly bond payload of the MissingEndpointMapping error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: BondValueError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SelectedBondCopyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SelectedBondCopyErrorKind(value)

Discriminants of SelectedBondCopyErrorKind.

Members: Stereo, MissingEndpointMapping, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
MissingEndpointMapping = SelectedBondCopyErrorKind.MissingEndpointMapping
Stereo = SelectedBondCopyErrorKind.Stereo
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Stereo': SelectedBondCopyErrorKind.Stereo, 'MissingEndpointMapping': SelectedBondCopyErrorKind.MissingEndpointMapping})
values = mappingproxy({0: SelectedBondCopyErrorKind.Stereo, 1: SelectedBondCopyErrorKind.MissingEndpointMapping})
exception cosmolkit.SelectedSubstanceGroupCopyError(*args, **kwargs)

Failure in the fragments domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SelectedSubstanceGroupCopyError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (13)
property atom: int | None

Readonly atom payload of the MissingAtomMapping error variant; None for other variants.

property atom_count: int | None

Readonly atom_count payload of the AtomOutOfRange error variant; None for other variants.

property bond: int | None

Readonly bond payload of the MissingBondMapping error variant; None for other variants.

property bond_count: int | None

Readonly bond_count payload of the BondOutOfRange error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property group: int

Group identifier involved in the failure. Applies to SelectedSubstanceGroupCopyError.MissingAtomMapping, SelectedSubstanceGroupCopyError.AtomOutOfRange, SelectedSubstanceGroupCopyError.MissingBondMapping, SelectedSubstanceGroupCopyError.BondOutOfRange.

property list: SubstanceGroupAtomList | None

“error_payload”} Name of the affected substance-group list. Present for SelectedSubstanceGroupCopyError.MissingAtomMapping, SelectedSubstanceGroupCopyError.AtomOutOfRange; None when unavailable.

Type:

{“role”

property mapped_atom: int | None

Readonly mapped_atom payload of the AtomOutOfRange error variant; None for other variants.

property mapped_bond: int | None

Readonly mapped_bond payload of the BondOutOfRange error variant; None for other variants.

property source_atom: int | None

Readonly source_atom payload of the AtomOutOfRange error variant; None for other variants.

property source_bond: int | None

Readonly source_bond payload of the BondOutOfRange error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SelectedSubstanceGroupCopyErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SelectedSubstanceGroupCopyErrorKind(value)

Discriminants of SelectedSubstanceGroupCopyErrorKind.

Members: MissingAtomMapping, AtomOutOfRange, MissingBondMapping, BondOutOfRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
AtomOutOfRange = SelectedSubstanceGroupCopyErrorKind.AtomOutOfRange
BondOutOfRange = SelectedSubstanceGroupCopyErrorKind.BondOutOfRange
MissingAtomMapping = SelectedSubstanceGroupCopyErrorKind.MissingAtomMapping
MissingBondMapping = SelectedSubstanceGroupCopyErrorKind.MissingBondMapping
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingAtomMapping': SelectedSubstanceGroupCopyErrorKind.MissingAtomMapping, 'AtomOutOfRange': SelectedSubstanceGroupCopyErrorKind.AtomOutOfRange, 'MissingBondMapping': SelectedSubstanceGroupCopyErrorKind.MissingBondMapping, 'BondOutOfRange': SelectedSubstanceGroupCopyErrorKind.BondOutOfRange})
values = mappingproxy({0: SelectedSubstanceGroupCopyErrorKind.MissingAtomMapping, 1: SelectedSubstanceGroupCopyErrorKind.AtomOutOfRange, 2: SelectedSubstanceGroupCopyErrorKind.MissingBondMapping, 3: SelectedSubstanceGroupCopyErrorKind.BondOutOfRange})
class cosmolkit.SerdeJsonCategory(value)

Discriminants of SerdeJsonCategory.

Members: Io, Syntax, Data, Eof, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
Data = SerdeJsonCategory.Data
Eof = SerdeJsonCategory.Eof
Io = SerdeJsonCategory.Io
Syntax = SerdeJsonCategory.Syntax
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Io': SerdeJsonCategory.Io, 'Syntax': SerdeJsonCategory.Syntax, 'Data': SerdeJsonCategory.Data, 'Eof': SerdeJsonCategory.Eof})
values = mappingproxy({0: SerdeJsonCategory.Io, 1: SerdeJsonCategory.Syntax, 2: SerdeJsonCategory.Data, 3: SerdeJsonCategory.Eof})
exception cosmolkit.SerdeJsonError(*args, **kwargs)

SerdeJsonError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property classify: SerdeJsonCategory

“error_payload”} Classify the failure as IO, syntax, data, or end-of-input.

Type:

{“role”

property column: int

Column reported by the native JSON parser.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property io_error_kind: IoErrorKind | None

“error_payload”} Underlying IO error category, or None for a non-IO failure.

Type:

{“role”

property is_data: bool

Whether JSON data was incompatible with the requested type.

property is_eof: bool

Whether input ended before parsing could complete.

property is_io: bool

Whether input reading failed.

property is_syntax: bool

Whether this is a JSON syntax error.

property line: int

Line reported by the native JSON parser.

property source: IoError | Utf8Error | FromUtf8Error | ExternalError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.SerialConformerOptimizationError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SerialConformerOptimizationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property conformer_id: int | None

Readonly conformer_id payload of the Optimization error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property input_index: int | None

Index of the failing input. Applies to SerialConformerOptimizationError.CoordinateCount, SerialConformerOptimizationError.Optimization. None when this payload is absent.

property source: SerialResultCapacityError | SerialCoordinateCountError | OptimizationStageError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SerialConformerOptimizationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SerialConformerOptimizationErrorKind(value)

Discriminants of SerialConformerOptimizationErrorKind.

Members: ResultCapacity, CoordinateCount, Optimization, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
CoordinateCount = SerialConformerOptimizationErrorKind.CoordinateCount
Optimization = SerialConformerOptimizationErrorKind.Optimization
ResultCapacity = SerialConformerOptimizationErrorKind.ResultCapacity
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ResultCapacity': SerialConformerOptimizationErrorKind.ResultCapacity, 'CoordinateCount': SerialConformerOptimizationErrorKind.CoordinateCount, 'Optimization': SerialConformerOptimizationErrorKind.Optimization})
values = mappingproxy({0: SerialConformerOptimizationErrorKind.ResultCapacity, 1: SerialConformerOptimizationErrorKind.CoordinateCount, 2: SerialConformerOptimizationErrorKind.Optimization})
exception cosmolkit.SerialCoordinateCountError(*args, **kwargs)

SerialCoordinateCountError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property atoms: int

Expected number of atom coordinates.

property conformer_id: int

Identifier of the conformer with an invalid coordinate count.

property coordinates: int

Number of coordinates actually present.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

exception cosmolkit.SerialResultCapacityError(*args, **kwargs)

SerialResultCapacityError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property conformers: int

Number of conformers requiring result slots.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property result_slots: int

Number of available result slots.

exception cosmolkit.SerialUffOptimizationError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SerialUffOptimizationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: AutomaticForceFieldConstructionError | SerialConformerOptimizationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SerialUffOptimizationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SerialUffOptimizationErrorKind(value)

Discriminants of SerialUffOptimizationErrorKind.

Members: Construction, Optimization, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Construction = SerialUffOptimizationErrorKind.Construction
Optimization = SerialUffOptimizationErrorKind.Optimization
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Construction': SerialUffOptimizationErrorKind.Construction, 'Optimization': SerialUffOptimizationErrorKind.Optimization})
values = mappingproxy({0: SerialUffOptimizationErrorKind.Construction, 1: SerialUffOptimizationErrorKind.Optimization})
class cosmolkit.SGroupBracket(points)

Three three-dimensional points defining an S-group display bracket.

Members (2)
static new(points) → SGroupBracket

Create a display bracket from three three-dimensional points.

points: list[list[float]]

Three three-component points defining the bracket geometry.

class cosmolkit.SGroupCState(bond, vector)

Crossing-bond identifier and associated three-component C-state vector.

Members (3)
bond: int

Zero-based bond identifier associated with the C-state vector.

static new(bond, vector) → SGroupCState

Create a crossing-bond C-state using a zero-based bond index and three-component vector.

vector: list[float]

Three-component crossing-bond C-state vector.

class cosmolkit.SGroupDisplay(*, brackets=None, field_position=None, display_tag=None)

Detached substance-group bracket and label-placement metadata.

Members (3)
brackets: list[SGroupBracket]

Independent list of substance-group display brackets.

display_tag: str | None

Source display tag, or None if unspecified.

field_position: list[float] | None

Two-dimensional label position, or None if unspecified.

exception cosmolkit.SingleConformerOptimizationError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SingleConformerOptimizationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: AutomaticForceFieldConstructionError | OptimizationStageError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SingleConformerOptimizationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SingleConformerOptimizationErrorKind(value)

Discriminants of SingleConformerOptimizationErrorKind.

Members: Construction, Optimization, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Construction = SingleConformerOptimizationErrorKind.Construction
Optimization = SingleConformerOptimizationErrorKind.Optimization
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Construction': SingleConformerOptimizationErrorKind.Construction, 'Optimization': SingleConformerOptimizationErrorKind.Optimization})
values = mappingproxy({0: SingleConformerOptimizationErrorKind.Construction, 1: SingleConformerOptimizationErrorKind.Optimization})
exception cosmolkit.SmartsParseError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SmartsParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property atom: int | None

Readonly atom payload of the SelfRingClosure error variant; None for other variants.

property begin_atom: int | None

Readonly begin_atom payload of the DuplicateRingBond error variant; None for other variants.

property carrier: int | None

Readonly carrier payload of the TemplateAttachmentRemap error variant; None for other variants.

property character: int | None

Readonly character payload of the UnexpectedCharacter error variant; None for other variants.

property context: str | None

Readonly context payload of the UnexpectedCharacter error variant; None for other variants.

property detail: str | None

Readonly detail payload of the InvalidAtomPrimitive error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end_atom: int | None

Readonly end_atom payload of the DuplicateRingBond error variant; None for other variants.

property feature: str | None

Unsupported feature identified by the native implementation. Present for SmartsParseError.UnsupportedFeature; None when unavailable.

property message: str | None

Native diagnostic message. Present for SmartsParseError.UnexpectedEnd, SmartsParseError.CxSmiles, SmartsParseError.Parse; None when unavailable.

property position: int | None

Position of the offending entry. Present for SmartsParseError.UnclosedBracket, SmartsParseError.UnclosedParenthesis, SmartsParseError.UnexpectedCharacter, SmartsParseError.InvalidAtomPrimitive; None when unavailable.

property ring: int | None

Ring-closure label involved in the failure, or None for another failure.

property source: StereoGroupError | CxQueryLoweringError | QueryGraphError | ParserCarrierError | AtomPropertyError | BondValueError | MoleculePropertyError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SmartsParseErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SmartsParseErrorKind(value)

Discriminants of SmartsParseErrorKind.

Members: StereoGroup, MissingRecursiveQueryGraph, CxLowering, QueryGraph, ParserCarrier, AtomProperty, BondProperty, MoleculeProperty, UnclosedBracket, UnexpectedCharacter, UnexpectedEnd, InvalidAtomPrimitive, UnclosedParenthesis, UnbalancedRingClosure, SelfRingClosure, DuplicateRingBond, CxSmiles, Parse, UnsupportedFeature, TemplateAttachmentRemap, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (23)
AtomProperty = SmartsParseErrorKind.AtomProperty
BondProperty = SmartsParseErrorKind.BondProperty
CxLowering = SmartsParseErrorKind.CxLowering
CxSmiles = SmartsParseErrorKind.CxSmiles
DuplicateRingBond = SmartsParseErrorKind.DuplicateRingBond
InvalidAtomPrimitive = SmartsParseErrorKind.InvalidAtomPrimitive
MissingRecursiveQueryGraph = SmartsParseErrorKind.MissingRecursiveQueryGraph
MoleculeProperty = SmartsParseErrorKind.MoleculeProperty
Parse = SmartsParseErrorKind.Parse
ParserCarrier = SmartsParseErrorKind.ParserCarrier
QueryGraph = SmartsParseErrorKind.QueryGraph
SelfRingClosure = SmartsParseErrorKind.SelfRingClosure
StereoGroup = SmartsParseErrorKind.StereoGroup
TemplateAttachmentRemap = SmartsParseErrorKind.TemplateAttachmentRemap
UnbalancedRingClosure = SmartsParseErrorKind.UnbalancedRingClosure
UnclosedBracket = SmartsParseErrorKind.UnclosedBracket
UnclosedParenthesis = SmartsParseErrorKind.UnclosedParenthesis
UnexpectedCharacter = SmartsParseErrorKind.UnexpectedCharacter
UnexpectedEnd = SmartsParseErrorKind.UnexpectedEnd
UnsupportedFeature = SmartsParseErrorKind.UnsupportedFeature
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': SmartsParseErrorKind.StereoGroup, 'MissingRecursiveQueryGraph': SmartsParseErrorKind.MissingRecursiveQueryGraph, 'CxLowering': SmartsParseErrorKind.CxLowering, 'QueryGraph': SmartsParseErrorKind.QueryGraph, 'ParserCarrier': SmartsParseErrorKind.ParserCarrier, 'AtomProperty': SmartsParseErrorKind.AtomProperty, 'BondProperty': SmartsParseErrorKind.BondProperty, 'MoleculeProperty': SmartsParseErrorKind.MoleculeProperty, 'UnclosedBracket': SmartsParseErrorKind.UnclosedBracket, 'UnexpectedCharacter': SmartsParseErrorKind.UnexpectedCharacter, 'UnexpectedEnd': SmartsParseErrorKind.UnexpectedEnd, 'InvalidAtomPrimitive': SmartsParseErrorKind.InvalidAtomPrimitive, 'UnclosedParenthesis': SmartsParseErrorKind.UnclosedParenthesis, 'UnbalancedRingClosure': SmartsParseErrorKind.UnbalancedRingClosure, 'SelfRingClosure': SmartsParseErrorKind.SelfRingClosure, 'DuplicateRingBond': SmartsParseErrorKind.DuplicateRingBond, 'CxSmiles': SmartsParseErrorKind.CxSmiles, 'Parse': SmartsParseErrorKind.Parse, 'UnsupportedFeature': SmartsParseErrorKind.UnsupportedFeature, 'TemplateAttachmentRemap': SmartsParseErrorKind.TemplateAttachmentRemap})
values = mappingproxy({0: SmartsParseErrorKind.StereoGroup, 1: SmartsParseErrorKind.MissingRecursiveQueryGraph, 2: SmartsParseErrorKind.CxLowering, 3: SmartsParseErrorKind.QueryGraph, 4: SmartsParseErrorKind.ParserCarrier, 5: SmartsParseErrorKind.AtomProperty, 6: SmartsParseErrorKind.BondProperty, 7: SmartsParseErrorKind.MoleculeProperty, 8: SmartsParseErrorKind.UnclosedBracket, 9: SmartsParseErrorKind.UnexpectedCharacter, 10: SmartsParseErrorKind.UnexpectedEnd, 11: SmartsParseErrorKind.InvalidAtomPrimitive, 12: SmartsParseErrorKind.UnclosedParenthesis, 13: SmartsParseErrorKind.UnbalancedRingClosure, 14: SmartsParseErrorKind.SelfRingClosure, 15: SmartsParseErrorKind.DuplicateRingBond, 16: SmartsParseErrorKind.CxSmiles, 17: SmartsParseErrorKind.Parse, 18: SmartsParseErrorKind.UnsupportedFeature, 19: SmartsParseErrorKind.TemplateAttachmentRemap})
class cosmolkit.SmartsParseParams(*, allow_cxsmiles=Ellipsis, strict_cxsmiles=Ellipsis, parse_name=Ellipsis, merge_hs=Ellipsis, skip_cleanup=Ellipsis, debug_parse=Ellipsis, replacements=Ellipsis)

RDKit source: SmilesParse.h lines 56-67 RDKit✔️✔️: struct RDKIT_SMILESPARSE_EXPORT SmartsParserParams { RDKit✔️✔️: bool allowCXSMILES = true; RDKit✔️✔️: bool strictCXSMILES = true; RDKit✔️✔️: bool parseName = true; RDKit✔️✔️: bool mergeHs = false; RDKit✔️✔️: bool skipCleanup = false; RDKit✔️✔️: bool debugParse = false; RDKit✔️✔️: std::map<std::string, std::string> replacements; RDKit✔️✔️: };

Members (7)
allow_cxsmiles: bool

Recognize CX extensions after the SMARTS graph.

debug_parse: bool

Enable native parser diagnostic output.

merge_hs: bool

Merge explicit hydrogen query atoms into their neighbors’ hydrogen-count queries.

parse_name: bool

Parse trailing name text after the query.

replacements: collections.abc.Mapping[str, str]

Text substitutions expanded before parsing the query.

skip_cleanup: bool

Skip the parser’s native cleanup stage.

strict_cxsmiles: bool

Raise an error when CX extension parsing fails.

exception cosmolkit.SmartsTraversalError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SmartsTraversalError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: ValenceError | LegacyStereoError | SmilesParseError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SmartsTraversalErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SmartsTraversalErrorKind(value)

Discriminants of SmartsTraversalErrorKind.

Members: Valence, Stereo, Traversal, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Stereo = SmartsTraversalErrorKind.Stereo
Traversal = SmartsTraversalErrorKind.Traversal
Valence = SmartsTraversalErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Valence': SmartsTraversalErrorKind.Valence, 'Stereo': SmartsTraversalErrorKind.Stereo, 'Traversal': SmartsTraversalErrorKind.Traversal})
values = mappingproxy({0: SmartsTraversalErrorKind.Valence, 1: SmartsTraversalErrorKind.Stereo, 2: SmartsTraversalErrorKind.Traversal})
exception cosmolkit.SmartsWriteError(*args, **kwargs)

SmartsWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (24)
property actual: int | PropertyValueKind | None

“error_payload”} Observed value reported by the native check. Applies to SmartsWriteError.CxCoordinateSelectionArity, SmartsWriteError.CxSgroupVectorCast. None when this payload is absent.

Type:

{“role”

property atom: int | None

Original atom index associated with this failure, or None when not applicable.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to SmartsWriteError.CxSourceAtomOutOfRange. None when this payload is absent.

property atomic_number: int | None

Atomic number involved in the failed chemistry operation. Applies to SmartsWriteError.AtomTypeAtomicNumber. None when this payload is absent.

property bond: int | None

Original bond index associated with this failure, or None when not applicable.

property bond_count: int | None

Bond count used when validating the reported bond reference. Applies to SmartsWriteError.CxSourceBondOutOfRange. None when this payload is absent.

property count: int | None

Count reported by the native failure. Applies to SmartsWriteError.CxRingAtomOrderIndex, SmartsWriteError.SourceAtomCount, SmartsWriteError.CxOutputOrder, SmartsWriteError.CxRowCount. None when this payload is absent.

property description: str | None

Native explanation of the rejected value or operation. Applies to SmartsWriteError.UnwritableBondQuery, SmartsWriteError.UnknownCombination. None when this payload is absent.

property detail: str | None

Additional native diagnostic detail. Applies to SmartsWriteError.QueryGraphTraversalUnsupported, SmartsWriteError.QueryGraphCxExtensionsUnsupported. None when this payload is absent.

property direction: BondDirection | None

“error_payload”} Mapping or bond direction associated with the failure. Present for SmartsWriteError.SourceBondDirection; None when unavailable.

Type:

{“role”

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property expected: int | str | None

Required value reported by the native check. Applies to SmartsWriteError.CxCoordinateSelectionArity, SmartsWriteError.CxSgroupVectorCast. None when this payload is absent.

property group: int | None

Group identifier involved in the failure. Applies to SmartsWriteError.CxSgroupVectorCast, SmartsWriteError.CxSgroupPropertyWrite, SmartsWriteError.CxSgroupPropertyUInt. None when this payload is absent.

property index: int | None

Index reported by the failing native check. Applies to SmartsWriteError.CxRingAtomOrderIndex, SmartsWriteError.SourceAtomToLeftIndex, SmartsWriteError.SourceBondBeginIndex. None when this payload is absent.

property kind: str | PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to SmartsWriteError.CxOutputOrder, SmartsWriteError.CxRowCount, SmartsWriteError.CompositeChildCount, SmartsWriteError.CxAtomPropertyKind, SmartsWriteError.InvalidPropertyKind. None when this payload is absent.

Type:

{“role”

property predicate: AtomQueryPredicate | BondQueryPredicate | None

“error_payload”} Unsupported atom or bond query predicate, or None for another failure.

Type:

{“role”

property property: str | None

Property name involved in this failure, or None when not applicable.

property row: int | None

Row reported by the native failure. Applies to SmartsWriteError.CxOutputOrder. None when this payload is absent.

property side: int | None

Probe/reference or source/target side identified by the native check. Applies to SmartsWriteError.CxRingStereoReferenceMissing. None when this payload is absent.

property source: StereoGroupError | SmartsTraversalError | CoordinateValidationError | RingFindingError | WedgeError | SmilesParseError | PropertyUIntReadError | MoleculePropertyError | AtropisomerError | AtomPropertyError | PropertyIntReadError | PropertyValueError | RequiredPropertyStringError | QueryGraphError | PropertyStringError | ValenceError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property source_message: str | None

Message of the immediate native cause, or None when no cause exists.

property template: int | None

Reaction template index associated with this failure, or None when not applicable.

property value: int | str | None

Value rejected or reported by the native operation. Applies to SmartsWriteError.ChargeMagnitudeOverflow, SmartsWriteError.InvalidGraph. None when this payload is absent.

property variant: SmartsWriteErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.SmartsWriteErrorKind(value)

Discriminants of SmartsWriteErrorKind.

Members: StereoGroup, Traversal, CxCoordinates, CxRingInfo, CxRingAtomOrderIndex, CxRingStereoReferenceMissing, CxWedge, CxBondConfigAtropMissingCarriers, CxAtomPropertyOutput, CxMissingConformer, CxCoordinateSource, CxCoordinateOutput, CxSourceBondOutOfRange, CxMoleculePropertyUInt, CxSgroupVectorCast, CxSgroupPropertyWrite, CxStereoGroup, CxSourceAtomOutOfRange, MoleculePropertyWrite, SourceAtomCount, AtomPropertyWrite, CanonicalTraversal, UnwritableBondQuery, SourceAtomToLeftIndex, SourceBondBeginIndex, AtomMapInt, AtomTypeAtomicNumber, ChargeMagnitudeOverflow, PropertyValue, CxRequiredProperty, CxPropertyList, CxCoordinateSelectionArity, CxMissingOutputOrder, CxOutputOrderPropertyType, CxAtomPropertyKind, CxAtomPropertyUInt, CxAtomPropertyWrite, CxCoordinateStorage, CxCoordinateSelection, CxComposition, CxOutputOrder, CxRowCount, CxBondPropertyUInt, InvalidPropertyKind, CxAtomPropertyInt, CxSgroupPropertyUInt, Property, Valence, InvalidGraph, QueryGraphTraversalUnsupported, OrAboveAndBelowAnd, UnknownCombination, MissingRecursiveQueryMolecule, SourceBondDirection, UnsupportedBondQuery, UnsupportedAtomQuery, CompositeChildCount, XorComposite, QueryGraphCxExtensionsUnsupported, RootedAtomOutOfRange, EmptyAtomSelection, EmptyBondSelection, FragmentAtomOutOfRange, FragmentBondOutOfRange, BondAtomNotEndpoint, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (68)
AtomMapInt = SmartsWriteErrorKind.AtomMapInt
AtomPropertyWrite = SmartsWriteErrorKind.AtomPropertyWrite
AtomTypeAtomicNumber = SmartsWriteErrorKind.AtomTypeAtomicNumber
BondAtomNotEndpoint = SmartsWriteErrorKind.BondAtomNotEndpoint
CanonicalTraversal = SmartsWriteErrorKind.CanonicalTraversal
ChargeMagnitudeOverflow = SmartsWriteErrorKind.ChargeMagnitudeOverflow
CompositeChildCount = SmartsWriteErrorKind.CompositeChildCount
CxAtomPropertyInt = SmartsWriteErrorKind.CxAtomPropertyInt
CxAtomPropertyKind = SmartsWriteErrorKind.CxAtomPropertyKind
CxAtomPropertyOutput = SmartsWriteErrorKind.CxAtomPropertyOutput
CxAtomPropertyUInt = SmartsWriteErrorKind.CxAtomPropertyUInt
CxAtomPropertyWrite = SmartsWriteErrorKind.CxAtomPropertyWrite
CxBondConfigAtropMissingCarriers = SmartsWriteErrorKind.CxBondConfigAtropMissingCarriers
CxBondPropertyUInt = SmartsWriteErrorKind.CxBondPropertyUInt
CxComposition = SmartsWriteErrorKind.CxComposition
CxCoordinateOutput = SmartsWriteErrorKind.CxCoordinateOutput
CxCoordinateSelection = SmartsWriteErrorKind.CxCoordinateSelection
CxCoordinateSelectionArity = SmartsWriteErrorKind.CxCoordinateSelectionArity
CxCoordinateSource = SmartsWriteErrorKind.CxCoordinateSource
CxCoordinateStorage = SmartsWriteErrorKind.CxCoordinateStorage
CxCoordinates = SmartsWriteErrorKind.CxCoordinates
CxMissingConformer = SmartsWriteErrorKind.CxMissingConformer
CxMissingOutputOrder = SmartsWriteErrorKind.CxMissingOutputOrder
CxMoleculePropertyUInt = SmartsWriteErrorKind.CxMoleculePropertyUInt
CxOutputOrder = SmartsWriteErrorKind.CxOutputOrder
CxOutputOrderPropertyType = SmartsWriteErrorKind.CxOutputOrderPropertyType
CxPropertyList = SmartsWriteErrorKind.CxPropertyList
CxRequiredProperty = SmartsWriteErrorKind.CxRequiredProperty
CxRingAtomOrderIndex = SmartsWriteErrorKind.CxRingAtomOrderIndex
CxRingInfo = SmartsWriteErrorKind.CxRingInfo
CxRingStereoReferenceMissing = SmartsWriteErrorKind.CxRingStereoReferenceMissing
CxRowCount = SmartsWriteErrorKind.CxRowCount
CxSgroupPropertyUInt = SmartsWriteErrorKind.CxSgroupPropertyUInt
CxSgroupPropertyWrite = SmartsWriteErrorKind.CxSgroupPropertyWrite
CxSgroupVectorCast = SmartsWriteErrorKind.CxSgroupVectorCast
CxSourceAtomOutOfRange = SmartsWriteErrorKind.CxSourceAtomOutOfRange
CxSourceBondOutOfRange = SmartsWriteErrorKind.CxSourceBondOutOfRange
CxStereoGroup = SmartsWriteErrorKind.CxStereoGroup
CxWedge = SmartsWriteErrorKind.CxWedge
EmptyAtomSelection = SmartsWriteErrorKind.EmptyAtomSelection
EmptyBondSelection = SmartsWriteErrorKind.EmptyBondSelection
FragmentAtomOutOfRange = SmartsWriteErrorKind.FragmentAtomOutOfRange
FragmentBondOutOfRange = SmartsWriteErrorKind.FragmentBondOutOfRange
InvalidGraph = SmartsWriteErrorKind.InvalidGraph
InvalidPropertyKind = SmartsWriteErrorKind.InvalidPropertyKind
MissingRecursiveQueryMolecule = SmartsWriteErrorKind.MissingRecursiveQueryMolecule
MoleculePropertyWrite = SmartsWriteErrorKind.MoleculePropertyWrite
OrAboveAndBelowAnd = SmartsWriteErrorKind.OrAboveAndBelowAnd
Property = SmartsWriteErrorKind.Property
PropertyValue = SmartsWriteErrorKind.PropertyValue
QueryGraphCxExtensionsUnsupported = SmartsWriteErrorKind.QueryGraphCxExtensionsUnsupported
QueryGraphTraversalUnsupported = SmartsWriteErrorKind.QueryGraphTraversalUnsupported
RootedAtomOutOfRange = SmartsWriteErrorKind.RootedAtomOutOfRange
SourceAtomCount = SmartsWriteErrorKind.SourceAtomCount
SourceAtomToLeftIndex = SmartsWriteErrorKind.SourceAtomToLeftIndex
SourceBondBeginIndex = SmartsWriteErrorKind.SourceBondBeginIndex
SourceBondDirection = SmartsWriteErrorKind.SourceBondDirection
StereoGroup = SmartsWriteErrorKind.StereoGroup
Traversal = SmartsWriteErrorKind.Traversal
UnknownCombination = SmartsWriteErrorKind.UnknownCombination
UnsupportedAtomQuery = SmartsWriteErrorKind.UnsupportedAtomQuery
UnsupportedBondQuery = SmartsWriteErrorKind.UnsupportedBondQuery
UnwritableBondQuery = SmartsWriteErrorKind.UnwritableBondQuery
Valence = SmartsWriteErrorKind.Valence
XorComposite = SmartsWriteErrorKind.XorComposite
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': SmartsWriteErrorKind.StereoGroup, 'Traversal': SmartsWriteErrorKind.Traversal, 'CxCoordinates': SmartsWriteErrorKind.CxCoordinates, 'CxRingInfo': SmartsWriteErrorKind.CxRingInfo, 'CxRingAtomOrderIndex': SmartsWriteErrorKind.CxRingAtomOrderIndex, 'CxRingStereoReferenceMissing': SmartsWriteErrorKind.CxRingStereoReferenceMissing, 'CxWedge': SmartsWriteErrorKind.CxWedge, 'CxBondConfigAtropMissingCarriers': SmartsWriteErrorKind.CxBondConfigAtropMissingCarriers, 'CxAtomPropertyOutput': SmartsWriteErrorKind.CxAtomPropertyOutput, 'CxMissingConformer': SmartsWriteErrorKind.CxMissingConformer, 'CxCoordinateSource': SmartsWriteErrorKind.CxCoordinateSource, 'CxCoordinateOutput': SmartsWriteErrorKind.CxCoordinateOutput, 'CxSourceBondOutOfRange': SmartsWriteErrorKind.CxSourceBondOutOfRange, 'CxMoleculePropertyUInt': SmartsWriteErrorKind.CxMoleculePropertyUInt, 'CxSgroupVectorCast': SmartsWriteErrorKind.CxSgroupVectorCast, 'CxSgroupPropertyWrite': SmartsWriteErrorKind.CxSgroupPropertyWrite, 'CxStereoGroup': SmartsWriteErrorKind.CxStereoGroup, 'CxSourceAtomOutOfRange': SmartsWriteErrorKind.CxSourceAtomOutOfRange, 'MoleculePropertyWrite': SmartsWriteErrorKind.MoleculePropertyWrite, 'SourceAtomCount': SmartsWriteErrorKind.SourceAtomCount, 'AtomPropertyWrite': SmartsWriteErrorKind.AtomPropertyWrite, 'CanonicalTraversal': SmartsWriteErrorKind.CanonicalTraversal, 'UnwritableBondQuery': SmartsWriteErrorKind.UnwritableBondQuery, 'SourceAtomToLeftIndex': SmartsWriteErrorKind.SourceAtomToLeftIndex, 'SourceBondBeginIndex': SmartsWriteErrorKind.SourceBondBeginIndex, 'AtomMapInt': SmartsWriteErrorKind.AtomMapInt, 'AtomTypeAtomicNumber': SmartsWriteErrorKind.AtomTypeAtomicNumber, 'ChargeMagnitudeOverflow': SmartsWriteErrorKind.ChargeMagnitudeOverflow, 'PropertyValue': SmartsWriteErrorKind.PropertyValue, 'CxRequiredProperty': SmartsWriteErrorKind.CxRequiredProperty, 'CxPropertyList': SmartsWriteErrorKind.CxPropertyList, 'CxCoordinateSelectionArity': SmartsWriteErrorKind.CxCoordinateSelectionArity, 'CxMissingOutputOrder': SmartsWriteErrorKind.CxMissingOutputOrder, 'CxOutputOrderPropertyType': SmartsWriteErrorKind.CxOutputOrderPropertyType, 'CxAtomPropertyKind': SmartsWriteErrorKind.CxAtomPropertyKind, 'CxAtomPropertyUInt': SmartsWriteErrorKind.CxAtomPropertyUInt, 'CxAtomPropertyWrite': SmartsWriteErrorKind.CxAtomPropertyWrite, 'CxCoordinateStorage': SmartsWriteErrorKind.CxCoordinateStorage, 'CxCoordinateSelection': SmartsWriteErrorKind.CxCoordinateSelection, 'CxComposition': SmartsWriteErrorKind.CxComposition, 'CxOutputOrder': SmartsWriteErrorKind.CxOutputOrder, 'CxRowCount': SmartsWriteErrorKind.CxRowCount, 'CxBondPropertyUInt': SmartsWriteErrorKind.CxBondPropertyUInt, 'InvalidPropertyKind': SmartsWriteErrorKind.InvalidPropertyKind, 'CxAtomPropertyInt': SmartsWriteErrorKind.CxAtomPropertyInt, 'CxSgroupPropertyUInt': SmartsWriteErrorKind.CxSgroupPropertyUInt, 'Property': SmartsWriteErrorKind.Property, 'Valence': SmartsWriteErrorKind.Valence, 'InvalidGraph': SmartsWriteErrorKind.InvalidGraph, 'QueryGraphTraversalUnsupported': SmartsWriteErrorKind.QueryGraphTraversalUnsupported, 'OrAboveAndBelowAnd': SmartsWriteErrorKind.OrAboveAndBelowAnd, 'UnknownCombination': SmartsWriteErrorKind.UnknownCombination, 'MissingRecursiveQueryMolecule': SmartsWriteErrorKind.MissingRecursiveQueryMolecule, 'SourceBondDirection': SmartsWriteErrorKind.SourceBondDirection, 'UnsupportedBondQuery': SmartsWriteErrorKind.UnsupportedBondQuery, 'UnsupportedAtomQuery': SmartsWriteErrorKind.UnsupportedAtomQuery, 'CompositeChildCount': SmartsWriteErrorKind.CompositeChildCount, 'XorComposite': SmartsWriteErrorKind.XorComposite, 'QueryGraphCxExtensionsUnsupported': SmartsWriteErrorKind.QueryGraphCxExtensionsUnsupported, 'RootedAtomOutOfRange': SmartsWriteErrorKind.RootedAtomOutOfRange, 'EmptyAtomSelection': SmartsWriteErrorKind.EmptyAtomSelection, 'EmptyBondSelection': SmartsWriteErrorKind.EmptyBondSelection, 'FragmentAtomOutOfRange': SmartsWriteErrorKind.FragmentAtomOutOfRange, 'FragmentBondOutOfRange': SmartsWriteErrorKind.FragmentBondOutOfRange, 'BondAtomNotEndpoint': SmartsWriteErrorKind.BondAtomNotEndpoint})
values = mappingproxy({0: SmartsWriteErrorKind.StereoGroup, 1: SmartsWriteErrorKind.Traversal, 2: SmartsWriteErrorKind.CxCoordinates, 3: SmartsWriteErrorKind.CxRingInfo, 4: SmartsWriteErrorKind.CxRingAtomOrderIndex, 5: SmartsWriteErrorKind.CxRingStereoReferenceMissing, 6: SmartsWriteErrorKind.CxWedge, 7: SmartsWriteErrorKind.CxBondConfigAtropMissingCarriers, 8: SmartsWriteErrorKind.CxAtomPropertyOutput, 9: SmartsWriteErrorKind.CxMissingConformer, 10: SmartsWriteErrorKind.CxCoordinateSource, 11: SmartsWriteErrorKind.CxCoordinateOutput, 12: SmartsWriteErrorKind.CxSourceBondOutOfRange, 13: SmartsWriteErrorKind.CxMoleculePropertyUInt, 14: SmartsWriteErrorKind.CxSgroupVectorCast, 15: SmartsWriteErrorKind.CxSgroupPropertyWrite, 16: SmartsWriteErrorKind.CxStereoGroup, 17: SmartsWriteErrorKind.CxSourceAtomOutOfRange, 18: SmartsWriteErrorKind.MoleculePropertyWrite, 19: SmartsWriteErrorKind.SourceAtomCount, 20: SmartsWriteErrorKind.AtomPropertyWrite, 21: SmartsWriteErrorKind.CanonicalTraversal, 22: SmartsWriteErrorKind.UnwritableBondQuery, 23: SmartsWriteErrorKind.SourceAtomToLeftIndex, 24: SmartsWriteErrorKind.SourceBondBeginIndex, 25: SmartsWriteErrorKind.AtomMapInt, 26: SmartsWriteErrorKind.AtomTypeAtomicNumber, 27: SmartsWriteErrorKind.ChargeMagnitudeOverflow, 28: SmartsWriteErrorKind.PropertyValue, 29: SmartsWriteErrorKind.CxRequiredProperty, 30: SmartsWriteErrorKind.CxPropertyList, 31: SmartsWriteErrorKind.CxCoordinateSelectionArity, 32: SmartsWriteErrorKind.CxMissingOutputOrder, 33: SmartsWriteErrorKind.CxOutputOrderPropertyType, 34: SmartsWriteErrorKind.CxAtomPropertyKind, 35: SmartsWriteErrorKind.CxAtomPropertyUInt, 36: SmartsWriteErrorKind.CxAtomPropertyWrite, 37: SmartsWriteErrorKind.CxCoordinateStorage, 38: SmartsWriteErrorKind.CxCoordinateSelection, 39: SmartsWriteErrorKind.CxComposition, 40: SmartsWriteErrorKind.CxOutputOrder, 41: SmartsWriteErrorKind.CxRowCount, 42: SmartsWriteErrorKind.CxBondPropertyUInt, 43: SmartsWriteErrorKind.InvalidPropertyKind, 44: SmartsWriteErrorKind.CxAtomPropertyInt, 45: SmartsWriteErrorKind.CxSgroupPropertyUInt, 46: SmartsWriteErrorKind.Property, 47: SmartsWriteErrorKind.Valence, 48: SmartsWriteErrorKind.InvalidGraph, 49: SmartsWriteErrorKind.QueryGraphTraversalUnsupported, 50: SmartsWriteErrorKind.OrAboveAndBelowAnd, 51: SmartsWriteErrorKind.UnknownCombination, 52: SmartsWriteErrorKind.MissingRecursiveQueryMolecule, 53: SmartsWriteErrorKind.SourceBondDirection, 54: SmartsWriteErrorKind.UnsupportedBondQuery, 55: SmartsWriteErrorKind.UnsupportedAtomQuery, 56: SmartsWriteErrorKind.CompositeChildCount, 57: SmartsWriteErrorKind.XorComposite, 58: SmartsWriteErrorKind.QueryGraphCxExtensionsUnsupported, 59: SmartsWriteErrorKind.RootedAtomOutOfRange, 60: SmartsWriteErrorKind.EmptyAtomSelection, 61: SmartsWriteErrorKind.EmptyBondSelection, 62: SmartsWriteErrorKind.FragmentAtomOutOfRange, 63: SmartsWriteErrorKind.FragmentBondOutOfRange, 64: SmartsWriteErrorKind.BondAtomNotEndpoint})
class cosmolkit.SmartsWriteParams(*, include_atom_maps=Ellipsis, isomeric_smiles=Ellipsis, include_dative_bonds=Ellipsis, rooted_at_atom=Ellipsis)

Options for QueryGraph-native SMARTS serialization.

Members (4)
include_atom_maps: bool

Emit atom-map labels stored on query atoms.

include_dative_bonds: bool

Preserve directional dative bond tokens.

isomeric_smiles: bool

Emit atom and bond stereochemistry.

rooted_at_atom: int | None

Start graph traversal at this atom index when present.

exception cosmolkit.SmilesError(*args, **kwargs)

Failure in the smiles domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SmilesError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: SmilesParseError | HydrogenError | SanitizeError | SmilesStereoError | OperationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SmilesErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SmilesErrorKind(value)

Discriminants of SmilesErrorKind.

Members: Parse, Hydrogen, Sanitize, Stereo, Construction, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
Construction = SmilesErrorKind.Construction
Hydrogen = SmilesErrorKind.Hydrogen
Parse = SmilesErrorKind.Parse
Sanitize = SmilesErrorKind.Sanitize
Stereo = SmilesErrorKind.Stereo
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Parse': SmilesErrorKind.Parse, 'Hydrogen': SmilesErrorKind.Hydrogen, 'Sanitize': SmilesErrorKind.Sanitize, 'Stereo': SmilesErrorKind.Stereo, 'Construction': SmilesErrorKind.Construction})
values = mappingproxy({0: SmilesErrorKind.Parse, 1: SmilesErrorKind.Hydrogen, 2: SmilesErrorKind.Sanitize, 3: SmilesErrorKind.Stereo, 4: SmilesErrorKind.Construction})
exception cosmolkit.SmilesParseError(*args, **kwargs)

Failure in the smiles domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SmilesParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (28)
property atom: int | None

Atom identifier implicated in the failure. Applies to SmilesParseError.CxLinkAtomOutOfRange, SmilesParseError.CxAtomPropertyAtomOutOfRange, SmilesParseError.CxCoordinateAtomOutOfRange, SmilesParseError.WriterRequiredProperty, SmilesParseError.WriterPropertyList. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to SmilesParseError.CxLinkAtomOutOfRange, SmilesParseError.CxAtomPropertyAtomOutOfRange, SmilesParseError.CxCoordinateAtomOutOfRange, SmilesParseError.WriterRootAtomOutOfRange. None when this payload is absent.

property atom_index: int | None

Readonly atom_index payload of the WriterRootAtomOutOfRange error variant; None for other variants.

property bond: int | None

Bond identifier implicated in the failure. Applies to SmilesParseError.CxZeroBondOutOfRange, SmilesParseError.CxTypedBondOutOfRange. None when this payload is absent.

property bond_count: int | None

Bond count used when validating the reported bond reference. Applies to SmilesParseError.CxZeroBondOutOfRange, SmilesParseError.CxTypedBondOutOfRange. None when this payload is absent.

property canonical_rank: str | None

Canonical rank implicated in the failed traversal. Applies to SmilesParseError.CanonicalRank. None when this payload is absent.

property count: int | None

Count reported by the native failure. Applies to SmilesParseError.CxLinkOrderOutOfRange, SmilesParseError.TraversalStateIndex. None when this payload is absent.

property cx: str | None

Native CXSMILES diagnostic, or None for another failure.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Index reported by the failing native check. Applies to SmilesParseError.CxLinkOrderOutOfRange, SmilesParseError.TraversalStateIndex, SmilesParseError.UnclosedRing. None when this payload is absent.

property key: str | None

Readonly key payload of the ReplacementCycle error variant; None for other variants.

property message: str | None

Readonly message payload of the Syntax error variant; None for other variants.

property model: str | None

Structural model involved in the failure. Applies to SmilesParseError.Model. None when this payload is absent.

property offset: int | None

Source offset reported by the native parser. Applies to SmilesParseError.Unsupported, SmilesParseError.Syntax, SmilesParseError.Atom. None when this payload is absent.

property selection: CxCoordinateSelection | None

“error_payload”} Requested CX coordinate set that was missing, or None for another failure.

Type:

{“role”

property source: StereoGroupError | TopologyEditError | CoordinateValidationError | AtomPropertyError | BondValueError | MoleculePropertyError | PropertyIntReadError | PropertyULongReadError | PropertyUIntReadError | PropertyValueError | RequiredPropertyStringError | PropertyStringError | LegacyStereoError | PotentialStereoError | ParserStereoOrderError | StereoOrderError | SmilesStereoError | AtropisomerError | RingFindingError | ParserCarrierError | KekulizeError | SanitizeError | HydrogenError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property state: str | None

Readonly state payload of the TraversalStateIndex error variant; None for other variants.

property text: str | None

Readonly text payload of the Atom error variant; None for other variants.

property three_d_count: int | None

Readonly three_d_count payload of the AmbiguousCoordinateSelection error variant; None for other variants.

property token: str | None

Readonly token payload of the Unsupported error variant; None for other variants.

property two_d_count: int | None

Readonly two_d_count payload of the AmbiguousCoordinateSelection error variant; None for other variants.

property unsupported_cx: str | None

Unsupported CXSMILES capability, or None for another failure.

property unsupported_writer: str | None

Unsupported SMILES writer capability, or None for another failure.

property variant: SmilesParseErrorKind

Exact Rust error variant, independent of the human-readable message.

property writer_canonical_invariant: str | None

Canonical writer invariant that failed, or None for another failure.

property writer_stereo: str | None

Native writer stereo diagnostic, or None for another failure.

property writer_valence: str | None

Native writer valence diagnostic, or None for another failure.

class cosmolkit.SmilesParseErrorKind(value)

Discriminants of SmilesParseErrorKind.

Members: StereoGroup, TopologyEdit, CxLinkAtomOutOfRange, CxLinkOrderOutOfRange, CxZeroBondOutOfRange, CxTypedBondOutOfRange, CxAtomPropertyAtomOutOfRange, CxCoordinateAtomOutOfRange, WriterCanonicalInvariant, WriterInt, WriterULong, WriterRings, WriterLegacyStereo, WriterPotentialStereo, WriterParserStereoOrder, TraversalTooManyOpenRings, TraversalStateIndex, WriterStereoOrder, WriterPropertyKind, Coordinates, WriterNumeric, WriterRequiredProperty, WriterPropertyList, AtomProperty, BondProperty, MoleculeProperty, PropertyKind, ParserCarrier, Unsupported, Syntax, Atom, UnclosedRing, Cx, UnsupportedCx, UnsupportedWriter, CanonicalRank, WriterValence, WriterKekulize, WriterProperty, WriterStereo, ParserSanitize, ParserRemoveHydrogens, ParserStereo, ParserAtropisomer, WriterStereoBond, AmbiguousCoordinateSelection, MissingCoordinateSelection, WriterRootAtomOutOfRange, Model, EmptyReplacementKey, ReplacementCycle, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (54)
AmbiguousCoordinateSelection = SmilesParseErrorKind.AmbiguousCoordinateSelection
Atom = SmilesParseErrorKind.Atom
AtomProperty = SmilesParseErrorKind.AtomProperty
BondProperty = SmilesParseErrorKind.BondProperty
CanonicalRank = SmilesParseErrorKind.CanonicalRank
Coordinates = SmilesParseErrorKind.Coordinates
Cx = SmilesParseErrorKind.Cx
CxAtomPropertyAtomOutOfRange = SmilesParseErrorKind.CxAtomPropertyAtomOutOfRange
CxCoordinateAtomOutOfRange = SmilesParseErrorKind.CxCoordinateAtomOutOfRange
CxLinkAtomOutOfRange = SmilesParseErrorKind.CxLinkAtomOutOfRange
CxLinkOrderOutOfRange = SmilesParseErrorKind.CxLinkOrderOutOfRange
CxTypedBondOutOfRange = SmilesParseErrorKind.CxTypedBondOutOfRange
CxZeroBondOutOfRange = SmilesParseErrorKind.CxZeroBondOutOfRange
EmptyReplacementKey = SmilesParseErrorKind.EmptyReplacementKey
MissingCoordinateSelection = SmilesParseErrorKind.MissingCoordinateSelection
Model = SmilesParseErrorKind.Model
MoleculeProperty = SmilesParseErrorKind.MoleculeProperty
ParserAtropisomer = SmilesParseErrorKind.ParserAtropisomer
ParserCarrier = SmilesParseErrorKind.ParserCarrier
ParserRemoveHydrogens = SmilesParseErrorKind.ParserRemoveHydrogens
ParserSanitize = SmilesParseErrorKind.ParserSanitize
ParserStereo = SmilesParseErrorKind.ParserStereo
PropertyKind = SmilesParseErrorKind.PropertyKind
ReplacementCycle = SmilesParseErrorKind.ReplacementCycle
StereoGroup = SmilesParseErrorKind.StereoGroup
Syntax = SmilesParseErrorKind.Syntax
TopologyEdit = SmilesParseErrorKind.TopologyEdit
TraversalStateIndex = SmilesParseErrorKind.TraversalStateIndex
TraversalTooManyOpenRings = SmilesParseErrorKind.TraversalTooManyOpenRings
UnclosedRing = SmilesParseErrorKind.UnclosedRing
Unsupported = SmilesParseErrorKind.Unsupported
UnsupportedCx = SmilesParseErrorKind.UnsupportedCx
UnsupportedWriter = SmilesParseErrorKind.UnsupportedWriter
WriterCanonicalInvariant = SmilesParseErrorKind.WriterCanonicalInvariant
WriterInt = SmilesParseErrorKind.WriterInt
WriterKekulize = SmilesParseErrorKind.WriterKekulize
WriterLegacyStereo = SmilesParseErrorKind.WriterLegacyStereo
WriterNumeric = SmilesParseErrorKind.WriterNumeric
WriterParserStereoOrder = SmilesParseErrorKind.WriterParserStereoOrder
WriterPotentialStereo = SmilesParseErrorKind.WriterPotentialStereo
WriterProperty = SmilesParseErrorKind.WriterProperty
WriterPropertyKind = SmilesParseErrorKind.WriterPropertyKind
WriterPropertyList = SmilesParseErrorKind.WriterPropertyList
WriterRequiredProperty = SmilesParseErrorKind.WriterRequiredProperty
WriterRings = SmilesParseErrorKind.WriterRings
WriterRootAtomOutOfRange = SmilesParseErrorKind.WriterRootAtomOutOfRange
WriterStereo = SmilesParseErrorKind.WriterStereo
WriterStereoBond = SmilesParseErrorKind.WriterStereoBond
WriterStereoOrder = SmilesParseErrorKind.WriterStereoOrder
WriterULong = SmilesParseErrorKind.WriterULong
WriterValence = SmilesParseErrorKind.WriterValence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': SmilesParseErrorKind.StereoGroup, 'TopologyEdit': SmilesParseErrorKind.TopologyEdit, 'CxLinkAtomOutOfRange': SmilesParseErrorKind.CxLinkAtomOutOfRange, 'CxLinkOrderOutOfRange': SmilesParseErrorKind.CxLinkOrderOutOfRange, 'CxZeroBondOutOfRange': SmilesParseErrorKind.CxZeroBondOutOfRange, 'CxTypedBondOutOfRange': SmilesParseErrorKind.CxTypedBondOutOfRange, 'CxAtomPropertyAtomOutOfRange': SmilesParseErrorKind.CxAtomPropertyAtomOutOfRange, 'CxCoordinateAtomOutOfRange': SmilesParseErrorKind.CxCoordinateAtomOutOfRange, 'WriterCanonicalInvariant': SmilesParseErrorKind.WriterCanonicalInvariant, 'WriterInt': SmilesParseErrorKind.WriterInt, 'WriterULong': SmilesParseErrorKind.WriterULong, 'WriterRings': SmilesParseErrorKind.WriterRings, 'WriterLegacyStereo': SmilesParseErrorKind.WriterLegacyStereo, 'WriterPotentialStereo': SmilesParseErrorKind.WriterPotentialStereo, 'WriterParserStereoOrder': SmilesParseErrorKind.WriterParserStereoOrder, 'TraversalTooManyOpenRings': SmilesParseErrorKind.TraversalTooManyOpenRings, 'TraversalStateIndex': SmilesParseErrorKind.TraversalStateIndex, 'WriterStereoOrder': SmilesParseErrorKind.WriterStereoOrder, 'WriterPropertyKind': SmilesParseErrorKind.WriterPropertyKind, 'Coordinates': SmilesParseErrorKind.Coordinates, 'WriterNumeric': SmilesParseErrorKind.WriterNumeric, 'WriterRequiredProperty': SmilesParseErrorKind.WriterRequiredProperty, 'WriterPropertyList': SmilesParseErrorKind.WriterPropertyList, 'AtomProperty': SmilesParseErrorKind.AtomProperty, 'BondProperty': SmilesParseErrorKind.BondProperty, 'MoleculeProperty': SmilesParseErrorKind.MoleculeProperty, 'PropertyKind': SmilesParseErrorKind.PropertyKind, 'ParserCarrier': SmilesParseErrorKind.ParserCarrier, 'Unsupported': SmilesParseErrorKind.Unsupported, 'Syntax': SmilesParseErrorKind.Syntax, 'Atom': SmilesParseErrorKind.Atom, 'UnclosedRing': SmilesParseErrorKind.UnclosedRing, 'Cx': SmilesParseErrorKind.Cx, 'UnsupportedCx': SmilesParseErrorKind.UnsupportedCx, 'UnsupportedWriter': SmilesParseErrorKind.UnsupportedWriter, 'CanonicalRank': SmilesParseErrorKind.CanonicalRank, 'WriterValence': SmilesParseErrorKind.WriterValence, 'WriterKekulize': SmilesParseErrorKind.WriterKekulize, 'WriterProperty': SmilesParseErrorKind.WriterProperty, 'WriterStereo': SmilesParseErrorKind.WriterStereo, 'ParserSanitize': SmilesParseErrorKind.ParserSanitize, 'ParserRemoveHydrogens': SmilesParseErrorKind.ParserRemoveHydrogens, 'ParserStereo': SmilesParseErrorKind.ParserStereo, 'ParserAtropisomer': SmilesParseErrorKind.ParserAtropisomer, 'WriterStereoBond': SmilesParseErrorKind.WriterStereoBond, 'AmbiguousCoordinateSelection': SmilesParseErrorKind.AmbiguousCoordinateSelection, 'MissingCoordinateSelection': SmilesParseErrorKind.MissingCoordinateSelection, 'WriterRootAtomOutOfRange': SmilesParseErrorKind.WriterRootAtomOutOfRange, 'Model': SmilesParseErrorKind.Model, 'EmptyReplacementKey': SmilesParseErrorKind.EmptyReplacementKey, 'ReplacementCycle': SmilesParseErrorKind.ReplacementCycle})
values = mappingproxy({0: SmilesParseErrorKind.StereoGroup, 1: SmilesParseErrorKind.TopologyEdit, 2: SmilesParseErrorKind.CxLinkAtomOutOfRange, 3: SmilesParseErrorKind.CxLinkOrderOutOfRange, 4: SmilesParseErrorKind.CxZeroBondOutOfRange, 5: SmilesParseErrorKind.CxTypedBondOutOfRange, 6: SmilesParseErrorKind.CxAtomPropertyAtomOutOfRange, 7: SmilesParseErrorKind.CxCoordinateAtomOutOfRange, 8: SmilesParseErrorKind.WriterCanonicalInvariant, 9: SmilesParseErrorKind.WriterInt, 10: SmilesParseErrorKind.WriterULong, 11: SmilesParseErrorKind.WriterRings, 12: SmilesParseErrorKind.WriterLegacyStereo, 13: SmilesParseErrorKind.WriterPotentialStereo, 14: SmilesParseErrorKind.WriterParserStereoOrder, 15: SmilesParseErrorKind.TraversalTooManyOpenRings, 16: SmilesParseErrorKind.TraversalStateIndex, 17: SmilesParseErrorKind.WriterStereoOrder, 18: SmilesParseErrorKind.WriterPropertyKind, 19: SmilesParseErrorKind.Coordinates, 20: SmilesParseErrorKind.WriterNumeric, 21: SmilesParseErrorKind.WriterRequiredProperty, 22: SmilesParseErrorKind.WriterPropertyList, 23: SmilesParseErrorKind.AtomProperty, 24: SmilesParseErrorKind.BondProperty, 25: SmilesParseErrorKind.MoleculeProperty, 26: SmilesParseErrorKind.PropertyKind, 27: SmilesParseErrorKind.ParserCarrier, 28: SmilesParseErrorKind.Unsupported, 29: SmilesParseErrorKind.Syntax, 30: SmilesParseErrorKind.Atom, 31: SmilesParseErrorKind.UnclosedRing, 32: SmilesParseErrorKind.Cx, 33: SmilesParseErrorKind.UnsupportedCx, 34: SmilesParseErrorKind.UnsupportedWriter, 35: SmilesParseErrorKind.CanonicalRank, 36: SmilesParseErrorKind.WriterValence, 37: SmilesParseErrorKind.WriterKekulize, 38: SmilesParseErrorKind.WriterProperty, 39: SmilesParseErrorKind.WriterStereo, 40: SmilesParseErrorKind.ParserSanitize, 41: SmilesParseErrorKind.ParserRemoveHydrogens, 42: SmilesParseErrorKind.ParserStereo, 43: SmilesParseErrorKind.ParserAtropisomer, 44: SmilesParseErrorKind.WriterStereoBond, 45: SmilesParseErrorKind.AmbiguousCoordinateSelection, 46: SmilesParseErrorKind.MissingCoordinateSelection, 47: SmilesParseErrorKind.WriterRootAtomOutOfRange, 48: SmilesParseErrorKind.Model, 49: SmilesParseErrorKind.EmptyReplacementKey, 50: SmilesParseErrorKind.ReplacementCycle})
class cosmolkit.SmilesParseParams(*, sanitize=Ellipsis, allow_cxsmiles=Ellipsis, strict_cxsmiles=Ellipsis, parse_name=Ellipsis, remove_hs=Ellipsis, skip_cleanup=Ellipsis, debug_parse=Ellipsis, replacements=Ellipsis)

SMILES and CXSMILES parsing options, including chemical cleanup and textual replacements.

Members (8)
allow_cxsmiles: bool

Recognize the CXSMILES extension following the core SMILES text.

debug_parse: bool

Enable parser diagnostic output.

parse_name: bool

Interpret trailing name text as the molecule name.

remove_hs: bool

Remove source-eligible explicit hydrogen atom rows after parsing.

replacements: collections.abc.Mapping[str, str]

Text replacements applied before parsing, such as a named fragment token and its SMILES expansion.

sanitize: bool

Run chemical sanitization after parsing.

skip_cleanup: bool

Skip the parser’s final cleanup stage.

strict_cxsmiles: bool

Report invalid CXSMILES extensions as errors instead of accepting a failed extension parse.

exception cosmolkit.SmilesStereoError(*args, **kwargs)

Failure in the smiles_stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SmilesStereoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property actual: int | None

Observed value reported by the native check. Applies to SmilesStereoError.ValenceRows, SmilesStereoError.RingRows. None when this payload is absent.

property assignment: LegacyStereoError | None

“error_payload”} Structured LegacyStereoError payload of SmilesStereoError.Assignment; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property coordinates: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of SmilesStereoError.Coordinates; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property dimension: str | None

Readonly dimension payload of the RingRows error variant; None for other variants.

property directions: DoubleBondStereoError | None

“error_payload”} Structured DoubleBondStereoError payload of SmilesStereoError.Directions; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Required value reported by the native check. Applies to SmilesStereoError.ValenceRows, SmilesStereoError.RingRows. None when this payload is absent.

property field: str | None

Readonly field payload of the ValenceRows error variant; None for other variants.

property id: int | None

Readonly id payload of the SelectedConformerMissing error variant; None for other variants.

property properties: MoleculePropertyError | None

“error_payload”} Structured MoleculePropertyError payload of SmilesStereoError.Properties; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property rings: RingFindingError | None

“error_payload”} Structured RingFindingError payload of SmilesStereoError.Rings; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | StereoOrderError | AtomPropertyError | PropertyIntReadError | TemplateAttachmentOrderError | MappingValidationError | PropertyUIntReadError | CanonicalRankError | DoubleBondStereoError | MoleculePropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of SmilesStereoError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: SmilesStereoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SmilesStereoErrorKind(value)

Discriminants of SmilesStereoErrorKind.

Members: Properties, SelectedConformerMissing, ValenceRows, RingRows, Coordinates, Directions, Assignment, Rings, Valence, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
Assignment = SmilesStereoErrorKind.Assignment
Coordinates = SmilesStereoErrorKind.Coordinates
Directions = SmilesStereoErrorKind.Directions
Properties = SmilesStereoErrorKind.Properties
RingRows = SmilesStereoErrorKind.RingRows
Rings = SmilesStereoErrorKind.Rings
SelectedConformerMissing = SmilesStereoErrorKind.SelectedConformerMissing
Valence = SmilesStereoErrorKind.Valence
ValenceRows = SmilesStereoErrorKind.ValenceRows
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Properties': SmilesStereoErrorKind.Properties, 'SelectedConformerMissing': SmilesStereoErrorKind.SelectedConformerMissing, 'ValenceRows': SmilesStereoErrorKind.ValenceRows, 'RingRows': SmilesStereoErrorKind.RingRows, 'Coordinates': SmilesStereoErrorKind.Coordinates, 'Directions': SmilesStereoErrorKind.Directions, 'Assignment': SmilesStereoErrorKind.Assignment, 'Rings': SmilesStereoErrorKind.Rings, 'Valence': SmilesStereoErrorKind.Valence})
values = mappingproxy({0: SmilesStereoErrorKind.Properties, 1: SmilesStereoErrorKind.SelectedConformerMissing, 2: SmilesStereoErrorKind.ValenceRows, 3: SmilesStereoErrorKind.RingRows, 4: SmilesStereoErrorKind.Coordinates, 5: SmilesStereoErrorKind.Directions, 6: SmilesStereoErrorKind.Assignment, 7: SmilesStereoErrorKind.Rings, 8: SmilesStereoErrorKind.Valence})
exception cosmolkit.SmilesWriteError(*args, **kwargs)

Failure in the smiles domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SmilesWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: SmilesParseError | FragmentWriteInputError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SmilesWriteErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SmilesWriteErrorKind(value)

Discriminants of SmilesWriteErrorKind.

Members: Write, Fragment, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Fragment = SmilesWriteErrorKind.Fragment
Write = SmilesWriteErrorKind.Write
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Write': SmilesWriteErrorKind.Write, 'Fragment': SmilesWriteErrorKind.Fragment})
values = mappingproxy({0: SmilesWriteErrorKind.Write, 1: SmilesWriteErrorKind.Fragment})
class cosmolkit.SmilesWriteParams(*, isomeric_smiles=Ellipsis, kekule=Ellipsis, canonical=Ellipsis, clean_stereo=Ellipsis, rooted_at_atom=Ellipsis, all_bonds_explicit=Ellipsis, all_hydrogens_explicit=Ellipsis, include_dative_bonds=Ellipsis, ignore_atom_map_numbers=Ellipsis)

SMILES output options controlling canonical order, explicit notation and stereochemistry.

Members (9)
all_bonds_explicit: bool

Write explicit bond symbols where implicit notation would otherwise suffice.

all_hydrogens_explicit: bool

Write hydrogen counts explicitly in atom notation.

canonical: bool

Use canonical atom ordering unless an explicit root constrains traversal.

clean_stereo: bool

Clean stereochemical annotations while preparing the output.

ignore_atom_map_numbers: bool

Ignore atom-mapping numbers when computing canonical order.

include_dative_bonds: bool

Preserve dative bond notation in the output.

isomeric_smiles: bool

Include isotope and stereochemical distinctions in the output.

kekule: bool

Write Kekule bond orders instead of aromatic notation.

rooted_at_atom: int | None

Optional atom from which traversal starts.

class cosmolkit.SourceNumericStreamState

Numeric input stream flags captured by a failed lexical conversion.

Members (3)
bad: bool

Whether the numeric stream recorded an underlying stream error.

eof: bool

Whether the numeric stream reached end-of-input.

fail: bool

Whether numeric extraction failed.

class cosmolkit.SparseBitFingerprint(n_bits)

Immutable sparse bit vector storing set positions without a dense bit buffer.

Members (2)
n_bits: int

Declared capacity of the sparse bit fingerprint.

on_bits: list[int]

Set bit indices returned as an independent list.

class cosmolkit.SparseCountFingerprint(length)

Mutable sparse integer counts with 64-bit indices and explicit index-space length.

Members (14)
fuzzy_and(other) → SparseCountFingerprint

Return a new fingerprint using the native componentwise fuzzy intersection.

fuzzy_or(other) → SparseCountFingerprint

Return a new fingerprint using the native componentwise fuzzy union.

length: int

Declared index-space length, not the number of stored nonzero entries.

static new(length) → SparseCountFingerprint

Create a sparse count vector with no nonzero entries and the given index-space length.

nonzero_elements: dict[int, int]

Independent dictionary mapping nonzero entry indices to their counts.

set_value(index, value) → None

Assign a count at an index; zero removes the stored entry. Out-of-range indices raise FingerprintError.

total_value(use_abs=False) → int

Sum stored counts, optionally using their absolute values; native arithmetic errors propagate.

value(index) → int

Return the count at an index; absent entries are zero and out-of-range indices raise FingerprintError.

with_added(other) → SparseCountFingerprint

Return a new fingerprint with corresponding counts added; both inputs remain unchanged.

with_added_scalar(value) → SparseCountFingerprint

Return a new fingerprint after adding the scalar using native sparse-vector semantics.

with_divided_scalar(value) → SparseCountFingerprint

Return a new fingerprint after dividing counts by the scalar; native arithmetic errors propagate.

with_multiplied_scalar(value) → SparseCountFingerprint

Return a new fingerprint after multiplying counts by the scalar.

with_subtracted(other) → SparseCountFingerprint

Return a new fingerprint with corresponding counts subtracted; both inputs remain unchanged.

with_subtracted_scalar(value) → SparseCountFingerprint

Return a new fingerprint after subtracting the scalar using native sparse-vector semantics.

class cosmolkit.SparseCountFingerprint32(length)

Mutable sparse integer counts with 32-bit indices and explicit index-space length.

Members (14)
fuzzy_and(other) → SparseCountFingerprint32

Return a new fingerprint using the native componentwise fuzzy intersection.

fuzzy_or(other) → SparseCountFingerprint32

Return a new fingerprint using the native componentwise fuzzy union.

length: int

Declared index-space length, not the number of stored nonzero entries.

static new(length) → SparseCountFingerprint32

Create a sparse count vector with no nonzero entries and the given index-space length.

nonzero_elements: dict[int, int]

Independent dictionary mapping nonzero entry indices to their counts.

set_value(index, value) → None

Assign a count at an index; zero removes the stored entry. Out-of-range indices raise FingerprintError.

total_value(use_abs=False) → int

Sum stored counts, optionally using their absolute values; native arithmetic errors propagate.

value(index) → int

Return the count at an index; absent entries are zero and out-of-range indices raise FingerprintError.

with_added(other) → SparseCountFingerprint32

Return a new fingerprint with corresponding counts added; both inputs remain unchanged.

with_added_scalar(value) → SparseCountFingerprint32

Return a new fingerprint after adding the scalar using native sparse-vector semantics.

with_divided_scalar(value) → SparseCountFingerprint32

Return a new fingerprint after dividing counts by the scalar; native arithmetic errors propagate.

with_multiplied_scalar(value) → SparseCountFingerprint32

Return a new fingerprint after multiplying counts by the scalar.

with_subtracted(other) → SparseCountFingerprint32

Return a new fingerprint with corresponding counts subtracted; both inputs remain unchanged.

with_subtracted_scalar(value) → SparseCountFingerprint32

Return a new fingerprint after subtracting the scalar using native sparse-vector semantics.

exception cosmolkit.StereoError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

StereoError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (18)
property actual: int | None

Readonly actual payload of the InvalidValence error variant; None for other variants.

property atom: int | None

Readonly atom payload of the InvalidValenceValue error variant; None for other variants.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to StereoError.ConformerAtomCountMismatch, StereoError.InvalidValence. None when this payload is absent.

property atropisomer: AtropisomerError | None

“error_payload”} Structured AtropisomerError payload of StereoError.Atropisomer; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property bond: int | None

Readonly bond payload of the UnknownStereoProperty error variant; None for other variants.

property center: int | None

Readonly center payload of the ZeroLengthVector error variant; None for other variants.

property conformer: int | None

Readonly conformer payload of the ConformerAtomCountMismatch error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property field: str | None

Field whose content or type caused the failure. Applies to StereoError.InvalidValence, StereoError.InvalidValenceValue. None when this payload is absent.

property hydrogen_count: ValenceError | None

“error_payload”} Structured ValenceError payload of StereoError.HydrogenCount; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property id: int | None

Readonly id payload of the DuplicateConformerId error variant; None for other variants.

property neighbor: int | None

Readonly neighbor payload of the ZeroLengthVector error variant; None for other variants.

property requested: int | None

Readonly requested payload of the ConformerNotFound error variant; None for other variants.

property rows: int | None

Readonly rows payload of the ConformerAtomCountMismatch error variant; None for other variants.

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | StereoOrderError | AtomPropertyError | PropertyIntReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: int | None

Readonly value payload of the InvalidValenceValue error variant; None for other variants.

property variant: StereoErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.StereoErrorKind(value)

Discriminants of StereoErrorKind.

Members: Atropisomer, StereoGroup, InvalidTopology, DuplicateConformerId, ConformerNotFound, ConformerAtomCountMismatch, InvalidValence, InvalidValenceValue, ZeroLengthVector, StereoOrder, AtomProperty, HydrogenCount, UnknownStereoProperty, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (16)
AtomProperty = StereoErrorKind.AtomProperty
Atropisomer = StereoErrorKind.Atropisomer
ConformerAtomCountMismatch = StereoErrorKind.ConformerAtomCountMismatch
ConformerNotFound = StereoErrorKind.ConformerNotFound
DuplicateConformerId = StereoErrorKind.DuplicateConformerId
HydrogenCount = StereoErrorKind.HydrogenCount
InvalidTopology = StereoErrorKind.InvalidTopology
InvalidValence = StereoErrorKind.InvalidValence
InvalidValenceValue = StereoErrorKind.InvalidValenceValue
StereoGroup = StereoErrorKind.StereoGroup
StereoOrder = StereoErrorKind.StereoOrder
UnknownStereoProperty = StereoErrorKind.UnknownStereoProperty
ZeroLengthVector = StereoErrorKind.ZeroLengthVector
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Atropisomer': StereoErrorKind.Atropisomer, 'StereoGroup': StereoErrorKind.StereoGroup, 'InvalidTopology': StereoErrorKind.InvalidTopology, 'DuplicateConformerId': StereoErrorKind.DuplicateConformerId, 'ConformerNotFound': StereoErrorKind.ConformerNotFound, 'ConformerAtomCountMismatch': StereoErrorKind.ConformerAtomCountMismatch, 'InvalidValence': StereoErrorKind.InvalidValence, 'InvalidValenceValue': StereoErrorKind.InvalidValenceValue, 'ZeroLengthVector': StereoErrorKind.ZeroLengthVector, 'StereoOrder': StereoErrorKind.StereoOrder, 'AtomProperty': StereoErrorKind.AtomProperty, 'HydrogenCount': StereoErrorKind.HydrogenCount, 'UnknownStereoProperty': StereoErrorKind.UnknownStereoProperty})
values = mappingproxy({0: StereoErrorKind.Atropisomer, 1: StereoErrorKind.StereoGroup, 2: StereoErrorKind.InvalidTopology, 3: StereoErrorKind.DuplicateConformerId, 4: StereoErrorKind.ConformerNotFound, 5: StereoErrorKind.ConformerAtomCountMismatch, 6: StereoErrorKind.InvalidValence, 7: StereoErrorKind.InvalidValenceValue, 8: StereoErrorKind.ZeroLengthVector, 9: StereoErrorKind.StereoOrder, 10: StereoErrorKind.AtomProperty, 11: StereoErrorKind.HydrogenCount, 12: StereoErrorKind.UnknownStereoProperty})
class cosmolkit.StereoGroup(kind, atoms, bonds)

Detached enhanced-stereochemistry group, with member atoms/bonds and source/output identifiers.

Members (8)
atoms: list[int]

Member atom identifiers in retained order.

bonds: list[int]

Member bond identifiers in retained order.

id: int | None

Optional source enhanced-stereo group identifier.

kind: StereoGroupKind

Absolute, OR or AND enhanced-stereochemistry relationship.

static new(kind, atoms, bonds) → StereoGroup

Create an enhanced-stereo group from zero-based atom/bond identifiers, applying native local validation.

with_id(id) → StereoGroup

Return an independent group with the source group identifier replaced.

with_write_id(write_id) → StereoGroup

Return an independent group with the output group identifier replaced.

write_id: int

Group identifier used by output writers.

exception cosmolkit.StereoGroupError(*args, **kwargs)

Failure in the model domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

StereoGroupError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: StereoGroupErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.StereoGroupErrorKind(value)

Discriminants of StereoGroupErrorKind.

Members: DuplicateAtom, DuplicateBond, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
DuplicateAtom = StereoGroupErrorKind.DuplicateAtom
DuplicateBond = StereoGroupErrorKind.DuplicateBond
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'DuplicateAtom': StereoGroupErrorKind.DuplicateAtom, 'DuplicateBond': StereoGroupErrorKind.DuplicateBond})
values = mappingproxy({0: StereoGroupErrorKind.DuplicateAtom, 1: StereoGroupErrorKind.DuplicateBond})
class cosmolkit.StereoGroupKind(value)

Typed StereoGroupKind values corresponding to the Rust enum.

Members: Absolute, Or, And, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
Absolute = StereoGroupKind.Absolute
And = StereoGroupKind.And
Or = StereoGroupKind.Or
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Absolute': StereoGroupKind.Absolute, 'Or': StereoGroupKind.Or, 'And': StereoGroupKind.And})
values = mappingproxy({0: StereoGroupKind.Absolute, 1: StereoGroupKind.Or, 2: StereoGroupKind.And})
class cosmolkit.StereoisomerIterator

Lazy iterator producing stereoisomer molecules while retaining its random source.

Members (2)
next() → Molecule | None

Return the next stereoisomer, or None when enumeration is exhausted.

yielded_count: int

Number of stereoisomers yielded so far.

class cosmolkit.StereoisomerOptions(*, try_embedding=Ellipsis, only_unassigned=Ellipsis, only_stereo_groups=Ellipsis, max_isomers=Ellipsis, unique=Ellipsis, random_source=None)

Editable stereoisomer enumeration options, including filtering and random-source policy.

Members (7)
static default() → StereoisomerOptions

Create options using the native enumeration defaults.

max_isomers: int

Maximum number of isomers to enumerate; zero removes this limit.

only_stereo_groups: bool

Restrict enumeration to centers in enhanced stereochemistry groups.

only_unassigned: bool

Enumerate only stereocenters whose stereochemistry is unspecified.

random_source: StereoisomerRandomSource | None

Random source retained by these options; None selects the native default seed.

try_embedding: bool

Attempt 3D embedding and discard candidates that cannot be embedded.

unique: bool

Remove duplicate stereoisomers from the output.

class cosmolkit.StereoisomerRandomSource

Stateful random-bit source for stereoisomer enumeration, created from a seed or callback.

Members (2)
static from_integer_seed(value) → StereoisomerRandomSource

Create a reproducible random source from an arbitrary-precision integer seed.

static from_random_bits(value) → StereoisomerRandomSource

Use a callback taking the requested bit count and returning a nonnegative integer.

exception cosmolkit.StereoOrderError(*args, **kwargs)

Failure in the stereo_order domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

StereoOrderError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (25)
property actual: int | None

Readonly actual payload of the TooManyLigands error variant; None for other variants.

property atom: int | None

Readonly atom payload of the ConflictingChiralPermutation error variant; None for other variants.

property atom_count: int | None

Readonly atom_count payload of the CenterOutOfRange error variant; None for other variants.

property bond: int | None

Bond identifier implicated in the failure. Applies to StereoOrderError.BondOutOfRange, StereoOrderError.BondNotIncident, StereoOrderError.DuplicateBondLigand, StereoOrderError.RemovedLigand, StereoOrderError.ImplicitReplacementOutOfRange, StereoOrderError.ImplicitReplacementRetained, StereoOrderError.ImplicitReplacementNotInSource. None when this payload is absent.

property bond_count: int | None

Readonly bond_count payload of the BondOutOfRange error variant; None for other variants.

property bond_index: int | None

Readonly bond_index payload of the BondIndexSourceWidth error variant; None for other variants.

property center: int | None

Stereochemical center reported by the native check. Applies to StereoOrderError.CenterOutOfRange, StereoOrderError.BondNotIncident, StereoOrderError.RemovedCenter. None when this payload is absent.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property first: int | None

Readonly first payload of the MultipleImplicitLigands error variant; None for other variants.

property mapped: int | None

Readonly mapped payload of the ImplicitReplacementRetained error variant; None for other variants.

property mapping: MappingValidationError | None

“error_payload”} Structured MappingValidationError payload of StereoOrderError.InvalidMapping; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property maximum: int | None

Readonly maximum payload of the TooManyLigands error variant; None for other variants.

property old_bond_count: int | None

Readonly old_bond_count payload of the ImplicitReplacementOutOfRange error variant; None for other variants.

property position: int | None

Readonly position payload of the DuplicateBondLigand error variant; None for other variants.

property probe: int | None

Readonly probe payload of the PermutationLength error variant; None for other variants.

property raw: int | None

Readonly raw payload of the ConflictingChiralPermutation error variant; None for other variants.

property reference: int | None

Readonly reference payload of the PermutationLength error variant; None for other variants.

property reference_position: int | None

Readonly reference_position payload of the MissingProbeValue error variant; None for other variants.

property second: int | None

Readonly second payload of the MultipleImplicitLigands error variant; None for other variants.

property source: PropertyUIntReadError | AtomPropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property tag: ChiralTag | None

Readonly tag payload of the UnsupportedTetrahedralTag error variant; None for other variants.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of StereoOrderError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property typed: int | None

Readonly typed payload of the ConflictingChiralPermutation error variant; None for other variants.

property variant: StereoOrderErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.StereoOrderErrorKind(value)

Discriminants of StereoOrderErrorKind.

Members: ChiralPermutationRead, ChiralPermutationWrite, ConflictingChiralPermutation, PermutationLength, MissingProbeValue, BondIndexSourceWidth, InvalidTopology, InvalidMapping, CenterOutOfRange, BondOutOfRange, BondNotIncident, TooManyLigands, DuplicateBondLigand, MultipleImplicitLigands, UnsupportedTetrahedralTag, RemovedCenter, RemovedLigand, ImplicitReplacementOutOfRange, ImplicitReplacementRetained, ImplicitReplacementNotInSource, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (23)
BondIndexSourceWidth = StereoOrderErrorKind.BondIndexSourceWidth
BondNotIncident = StereoOrderErrorKind.BondNotIncident
BondOutOfRange = StereoOrderErrorKind.BondOutOfRange
CenterOutOfRange = StereoOrderErrorKind.CenterOutOfRange
ChiralPermutationRead = StereoOrderErrorKind.ChiralPermutationRead
ChiralPermutationWrite = StereoOrderErrorKind.ChiralPermutationWrite
ConflictingChiralPermutation = StereoOrderErrorKind.ConflictingChiralPermutation
DuplicateBondLigand = StereoOrderErrorKind.DuplicateBondLigand
ImplicitReplacementNotInSource = StereoOrderErrorKind.ImplicitReplacementNotInSource
ImplicitReplacementOutOfRange = StereoOrderErrorKind.ImplicitReplacementOutOfRange
ImplicitReplacementRetained = StereoOrderErrorKind.ImplicitReplacementRetained
InvalidMapping = StereoOrderErrorKind.InvalidMapping
InvalidTopology = StereoOrderErrorKind.InvalidTopology
MissingProbeValue = StereoOrderErrorKind.MissingProbeValue
MultipleImplicitLigands = StereoOrderErrorKind.MultipleImplicitLigands
PermutationLength = StereoOrderErrorKind.PermutationLength
RemovedCenter = StereoOrderErrorKind.RemovedCenter
RemovedLigand = StereoOrderErrorKind.RemovedLigand
TooManyLigands = StereoOrderErrorKind.TooManyLigands
UnsupportedTetrahedralTag = StereoOrderErrorKind.UnsupportedTetrahedralTag
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ChiralPermutationRead': StereoOrderErrorKind.ChiralPermutationRead, 'ChiralPermutationWrite': StereoOrderErrorKind.ChiralPermutationWrite, 'ConflictingChiralPermutation': StereoOrderErrorKind.ConflictingChiralPermutation, 'PermutationLength': StereoOrderErrorKind.PermutationLength, 'MissingProbeValue': StereoOrderErrorKind.MissingProbeValue, 'BondIndexSourceWidth': StereoOrderErrorKind.BondIndexSourceWidth, 'InvalidTopology': StereoOrderErrorKind.InvalidTopology, 'InvalidMapping': StereoOrderErrorKind.InvalidMapping, 'CenterOutOfRange': StereoOrderErrorKind.CenterOutOfRange, 'BondOutOfRange': StereoOrderErrorKind.BondOutOfRange, 'BondNotIncident': StereoOrderErrorKind.BondNotIncident, 'TooManyLigands': StereoOrderErrorKind.TooManyLigands, 'DuplicateBondLigand': StereoOrderErrorKind.DuplicateBondLigand, 'MultipleImplicitLigands': StereoOrderErrorKind.MultipleImplicitLigands, 'UnsupportedTetrahedralTag': StereoOrderErrorKind.UnsupportedTetrahedralTag, 'RemovedCenter': StereoOrderErrorKind.RemovedCenter, 'RemovedLigand': StereoOrderErrorKind.RemovedLigand, 'ImplicitReplacementOutOfRange': StereoOrderErrorKind.ImplicitReplacementOutOfRange, 'ImplicitReplacementRetained': StereoOrderErrorKind.ImplicitReplacementRetained, 'ImplicitReplacementNotInSource': StereoOrderErrorKind.ImplicitReplacementNotInSource})
values = mappingproxy({0: StereoOrderErrorKind.ChiralPermutationRead, 1: StereoOrderErrorKind.ChiralPermutationWrite, 2: StereoOrderErrorKind.ConflictingChiralPermutation, 3: StereoOrderErrorKind.PermutationLength, 4: StereoOrderErrorKind.MissingProbeValue, 5: StereoOrderErrorKind.BondIndexSourceWidth, 6: StereoOrderErrorKind.InvalidTopology, 7: StereoOrderErrorKind.InvalidMapping, 8: StereoOrderErrorKind.CenterOutOfRange, 9: StereoOrderErrorKind.BondOutOfRange, 10: StereoOrderErrorKind.BondNotIncident, 11: StereoOrderErrorKind.TooManyLigands, 12: StereoOrderErrorKind.DuplicateBondLigand, 13: StereoOrderErrorKind.MultipleImplicitLigands, 14: StereoOrderErrorKind.UnsupportedTetrahedralTag, 15: StereoOrderErrorKind.RemovedCenter, 16: StereoOrderErrorKind.RemovedLigand, 17: StereoOrderErrorKind.ImplicitReplacementOutOfRange, 18: StereoOrderErrorKind.ImplicitReplacementRetained, 19: StereoOrderErrorKind.ImplicitReplacementNotInSource})
exception cosmolkit.StereoReadError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

StereoReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property atom: int | None

Readonly atom payload of the CipLabelEncoding error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | StereoOrderError | AtomPropertyError | PropertyIntReadError | TemplateAttachmentOrderError | MappingValidationError | PropertyUIntReadError | CanonicalRankError | DoubleBondStereoError | MoleculePropertyError | PotentialStereoError | CipLabelerError | PropertyStringError | FromUtf8Error | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of StereoReadError.InvalidTopology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: StereoReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.StereoReadErrorKind(value)

Discriminants of StereoReadErrorKind.

Members: InvalidTopology, Valence, Rings, PotentialStereo, CipLabeler, PropertyString, CipLabelEncoding, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (10)
CipLabelEncoding = StereoReadErrorKind.CipLabelEncoding
CipLabeler = StereoReadErrorKind.CipLabeler
InvalidTopology = StereoReadErrorKind.InvalidTopology
PotentialStereo = StereoReadErrorKind.PotentialStereo
PropertyString = StereoReadErrorKind.PropertyString
Rings = StereoReadErrorKind.Rings
Valence = StereoReadErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': StereoReadErrorKind.InvalidTopology, 'Valence': StereoReadErrorKind.Valence, 'Rings': StereoReadErrorKind.Rings, 'PotentialStereo': StereoReadErrorKind.PotentialStereo, 'CipLabeler': StereoReadErrorKind.CipLabeler, 'PropertyString': StereoReadErrorKind.PropertyString, 'CipLabelEncoding': StereoReadErrorKind.CipLabelEncoding})
values = mappingproxy({0: StereoReadErrorKind.InvalidTopology, 1: StereoReadErrorKind.Valence, 2: StereoReadErrorKind.Rings, 3: StereoReadErrorKind.PotentialStereo, 4: StereoReadErrorKind.CipLabeler, 5: StereoReadErrorKind.PropertyString, 6: StereoReadErrorKind.CipLabelEncoding})
class cosmolkit.StructureTagParams(*, conformer_id=Ellipsis, replace_existing_tags=Ellipsis)

Conformer selection and overwrite policy for stereochemical tags from coordinates.

Members (2)
conformer_id: int

Native conformer selector; -1 requests the default conformer.

replace_existing_tags: bool

Replace existing stereochemical tags using the selected geometry.

class cosmolkit.SubstanceGroup(id, kind)

Detached substance-group identity, type, crossing-bond and display information.

Members (7)
crossing_bond_correspondence: list[int]

Stored correspondence between crossing bonds.

cstates: list[SGroupCState]

Independent crossing-bond C-state records.

display: SGroupDisplay | None

Detached display settings, or None if absent.

head_crossing_bonds: list[int]

Zero-based identifiers of head crossing bonds.

id: SubstanceGroupId

Identifier of the substance group.

kind: SubstanceGroupKind

Native substance-group classification.

static new(id, kind) → SubstanceGroup

Create an empty substance group with the supplied identifier and kind.

class cosmolkit.SubstanceGroupAtomList(value)

Typed SubstanceGroupAtomList values corresponding to the Rust enum.

Members: Atoms, ParentAtoms, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Atoms = SubstanceGroupAtomList.Atoms
ParentAtoms = SubstanceGroupAtomList.ParentAtoms
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Atoms': SubstanceGroupAtomList.Atoms, 'ParentAtoms': SubstanceGroupAtomList.ParentAtoms})
values = mappingproxy({0: SubstanceGroupAtomList.Atoms, 1: SubstanceGroupAtomList.ParentAtoms})
class cosmolkit.SubstanceGroupId(index)

Local zero-based identifier of a substance group.

Members (2)
index: int

Zero-based substance-group identifier.

static new(index) → SubstanceGroupId

Create a local substance-group identifier from a zero-based index.

class cosmolkit.SubstanceGroupKind

Native substance-group classification, including explicitly named generic groups.

Members (16)
AnyPolymer = <cosmolkit.SubstanceGroupKind object>
Copolymer = <cosmolkit.SubstanceGroupKind object>
Data = <cosmolkit.SubstanceGroupKind object>
Formulation = <cosmolkit.SubstanceGroupKind object>
static Generic(value) → SubstanceGroupKind

Create a substance-group kind with an explicit custom name.

Graft = <cosmolkit.SubstanceGroupKind object>
Mer = <cosmolkit.SubstanceGroupKind object>
Mixture = <cosmolkit.SubstanceGroupKind object>
MixtureComponent = <cosmolkit.SubstanceGroupKind object>
Modification = <cosmolkit.SubstanceGroupKind object>
Monomer = <cosmolkit.SubstanceGroupKind object>
MultipleGroup = <cosmolkit.SubstanceGroupKind object>
StructuralRepeatUnit = <cosmolkit.SubstanceGroupKind object>
Superatom = <cosmolkit.SubstanceGroupKind object>
generic_value: str | None

Custom group name for Generic groups; None for a standard group kind.

exception cosmolkit.SubstructMatchError(*args, **kwargs)

Failure in the search domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SubstructMatchError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (24)
property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to SubstructMatchError.FinalCheckMappingIndex, SubstructMatchError.FinalCheckBondEndpoint. None when this payload is absent.

property begin: int | None

Readonly begin payload of the FinalCheckMissingBond error variant; None for other variants.

property branch: str | None

Readonly branch payload of the Unsupported error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the FinalCheckMissingBond error variant; None for other variants.

property endpoint: str | None

Readonly endpoint payload of the FinalCheckBondEndpoint error variant; None for other variants.

property index: int | None

Index reported by the failing native check. Applies to SubstructMatchError.FinalCheckMappingIndex, SubstructMatchError.FinalCheckBondEndpoint. None when this payload is absent.

property invariant: str | None

Readonly invariant payload of the FinalCheckInvariant error variant; None for other variants.

property periodic_table: PeriodicTableError | None

“error_payload”} Structured PeriodicTableError payload of SubstructMatchError.PeriodicTable; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property position: int | None

Readonly position payload of the FinalCheckMappingIndex error variant; None for other variants.

property property: str | None

Readonly property payload of the PropertyInteger error variant; None for other variants.

property property_string: PropertyStringError | None

“error_payload”} Structured PropertyStringError payload of SubstructMatchError.PropertyString; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property query_atom: int | None

Readonly query_atom payload of the FinalCheckInvariant error variant; None for other variants.

property query_atoms: int | None

Readonly query_atoms payload of the FinalCheckMappingLength error variant; None for other variants.

property query_bond: int | None

Readonly query_bond payload of the FinalCheckMissingBond error variant; None for other variants.

property query_context: QueryMatchContextError | None

“error_payload”} Structured QueryMatchContextError payload of SubstructMatchError.QueryContext; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property query_mapping: int | None

Readonly query_mapping payload of the FinalCheckMappingLength error variant; None for other variants.

property rdkit_function: str | None

Readonly rdkit_function payload of the Unsupported error variant; None for other variants.

property side: str | None

Probe/reference or source/target side identified by the native check. Applies to SubstructMatchError.FinalCheckMappingIndex, SubstructMatchError.FinalCheckBondEndpoint. None when this payload is absent.

property source: PropertyUIntReadError | AtomPropertyError | PropertyIntReadError | TopologyValidationError | RingFindingError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stereo_order: StereoOrderError | None

“error_payload”} Structured StereoOrderError payload of SubstructMatchError.StereoOrder; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property target_mapping: int | None

Readonly target_mapping payload of the FinalCheckMappingLength error variant; None for other variants.

property variant: SubstructMatchErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SubstructMatchErrorKind(value)

Discriminants of SubstructMatchErrorKind.

Members: Unsupported, FinalCheckMappingLength, FinalCheckMappingIndex, FinalCheckInvariant, FinalCheckBondEndpoint, FinalCheckMissingBond, PeriodicTable, StereoOrder, PropertyString, PropertyInteger, QueryContext, UninitializedRecursiveQuery, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (15)
FinalCheckBondEndpoint = SubstructMatchErrorKind.FinalCheckBondEndpoint
FinalCheckInvariant = SubstructMatchErrorKind.FinalCheckInvariant
FinalCheckMappingIndex = SubstructMatchErrorKind.FinalCheckMappingIndex
FinalCheckMappingLength = SubstructMatchErrorKind.FinalCheckMappingLength
FinalCheckMissingBond = SubstructMatchErrorKind.FinalCheckMissingBond
PeriodicTable = SubstructMatchErrorKind.PeriodicTable
PropertyInteger = SubstructMatchErrorKind.PropertyInteger
PropertyString = SubstructMatchErrorKind.PropertyString
QueryContext = SubstructMatchErrorKind.QueryContext
StereoOrder = SubstructMatchErrorKind.StereoOrder
UninitializedRecursiveQuery = SubstructMatchErrorKind.UninitializedRecursiveQuery
Unsupported = SubstructMatchErrorKind.Unsupported
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Unsupported': SubstructMatchErrorKind.Unsupported, 'FinalCheckMappingLength': SubstructMatchErrorKind.FinalCheckMappingLength, 'FinalCheckMappingIndex': SubstructMatchErrorKind.FinalCheckMappingIndex, 'FinalCheckInvariant': SubstructMatchErrorKind.FinalCheckInvariant, 'FinalCheckBondEndpoint': SubstructMatchErrorKind.FinalCheckBondEndpoint, 'FinalCheckMissingBond': SubstructMatchErrorKind.FinalCheckMissingBond, 'PeriodicTable': SubstructMatchErrorKind.PeriodicTable, 'StereoOrder': SubstructMatchErrorKind.StereoOrder, 'PropertyString': SubstructMatchErrorKind.PropertyString, 'PropertyInteger': SubstructMatchErrorKind.PropertyInteger, 'QueryContext': SubstructMatchErrorKind.QueryContext, 'UninitializedRecursiveQuery': SubstructMatchErrorKind.UninitializedRecursiveQuery})
values = mappingproxy({0: SubstructMatchErrorKind.Unsupported, 1: SubstructMatchErrorKind.FinalCheckMappingLength, 2: SubstructMatchErrorKind.FinalCheckMappingIndex, 3: SubstructMatchErrorKind.FinalCheckInvariant, 4: SubstructMatchErrorKind.FinalCheckBondEndpoint, 5: SubstructMatchErrorKind.FinalCheckMissingBond, 6: SubstructMatchErrorKind.PeriodicTable, 7: SubstructMatchErrorKind.StereoOrder, 8: SubstructMatchErrorKind.PropertyString, 9: SubstructMatchErrorKind.PropertyInteger, 10: SubstructMatchErrorKind.QueryContext, 11: SubstructMatchErrorKind.UninitializedRecursiveQuery})
class cosmolkit.SubstructMatchParams(*, max_matches=Ellipsis, uniquify=Ellipsis, use_chirality=Ellipsis, use_enhanced_stereo=Ellipsis, specified_stereo_query_matches_unspecified=Ellipsis, use_query_query_matches=Ellipsis, recursion_possible=Ellipsis, max_recursive_matches=Ellipsis, num_threads=Ellipsis, aromatic_matches_conjugated=Ellipsis, aromatic_matches_single_or_double=Ellipsis, extra_atom_check_overrides_default_check=Ellipsis, extra_bond_check_overrides_default_check=Ellipsis, use_generic_matchers=Ellipsis, atom_properties=None, bond_properties=None, final_match=None, atom_match=None, bond_match=None, extra_final_check=None, extra_atom_check=None, extra_bond_check=None)

Reusable native substructure matching options and typed optional match callbacks.

Members (22)
aromatic_matches_conjugated: bool

Whether aromatic bonds may match conjugated single or double bonds.

aromatic_matches_single_or_double: bool

Whether aromatic bonds may match any single or double bond.

atom_match: collections.abc.Callable[[QueryGraph, QueryAtom, Molecule, Atom], bool] | None

Optional callback(query, query_atom, target, target_atom) accepting an atom pair. query retains the actual query graph, including recursive queries. target is an independent COW Molecule; changes do not affect matching or later callbacks. Atom records are detached; use target.atom(target_atom.id) for contextual reads. Callback exceptions propagate unchanged to the caller.

atom_properties: tuple[str, ...]

Atom property names required to have equal string values; assign the complete field to change it.

bond_match: collections.abc.Callable[[Bond, Bond], bool] | None

Optional callback(query_bond, target_bond) returning whether to accept a bond pair. Receives detached Bond values. Callback exceptions propagate unchanged to the caller.

bond_properties: tuple[str, ...]

Bond property names required to have equal string values; assign the complete field to change it.

extra_atom_check: collections.abc.Callable[[QueryGraph, QueryAtom, Molecule, Atom], bool] | None

Optional callback(query, query_atom, target, target_atom) accepting an atom pair. query retains the actual query graph, including recursive queries. target is an independent COW Molecule; changes do not affect matching or later callbacks. Atom records are detached; use target.atom(target_atom.id) for contextual reads. Callback exceptions propagate unchanged to the caller.

extra_atom_check_overrides_default_check: bool

Whether extra_atom_check replaces the default atom comparison.

extra_bond_check: collections.abc.Callable[[Bond, Bond], bool] | None

Optional callback(query_bond, target_bond) returning whether to accept a bond pair. Receives detached Bond values. Callback exceptions propagate unchanged to the caller.

extra_bond_check_overrides_default_check: bool

Whether extra_bond_check replaces the default bond comparison.

extra_final_check: collections.abc.Callable[[Molecule, collections.abc.Sequence[int]], bool] | None

Optional callback(target, atom_indices) returning whether to accept a complete match. target is an independent COW Molecule value; indices follow query-atom order. Callback exceptions propagate unchanged to the caller.

final_match: collections.abc.Callable[[Molecule, collections.abc.Sequence[int]], bool] | None

Optional callback(target, atom_indices) returning whether to accept a complete match. target is an independent COW Molecule value; indices follow query-atom order. Callback exceptions propagate unchanged to the caller.

max_matches: int

1000).

Type:

Maximum number of matches to return (default

max_recursive_matches: int

Maximum matches used while evaluating recursive query nodes.

num_threads: int

Requested matcher thread count; matching is currently single-threaded.

recursion_possible: bool

Whether recursive query nodes may be evaluated.

specified_stereo_query_matches_unspecified: bool

Whether specified query stereo may match unspecified molecule stereo.

uniquify: bool

true).

Type:

Whether to uniquify results (default

use_chirality: bool

Whether atom/bond stereochemistry participates in matching.

use_enhanced_stereo: bool

Whether enhanced stereo groups participate in final matching.

use_generic_matchers: bool

Whether generic-group labels participate in final matching.

use_query_query_matches: bool

Whether two query atoms are compared as query trees.

class cosmolkit.SupportMatrixEntry

Feature-to-operation link in the generated support matrix.

Members (2)
feature: FeatureSpec

Public feature declaration associated with this matrix entry.

operation: MoleculeOpSpec | None

Associated molecule operation; None when a support entry does not name an operation.

exception cosmolkit.SvgParseError(*args, **kwargs)

Failure in the depict domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

SvgParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property parsing_failed: XmlParseError | None

“error_payload”} Structured XmlParseError payload of SvgParseError.ParsingFailed; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: SvgParseErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.SvgParseErrorKind(value)

Discriminants of SvgParseErrorKind.

Members: NotAnUtf8Str, SvgzFeatureNotEnabled, MalformedGZip, ElementsLimitReached, InvalidSize, ParsingFailed, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
ElementsLimitReached = SvgParseErrorKind.ElementsLimitReached
InvalidSize = SvgParseErrorKind.InvalidSize
MalformedGZip = SvgParseErrorKind.MalformedGZip
NotAnUtf8Str = SvgParseErrorKind.NotAnUtf8Str
ParsingFailed = SvgParseErrorKind.ParsingFailed
SvgzFeatureNotEnabled = SvgParseErrorKind.SvgzFeatureNotEnabled
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NotAnUtf8Str': SvgParseErrorKind.NotAnUtf8Str, 'SvgzFeatureNotEnabled': SvgParseErrorKind.SvgzFeatureNotEnabled, 'MalformedGZip': SvgParseErrorKind.MalformedGZip, 'ElementsLimitReached': SvgParseErrorKind.ElementsLimitReached, 'InvalidSize': SvgParseErrorKind.InvalidSize, 'ParsingFailed': SvgParseErrorKind.ParsingFailed})
values = mappingproxy({0: SvgParseErrorKind.NotAnUtf8Str, 1: SvgParseErrorKind.SvgzFeatureNotEnabled, 2: SvgParseErrorKind.MalformedGZip, 3: SvgParseErrorKind.ElementsLimitReached, 4: SvgParseErrorKind.InvalidSize, 5: SvgParseErrorKind.ParsingFailed})
exception cosmolkit.TautomerCatalogError(*args, **kwargs)

TautomerCatalogError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property index: int | None

Index reported by the failing native check. Applies to TautomerCatalogError.TransformIndexOutOfRange. None when this payload is absent.

property len: int | None

Length reported by the native failure. Applies to TautomerCatalogError.TransformIndexOutOfRange. None when this payload is absent.

property path: pathlib.Path | None

Filesystem path involved in the operation. Applies to TautomerCatalogError.BadInputFile. None when this payload is absent.

property source: IoError | FromUtf8Error | SmartsParseError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property transform: TautomerTransformError | None

“error_payload”} Structured TautomerTransformError payload of TautomerCatalogError.Transform; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: TautomerCatalogErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.TautomerCatalogErrorKind(value)

Discriminants of TautomerCatalogErrorKind.

Members: BadInputFile, BadStreamContents, InvalidUtf8, Transform, TransformIndexOutOfRange, DeserializationUnderConstruction, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
BadInputFile = TautomerCatalogErrorKind.BadInputFile
BadStreamContents = TautomerCatalogErrorKind.BadStreamContents
DeserializationUnderConstruction = TautomerCatalogErrorKind.DeserializationUnderConstruction
InvalidUtf8 = TautomerCatalogErrorKind.InvalidUtf8
Transform = TautomerCatalogErrorKind.Transform
TransformIndexOutOfRange = TautomerCatalogErrorKind.TransformIndexOutOfRange
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'BadInputFile': TautomerCatalogErrorKind.BadInputFile, 'BadStreamContents': TautomerCatalogErrorKind.BadStreamContents, 'InvalidUtf8': TautomerCatalogErrorKind.InvalidUtf8, 'Transform': TautomerCatalogErrorKind.Transform, 'TransformIndexOutOfRange': TautomerCatalogErrorKind.TransformIndexOutOfRange, 'DeserializationUnderConstruction': TautomerCatalogErrorKind.DeserializationUnderConstruction})
values = mappingproxy({0: TautomerCatalogErrorKind.BadInputFile, 1: TautomerCatalogErrorKind.BadStreamContents, 2: TautomerCatalogErrorKind.InvalidUtf8, 3: TautomerCatalogErrorKind.Transform, 4: TautomerCatalogErrorKind.TransformIndexOutOfRange, 5: TautomerCatalogErrorKind.DeserializationUnderConstruction})
class cosmolkit.TautomerEnumeration

Retained tautomer candidates, enumeration status and modification indices; candidate molecules use COW value semantics.

Members (11)
canonical_smiles: list[str]

Canonical SMILES keys in the same order as the retained candidates.

canonical_tautomer(*, max_tautomers: SupportsIndex | None = None, max_transforms: SupportsIndex | None = None, remove_sp3_stereo: bool | None = None, remove_bond_stereo: bool | None = None, remove_isotopic_hydrogens: bool | None = None, reassign_stereo: bool | None = None, callback: collections.abc.Callable[[TautomerMoleculeView, TautomerProgress], bool] | None = None, scorer: collections.abc.Callable[[TautomerMoleculeView], int] | None = None, score_params: TautomerScoreParams | None = None) → Molecule
canonical_tautomer(params: TautomerParams | None = None) → Molecule

Select the canonical tautomer from these candidates using native scoring and tie-breaking; accept parameters or keyword options, not both.

canonical_tautomer_with_params(params) → Molecule

Select the canonical candidate using the supplied scoring configuration.

entries() → collections.abc.Iterator[tuple[str, Molecule]]

Iterate over canonical-SMILES/molecule pairs in retained order, keeping the enumeration alive.

get(index) → Molecule | None

Return the candidate at a zero-based index, or None when out of range; the returned molecule has COW value semantics.

is_empty: bool

Whether enumeration retained no candidates.

iter() → collections.abc.Iterator[Molecule]

Iterate over candidate molecules in retained order, keeping the enumeration alive.

len: int

Number of retained tautomer candidates.

modified_atoms: set[int]

Set of zero-based atom indices modified during enumeration.

modified_bonds: set[int]

Set of zero-based bond indices modified during enumeration.

status: TautomerEnumerationStatus

Enumeration completion reason, including configured limits or cancellation.

class cosmolkit.TautomerEnumerationStatus(value)

Typed TautomerEnumerationStatus values corresponding to the Rust enum.

Members: Completed, MaxTautomersReached, MaxTransformsReached, Canceled, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
Canceled = TautomerEnumerationStatus.Canceled
Completed = TautomerEnumerationStatus.Completed
MaxTautomersReached = TautomerEnumerationStatus.MaxTautomersReached
MaxTransformsReached = TautomerEnumerationStatus.MaxTransformsReached
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Completed': TautomerEnumerationStatus.Completed, 'MaxTautomersReached': TautomerEnumerationStatus.MaxTautomersReached, 'MaxTransformsReached': TautomerEnumerationStatus.MaxTransformsReached, 'Canceled': TautomerEnumerationStatus.Canceled})
values = mappingproxy({0: TautomerEnumerationStatus.Completed, 1: TautomerEnumerationStatus.MaxTautomersReached, 2: TautomerEnumerationStatus.MaxTransformsReached, 3: TautomerEnumerationStatus.Canceled})
class cosmolkit.TautomerMoleculeView

Scoped enumeration molecule view. Call snapshot() during the callback to retain shared native ownership; expired live views raise ReferenceError.

Members (13)
atom(id) → Atom | None

Return a detached atom value by zero-based identifier, or None if absent.

atom_degree(id) → int | None

Return the degree of the requested atom, or None for an absent atom identifier.

atom_metadata() → list[AtomMetadata]

Compute detached valence and hydrogen metadata in atom order.

atoms: list[Atom]

Return detached atom values, not borrowed Python views.

bond(id) → Bond | None

Return a detached bond value by zero-based identifier, or None if absent.

bonds: list[Bond]

Independent detached bond values in stored order.

num_atoms: int

Number of atoms in this molecule view; expired callback views raise ReferenceError.

num_bonds: int

Number of bonds in this molecule view; expired callback views raise ReferenceError.

properties: MoleculeProperties

Copy the detached property value; this is not a zero-copy query.

snapshot() → TautomerMoleculeView

Explicitly own source blocks, or share the actual candidate snapshot.

tautomer_score() → TautomerScore

Evaluate the native tautomer score, allowing its native score-cache updates.

to_owned() → TautomerMoleculeView

Create an owned snapshot that remains accessible after the callback ends.

to_smiles() → str

Write the viewed molecule using the native SMILES writer.

class cosmolkit.TautomerParams(*, max_tautomers=Ellipsis, max_transforms=Ellipsis, remove_sp3_stereo=Ellipsis, remove_bond_stereo=Ellipsis, remove_isotopic_hydrogens=Ellipsis, reassign_stereo=Ellipsis, callback=None, scorer=None, score_params=None)

Reusable tautomer enumeration limits, stereochemistry policy, transform catalogue and scoring callbacks.

Members (27)
callback: collections.abc.Callable[[TautomerMoleculeView, TautomerProgress], bool] | None

Optional enumeration callback receiving source and scoped progress. Return False to cancel; exceptions propagate.

static from_transform_data(data) → TautomerParams

Compile transform rows containing name, SMARTS, bond changes and charge changes.

static from_transform_file(path) → TautomerParams

Load the native tautomer transform catalogue from a file; parsing errors propagate.

max_tautomers: int

Maximum number of retained tautomer candidates.

max_transforms: int

Maximum number of transform applications during enumeration.

reassign_stereo: bool

Reassign stereochemistry after enumeration changes.

remove_bond_stereo: bool

Remove affected double-bond stereochemistry during tautomerization.

remove_isotopic_hydrogens: bool

Remove isotopic hydrogens from affected atoms.

remove_sp3_stereo: bool

Remove tetrahedral stereochemistry at atoms affected by tautomerization.

score_params: TautomerScoreParams

Scoring configuration owned by these parameters; field assignment updates this configuration.

scorer: collections.abc.Callable[[TautomerMoleculeView], int] | None

Optional custom scorer receiving a tautomer view and returning a signed integer score.

set_callback(callback) → None

Replace the enumeration callback, or disable it with None.

set_max_tautomers(value) → None

Set max_tautomers on this configuration. See the corresponding property for its meaning.

set_max_transforms(value) → None

Set max_transforms on this configuration. See the corresponding property for its meaning.

set_reassign_stereo(value) → None

Set reassign_stereo on this configuration. See the corresponding property for its meaning.

set_remove_bond_stereo(value) → None

Set remove_bond_stereo on this configuration. See the corresponding property for its meaning.

set_remove_isotopic_hydrogens(value) → None

Set remove_isotopic_hydrogens on this configuration. See the corresponding property for its meaning.

set_remove_sp3_stereo(value) → None

Set remove_sp3_stereo on this configuration. See the corresponding property for its meaning.

set_scorer(scorer) → None

Replace the custom scorer, or restore native scoring with None.

transform_count: int

Number of transform rules in the retained enumeration catalogue.

static v1() → TautomerParams

Construct configuration using the version-one tautomer transform catalogue.

with_max_tautomers(value) → TautomerParams

Return an independent configuration with max_tautomers replaced, preserving the catalogue and callback owners.

with_max_transforms(value) → TautomerParams

Return an independent configuration with max_transforms replaced, preserving the catalogue and callback owners.

with_reassign_stereo(value) → TautomerParams

Return an independent configuration with reassign_stereo replaced, preserving the catalogue and callback owners.

with_remove_bond_stereo(value) → TautomerParams

Return an independent configuration with remove_bond_stereo replaced, preserving the catalogue and callback owners.

with_remove_isotopic_hydrogens(value) → TautomerParams

Return an independent configuration with remove_isotopic_hydrogens replaced, preserving the catalogue and callback owners.

with_remove_sp3_stereo(value) → TautomerParams

Return an independent configuration with remove_sp3_stereo replaced, preserving the catalogue and callback owners.

class cosmolkit.TautomerProgress

Scoped enumeration progress and candidate access. Explicit snapshots retain a fixed candidate set after the callback returns.

Members (10)
entries() → collections.abc.Iterator[tuple[str, TautomerMoleculeView]]

Iterate over canonical-key/candidate-view pairs; a live callback iterator expires when its callback returns.

entry(index) → tuple[str, TautomerMoleculeView] | None

Return the canonical key and candidate view at an index, or None if absent. A live callback entry expires with its callback.

is_empty: bool

Whether no candidate is currently retained.

len: int

Number of candidates currently retained by the enumeration.

modified_atoms: set[int]

Zero-based identifiers of atoms modified during enumeration.

modified_bonds: set[int]

Zero-based identifiers of bonds modified during enumeration.

num_transforms: int

Number of transform applications performed so far.

snapshot() → TautomerProgress

Retain this candidate set and progress metadata as an owned shared snapshot; subsequent enumeration does not alter it.

status: TautomerEnumerationStatus

Current enumeration completion or stopping status.

to_owned() → TautomerProgress

Create an owned snapshot that remains accessible after the callback ends.

exception cosmolkit.TautomerRunError(*args, **kwargs)

Failure in the tautomer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TautomerRunError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (30)
property actual: int | None

Observed value reported by the native check. Applies to TautomerRunError.AtomMappingCount, TautomerRunError.BondMappingCount, TautomerRunError.AtomCountMismatch, TautomerRunError.BondCountMismatch, TautomerRunError.EditCount. None when this payload is absent.

property atom: int | None

Atom identifier implicated in the failure. Applies to TautomerRunError.AtomOutOfRange, TautomerRunError.HydrogenCountOutOfRange, TautomerRunError.FormalChargeOutOfRange, TautomerRunError.MissingValence. None when this payload is absent.

property atom_count: int | None

Readonly atom_count payload of the AtomOutOfRange error variant; None for other variants.

property atom_property: AtomPropertyError | None

“error_payload”} Structured AtomPropertyError payload of TautomerRunError.AtomProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property bond: int | None

Bond identifier implicated in the failure. Applies to TautomerRunError.BondOutOfRange, TautomerRunError.MissingMappedBond. None when this payload is absent.

property bond_count: int | None

Readonly bond_count payload of the BondOutOfRange error variant; None for other variants.

property bond_value: BondValueError | None

“error_payload”} Structured BondValueError payload of TautomerRunError.BondValue; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property callback: str | None

Native callback failure message, or None for another failure.

property charge: int | None

Readonly charge payload of the FormalChargeOutOfRange error variant; None for other variants.

property control: str | None

Stereo control reference involved in the native check. Applies to TautomerRunError.Control. None when this payload is absent.

property coordinates: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of TautomerRunError.Coordinates; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property count: int | None

Readonly count payload of the HydrogenCountOutOfRange error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Required value reported by the native check. Applies to TautomerRunError.AtomMappingCount, TautomerRunError.BondMappingCount, TautomerRunError.AtomCountMismatch, TautomerRunError.BondCountMismatch, TautomerRunError.EditCount. None when this payload is absent.

property field: str | None

Readonly field payload of the EditCount error variant; None for other variants.

property kekulize: KekulizeError | None

“error_payload”} Structured KekulizeError payload of TautomerRunError.Kekulize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property legacy_stereo: LegacyStereoError | None

“error_payload”} Structured LegacyStereoError payload of TautomerRunError.LegacyStereo; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property match_context: QueryMatchContextError | None

“error_payload”} Structured QueryMatchContextError payload of TautomerRunError.MatchContext; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property match_error: SubstructMatchError | None

“error_payload”} Structured SubstructMatchError payload of TautomerRunError.Match; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property molecule_property: MoleculePropertyError | None

“error_payload”} Structured MoleculePropertyError payload of TautomerRunError.MoleculeProperty; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property property_string: PropertyStringError | None

“error_payload”} Structured PropertyStringError payload of TautomerRunError.PropertyString; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property query_compile: QueryCompileError | None

“error_payload”} Structured QueryCompileError payload of TautomerRunError.QueryCompile; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property rings: RingFindingError | None

“error_payload”} Structured RingFindingError payload of TautomerRunError.Rings; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property sanitize: SanitizeError | None

“error_payload”} Structured SanitizeError payload of TautomerRunError.Sanitize; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property smiles: SmilesParseError | None

“error_payload”} Structured SmilesParseError payload of TautomerRunError.Smiles; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | TopologyEditError | CoordinateValidationError | AtomPropertyError | BondValueError | MoleculePropertyError | PropertyIntReadError | PropertyULongReadError | PropertyUIntReadError | PropertyValueError | RequiredPropertyStringError | PropertyStringError | LegacyStereoError | PotentialStereoError | ParserStereoOrderError | StereoOrderError | SmilesStereoError | AtropisomerError | RingFindingError | ParserCarrierError | KekulizeError | SanitizeError | HydrogenError | ValenceError | ConjugationError | HybridizationError | TopologyValidationError | TemplateAttachmentOrderError | MappingValidationError | CanonicalRankError | DoubleBondStereoError | QueryStateError | CleanupError | PropertyCacheError | RadicalError | AromaticityError | StereoError | AdjustHsError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of TautomerRunError.Topology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property valence: ValenceError | None

“error_payload”} Structured ValenceError payload of TautomerRunError.Valence; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property variant: TautomerRunErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TautomerRunErrorKind(value)

Discriminants of TautomerRunErrorKind.

Members: Smiles, Valence, Rings, Kekulize, Sanitize, LegacyStereo, QueryCompile, Match, MatchContext, Coordinates, Topology, AtomProperty, MoleculeProperty, BondValue, PropertyString, AtomMappingCount, BondMappingCount, AtomCountMismatch, BondCountMismatch, AtomOutOfRange, BondOutOfRange, EmptyTransformMatch, EditCount, HydrogenCountOutOfRange, FormalChargeOutOfRange, MissingMappedBond, MissingValence, NoCanonicalTautomer, SourceCacheCommit, ScoreCacheTargetMismatch, Control, Callback, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (35)
AtomCountMismatch = TautomerRunErrorKind.AtomCountMismatch
AtomMappingCount = TautomerRunErrorKind.AtomMappingCount
AtomOutOfRange = TautomerRunErrorKind.AtomOutOfRange
AtomProperty = TautomerRunErrorKind.AtomProperty
BondCountMismatch = TautomerRunErrorKind.BondCountMismatch
BondMappingCount = TautomerRunErrorKind.BondMappingCount
BondOutOfRange = TautomerRunErrorKind.BondOutOfRange
BondValue = TautomerRunErrorKind.BondValue
Callback = TautomerRunErrorKind.Callback
Control = TautomerRunErrorKind.Control
Coordinates = TautomerRunErrorKind.Coordinates
EditCount = TautomerRunErrorKind.EditCount
EmptyTransformMatch = TautomerRunErrorKind.EmptyTransformMatch
FormalChargeOutOfRange = TautomerRunErrorKind.FormalChargeOutOfRange
HydrogenCountOutOfRange = TautomerRunErrorKind.HydrogenCountOutOfRange
Kekulize = TautomerRunErrorKind.Kekulize
LegacyStereo = TautomerRunErrorKind.LegacyStereo
Match = TautomerRunErrorKind.Match
MatchContext = TautomerRunErrorKind.MatchContext
MissingMappedBond = TautomerRunErrorKind.MissingMappedBond
MissingValence = TautomerRunErrorKind.MissingValence
MoleculeProperty = TautomerRunErrorKind.MoleculeProperty
NoCanonicalTautomer = TautomerRunErrorKind.NoCanonicalTautomer
PropertyString = TautomerRunErrorKind.PropertyString
QueryCompile = TautomerRunErrorKind.QueryCompile
Rings = TautomerRunErrorKind.Rings
Sanitize = TautomerRunErrorKind.Sanitize
ScoreCacheTargetMismatch = TautomerRunErrorKind.ScoreCacheTargetMismatch
Smiles = TautomerRunErrorKind.Smiles
SourceCacheCommit = TautomerRunErrorKind.SourceCacheCommit
Topology = TautomerRunErrorKind.Topology
Valence = TautomerRunErrorKind.Valence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Smiles': TautomerRunErrorKind.Smiles, 'Valence': TautomerRunErrorKind.Valence, 'Rings': TautomerRunErrorKind.Rings, 'Kekulize': TautomerRunErrorKind.Kekulize, 'Sanitize': TautomerRunErrorKind.Sanitize, 'LegacyStereo': TautomerRunErrorKind.LegacyStereo, 'QueryCompile': TautomerRunErrorKind.QueryCompile, 'Match': TautomerRunErrorKind.Match, 'MatchContext': TautomerRunErrorKind.MatchContext, 'Coordinates': TautomerRunErrorKind.Coordinates, 'Topology': TautomerRunErrorKind.Topology, 'AtomProperty': TautomerRunErrorKind.AtomProperty, 'MoleculeProperty': TautomerRunErrorKind.MoleculeProperty, 'BondValue': TautomerRunErrorKind.BondValue, 'PropertyString': TautomerRunErrorKind.PropertyString, 'AtomMappingCount': TautomerRunErrorKind.AtomMappingCount, 'BondMappingCount': TautomerRunErrorKind.BondMappingCount, 'AtomCountMismatch': TautomerRunErrorKind.AtomCountMismatch, 'BondCountMismatch': TautomerRunErrorKind.BondCountMismatch, 'AtomOutOfRange': TautomerRunErrorKind.AtomOutOfRange, 'BondOutOfRange': TautomerRunErrorKind.BondOutOfRange, 'EmptyTransformMatch': TautomerRunErrorKind.EmptyTransformMatch, 'EditCount': TautomerRunErrorKind.EditCount, 'HydrogenCountOutOfRange': TautomerRunErrorKind.HydrogenCountOutOfRange, 'FormalChargeOutOfRange': TautomerRunErrorKind.FormalChargeOutOfRange, 'MissingMappedBond': TautomerRunErrorKind.MissingMappedBond, 'MissingValence': TautomerRunErrorKind.MissingValence, 'NoCanonicalTautomer': TautomerRunErrorKind.NoCanonicalTautomer, 'SourceCacheCommit': TautomerRunErrorKind.SourceCacheCommit, 'ScoreCacheTargetMismatch': TautomerRunErrorKind.ScoreCacheTargetMismatch, 'Control': TautomerRunErrorKind.Control, 'Callback': TautomerRunErrorKind.Callback})
values = mappingproxy({0: TautomerRunErrorKind.Smiles, 1: TautomerRunErrorKind.Valence, 2: TautomerRunErrorKind.Rings, 3: TautomerRunErrorKind.Kekulize, 4: TautomerRunErrorKind.Sanitize, 5: TautomerRunErrorKind.LegacyStereo, 6: TautomerRunErrorKind.QueryCompile, 7: TautomerRunErrorKind.Match, 8: TautomerRunErrorKind.MatchContext, 9: TautomerRunErrorKind.Coordinates, 10: TautomerRunErrorKind.Topology, 11: TautomerRunErrorKind.AtomProperty, 12: TautomerRunErrorKind.MoleculeProperty, 13: TautomerRunErrorKind.BondValue, 14: TautomerRunErrorKind.PropertyString, 15: TautomerRunErrorKind.AtomMappingCount, 16: TautomerRunErrorKind.BondMappingCount, 17: TautomerRunErrorKind.AtomCountMismatch, 18: TautomerRunErrorKind.BondCountMismatch, 19: TautomerRunErrorKind.AtomOutOfRange, 20: TautomerRunErrorKind.BondOutOfRange, 21: TautomerRunErrorKind.EmptyTransformMatch, 22: TautomerRunErrorKind.EditCount, 23: TautomerRunErrorKind.HydrogenCountOutOfRange, 24: TautomerRunErrorKind.FormalChargeOutOfRange, 25: TautomerRunErrorKind.MissingMappedBond, 26: TautomerRunErrorKind.MissingValence, 27: TautomerRunErrorKind.NoCanonicalTautomer, 28: TautomerRunErrorKind.SourceCacheCommit, 29: TautomerRunErrorKind.ScoreCacheTargetMismatch, 30: TautomerRunErrorKind.Control, 31: TautomerRunErrorKind.Callback})
class cosmolkit.TautomerScore

Read-only native tautomer score and its ring, substructure and heteroatom-hydrogen contributions.

Members (4)
hetero_hydrogen: int

Contribution from hydrogens attached to heteroatoms.

ring: int

Contribution from ring scoring.

substructure: int

Contribution from matched substructure scoring terms.

total: int

Sum of all contributions to this tautomer score.

class cosmolkit.TautomerScoreParams(*, terms=Ellipsis)

Terms used by the score query or restricted callback score. None selects the source defaults.

Members (1)
terms: tuple[TautomerScoreTerm, ...] | None

Explicit score terms in evaluation order; None selects the native defaults.

class cosmolkit.TautomerScoreTerm(name, smarts, score)

Named SMARTS pattern and signed weight used by tautomer scoring.

Members (4)
name: str

Human-readable name of the scoring term.

static new(name, smarts, score) → TautomerScoreTerm

Create a named SMARTS scoring term with a signed integer weight.

score: int

Signed integer weight assigned to a match of this term.

smarts: str

SMARTS pattern matched by this scoring term.

exception cosmolkit.TautomerTransformError(*args, **kwargs)

Failure in the tautomer domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TautomerTransformError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property query_compile_error: QueryCompileError | None

“error_payload”} Structured QueryCompileError payload of TautomerTransformError.QueryCompile; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property smarts: str | None

Readonly smarts payload of the CannotParseSmarts error variant; None for other variants.

property source: SmartsParseError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: TautomerTransformErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TautomerTransformErrorKind(value)

Discriminants of TautomerTransformErrorKind.

Members: ChargeSymbolNotRecognised, CannotParseSmarts, QueryCompile, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
CannotParseSmarts = TautomerTransformErrorKind.CannotParseSmarts
ChargeSymbolNotRecognised = TautomerTransformErrorKind.ChargeSymbolNotRecognised
QueryCompile = TautomerTransformErrorKind.QueryCompile
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ChargeSymbolNotRecognised': TautomerTransformErrorKind.ChargeSymbolNotRecognised, 'CannotParseSmarts': TautomerTransformErrorKind.CannotParseSmarts, 'QueryCompile': TautomerTransformErrorKind.QueryCompile})
values = mappingproxy({0: TautomerTransformErrorKind.ChargeSymbolNotRecognised, 1: TautomerTransformErrorKind.CannotParseSmarts, 2: TautomerTransformErrorKind.QueryCompile})
class cosmolkit.TemplateAttachment(target, label)

Named attachment to a target atom.

Members (2)
label: str

Unique attachment label.

target: int

Zero-based target atom identifier for this attachment.

class cosmolkit.TemplateAttachmentOrder(entries)

Ordered, validated set of template attachment targets and labels.

Members (2)
entries: list[TemplateAttachment]

Ordered independent attachment entries.

validate_for_atom_count(atom_count) → None

Check that all attachment targets belong to the specified atom count; raise TemplateAttachmentOrderError on violation.

exception cosmolkit.TemplateAttachmentOrderError(*args, **kwargs)

TemplateAttachmentOrderError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (9)
property atom_count: int | None

Number of atoms available to the operation. Present for TemplateAttachmentOrderError.TargetOutOfRange; None when unavailable.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property duplicate_position: int | None

Position of the duplicate occurrence. Present for TemplateAttachmentOrderError.DuplicateTarget, TemplateAttachmentOrderError.DuplicateLabel; None when unavailable.

property first_position: int | None

Position of the first occurrence. Present for TemplateAttachmentOrderError.DuplicateTarget, TemplateAttachmentOrderError.DuplicateLabel; None when unavailable.

property label: str | None

Attachment-point label associated with the failure. Present for TemplateAttachmentOrderError.DuplicateLabel; None when unavailable.

property mapping_len: int | None

Length of the supplied mapping. Present for TemplateAttachmentOrderError.MappingTargetOutOfRange; None when unavailable.

property position: int | None

Position of the offending entry. Present for TemplateAttachmentOrderError.TargetOutOfRange, TemplateAttachmentOrderError.MappingTargetOutOfRange, TemplateAttachmentOrderError.TargetRemoved; None when unavailable.

property target: int | None

Target atom identifier associated with the failure. Present for TemplateAttachmentOrderError.DuplicateTarget, TemplateAttachmentOrderError.TargetOutOfRange, TemplateAttachmentOrderError.MappingTargetOutOfRange, TemplateAttachmentOrderError.TargetRemoved; None when unavailable.

property variant: TemplateAttachmentOrderErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.TemplateAttachmentOrderErrorKind(value)

Discriminants of TemplateAttachmentOrderErrorKind.

Members: Empty, DuplicateTarget, DuplicateLabel, TargetOutOfRange, MappingTargetOutOfRange, TargetRemoved, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
DuplicateLabel = TemplateAttachmentOrderErrorKind.DuplicateLabel
DuplicateTarget = TemplateAttachmentOrderErrorKind.DuplicateTarget
Empty = TemplateAttachmentOrderErrorKind.Empty
MappingTargetOutOfRange = TemplateAttachmentOrderErrorKind.MappingTargetOutOfRange
TargetOutOfRange = TemplateAttachmentOrderErrorKind.TargetOutOfRange
TargetRemoved = TemplateAttachmentOrderErrorKind.TargetRemoved
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Empty': TemplateAttachmentOrderErrorKind.Empty, 'DuplicateTarget': TemplateAttachmentOrderErrorKind.DuplicateTarget, 'DuplicateLabel': TemplateAttachmentOrderErrorKind.DuplicateLabel, 'TargetOutOfRange': TemplateAttachmentOrderErrorKind.TargetOutOfRange, 'MappingTargetOutOfRange': TemplateAttachmentOrderErrorKind.MappingTargetOutOfRange, 'TargetRemoved': TemplateAttachmentOrderErrorKind.TargetRemoved})
values = mappingproxy({0: TemplateAttachmentOrderErrorKind.Empty, 1: TemplateAttachmentOrderErrorKind.DuplicateTarget, 2: TemplateAttachmentOrderErrorKind.DuplicateLabel, 3: TemplateAttachmentOrderErrorKind.TargetOutOfRange, 4: TemplateAttachmentOrderErrorKind.MappingTargetOutOfRange, 5: TemplateAttachmentOrderErrorKind.TargetRemoved})
class cosmolkit.TetrahedralStereo(center, ligands=None)

Tetrahedral center with an ordered configuration, or None when undetermined.

Members (2)
center: int

Zero-based atom identifier of the tetrahedral center.

ligands: list[LigandRef] | None

Four ordered ligand references, or None for an undetermined configuration.

exception cosmolkit.ThreadCountError(*args, **kwargs)

ThreadCountError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property platform: str | None

Platform associated with native thread selection. Present for ThreadCountError.AutomaticObservationUnavailable; None when unavailable.

property reason: str | None

Native explanation for rejecting the input. Present for ThreadCountError.InvalidCpuList; None when unavailable.

property segment: int | None

CPU-list segment containing the invalid value. Present for ThreadCountError.InvalidCpuList; None when unavailable.

property source: IoError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

property variant: ThreadCountErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.ThreadCountErrorKind(value)

Discriminants of ThreadCountErrorKind.

Members: UndefinedSignedNegation, ObservationIo, InvalidCpuList, AutomaticObservationUnavailable, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
AutomaticObservationUnavailable = ThreadCountErrorKind.AutomaticObservationUnavailable
InvalidCpuList = ThreadCountErrorKind.InvalidCpuList
ObservationIo = ThreadCountErrorKind.ObservationIo
UndefinedSignedNegation = ThreadCountErrorKind.UndefinedSignedNegation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UndefinedSignedNegation': ThreadCountErrorKind.UndefinedSignedNegation, 'ObservationIo': ThreadCountErrorKind.ObservationIo, 'InvalidCpuList': ThreadCountErrorKind.InvalidCpuList, 'AutomaticObservationUnavailable': ThreadCountErrorKind.AutomaticObservationUnavailable})
values = mappingproxy({0: ThreadCountErrorKind.UndefinedSignedNegation, 1: ThreadCountErrorKind.ObservationIo, 2: ThreadCountErrorKind.InvalidCpuList, 3: ThreadCountErrorKind.AutomaticObservationUnavailable})
exception cosmolkit.ThreadSelectionError(*args, **kwargs)

ThreadSelectionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: ThreadCountError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.TopologicalFingerprintError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TopologicalFingerprintError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property field: str | None

Readonly field payload of the OutputNotRequested error variant; None for other variants.

property reason: str | None

Readonly reason payload of the InvalidArguments error variant; None for other variants.

property source: TopologyValidationError | QueryGraphError | LayeredFingerprintError | FingerprintError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: TopologicalFingerprintErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TopologicalFingerprintErrorKind(value)

Discriminants of TopologicalFingerprintErrorKind.

Members: InvalidArguments, OutputNotRequested, Topology, Query, Paths, Value, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
InvalidArguments = TopologicalFingerprintErrorKind.InvalidArguments
OutputNotRequested = TopologicalFingerprintErrorKind.OutputNotRequested
Paths = TopologicalFingerprintErrorKind.Paths
Query = TopologicalFingerprintErrorKind.Query
Topology = TopologicalFingerprintErrorKind.Topology
Value = TopologicalFingerprintErrorKind.Value
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidArguments': TopologicalFingerprintErrorKind.InvalidArguments, 'OutputNotRequested': TopologicalFingerprintErrorKind.OutputNotRequested, 'Topology': TopologicalFingerprintErrorKind.Topology, 'Query': TopologicalFingerprintErrorKind.Query, 'Paths': TopologicalFingerprintErrorKind.Paths, 'Value': TopologicalFingerprintErrorKind.Value})
values = mappingproxy({0: TopologicalFingerprintErrorKind.InvalidArguments, 1: TopologicalFingerprintErrorKind.OutputNotRequested, 2: TopologicalFingerprintErrorKind.Topology, 3: TopologicalFingerprintErrorKind.Query, 4: TopologicalFingerprintErrorKind.Paths, 5: TopologicalFingerprintErrorKind.Value})
class cosmolkit.TopologicalFingerprintOutput(atom_bits, bit_info)

Optional atom-to-bit and bit-to-path provenance collected during a topological fingerprint call.

Members (2)
atom_bits: list[list[int]] | None

Independent per-atom lists of associated fingerprint bits, or None if not collected.

bit_info: dict[int, list[list[int]]] | None

Independent map from fingerprint bit to bond-index paths, or None if not collected.

class cosmolkit.TopologicalFingerprintOutputRequest(*, atom_bits=Ellipsis, bit_info=Ellipsis)

Select which path-to-bit explanations accompany a topological fingerprint.

Members (2)
atom_bits: bool

Collect the fingerprint bits associated with each atom.

bit_info: bool

Collect the bond paths associated with each fingerprint bit.

class cosmolkit.TopologicalFingerprintParams(*, min_path=Ellipsis, max_path=Ellipsis, fp_size=Ellipsis, num_bits_per_feature=Ellipsis, use_hs=Ellipsis, target_density=Ellipsis, min_size=Ellipsis, branched_paths=Ellipsis, use_bond_order=Ellipsis, atom_invariants=Ellipsis, from_atoms=Ellipsis, ignore_atoms=Ellipsis)

Path-based fingerprint settings, including folding and optional atom selection.

Members (12)
atom_invariants: tuple[int, ...] | None

Optional caller-provided atom invariants, indexed by atom position.

branched_paths: bool

Include branched subgraphs instead of restricting enumeration to linear paths.

fp_size: int

Initial fingerprint length in bits, before optional density-based folding.

from_atoms: tuple[int, ...] | None

Optional atom indices from which path enumeration starts.

ignore_atoms: tuple[int, ...] | None

Optional atom indices excluded from path enumeration.

max_path: int

Maximum path length measured in bonds.

min_path: int

Minimum path length measured in bonds.

min_size: int

Minimum fingerprint size allowed during density-based folding.

num_bits_per_feature: int

Number of hash-derived bits set by each path feature.

target_density: float

Requested set-bit density for folding; zero disables density-based folding.

use_bond_order: bool

Distinguish bond orders in path feature hashes.

use_hs: bool

Include explicit hydrogen atoms in paths.

class cosmolkit.TopologicalFingerprintResult(fingerprint, output)

Topological fingerprint together with explicitly requested contribution metadata.

Members (3)
atom_bits: list[list[int]]

Bit identifiers attributed to each atom; raises the native error if this output was not collected.

bit_info: dict[int, list[list[int]]]

Contributing bond paths keyed by fingerprint bit; raises the native error if this output was not collected.

fingerprint: Fingerprint

Generated topological bit fingerprint.

class cosmolkit.TopologicalTorsionCallParams(*, from_atoms=Ellipsis, ignore_atoms=Ellipsis, custom_atom_invariants=Ellipsis, custom_bond_invariants=Ellipsis, use_legacy_stereo_perception=Ellipsis)

Immutable call selections independent of reusable generator configuration.

Members (5)
custom_atom_invariants: tuple[int, ...] | None

Optional per-atom invariant values overriding the atom provider.

custom_bond_invariants: tuple[int, ...] | None

Optional per-bond invariant values supplied to the generator.

from_atoms: tuple[int, ...] | None

Optional atom indices restricting torsion endpoints.

ignore_atoms: tuple[int, ...] | None

Optional atom indices excluded from torsion paths.

use_legacy_stereo_perception: bool

Use legacy stereo perception when preparing the molecule for this call.

exception cosmolkit.TopologicalTorsionError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TopologicalTorsionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: FingerprintError | AtomPairError | PathError | MorganError | FingerprintJsonError | ThreadCountError | IoError | TryReserveError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: TopologicalTorsionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TopologicalTorsionErrorKind(value)

Discriminants of TopologicalTorsionErrorKind.

Members: Fingerprint, AtomInvariants, Path, Preparation, Json, StatePoisoned, ThreadCount, ThreadSpawn, WorkerPanic, WorkerProtocol, OutputAllocation, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (14)
AtomInvariants = TopologicalTorsionErrorKind.AtomInvariants
Fingerprint = TopologicalTorsionErrorKind.Fingerprint
Json = TopologicalTorsionErrorKind.Json
OutputAllocation = TopologicalTorsionErrorKind.OutputAllocation
Path = TopologicalTorsionErrorKind.Path
Preparation = TopologicalTorsionErrorKind.Preparation
StatePoisoned = TopologicalTorsionErrorKind.StatePoisoned
ThreadCount = TopologicalTorsionErrorKind.ThreadCount
ThreadSpawn = TopologicalTorsionErrorKind.ThreadSpawn
WorkerPanic = TopologicalTorsionErrorKind.WorkerPanic
WorkerProtocol = TopologicalTorsionErrorKind.WorkerProtocol
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Fingerprint': TopologicalTorsionErrorKind.Fingerprint, 'AtomInvariants': TopologicalTorsionErrorKind.AtomInvariants, 'Path': TopologicalTorsionErrorKind.Path, 'Preparation': TopologicalTorsionErrorKind.Preparation, 'Json': TopologicalTorsionErrorKind.Json, 'StatePoisoned': TopologicalTorsionErrorKind.StatePoisoned, 'ThreadCount': TopologicalTorsionErrorKind.ThreadCount, 'ThreadSpawn': TopologicalTorsionErrorKind.ThreadSpawn, 'WorkerPanic': TopologicalTorsionErrorKind.WorkerPanic, 'WorkerProtocol': TopologicalTorsionErrorKind.WorkerProtocol, 'OutputAllocation': TopologicalTorsionErrorKind.OutputAllocation})
values = mappingproxy({0: TopologicalTorsionErrorKind.Fingerprint, 1: TopologicalTorsionErrorKind.AtomInvariants, 2: TopologicalTorsionErrorKind.Path, 3: TopologicalTorsionErrorKind.Preparation, 4: TopologicalTorsionErrorKind.Json, 5: TopologicalTorsionErrorKind.StatePoisoned, 6: TopologicalTorsionErrorKind.ThreadCount, 7: TopologicalTorsionErrorKind.ThreadSpawn, 8: TopologicalTorsionErrorKind.WorkerPanic, 9: TopologicalTorsionErrorKind.WorkerProtocol, 10: TopologicalTorsionErrorKind.OutputAllocation})
class cosmolkit.TopologicalTorsionFingerprintGenerator(params=None, atom_invariants=None)

Reusable native TopologicalTorsion fingerprint generator retaining its invariant providers and editable settings.

Members (9)
counts(molecules, num_threads=1) → list[SparseCountFingerprint32 | None]

Compute folded sparse count fingerprints in input order, retaining None entries.

fingerprints(molecules, num_threads=1) → FingerprintBatch

Compute fixed-size bit fingerprints in input order; retain None entries and use the requested native worker count.

static from_json(json) → TopologicalTorsionFingerprintGenerator

Restore generator configuration using the native JSON reader.

info_string() → str

Return the native summary of the generator and invariant-provider settings.

static new(params=None, atom_invariants=None) → TopologicalTorsionFingerprintGenerator

Create a reusable TopologicalTorsion fingerprint generator with native parameter defaults and optional invariant providers.

settings: TopologicalTorsionSettings

Live generator settings; edits affect subsequent calculations, not previously returned fingerprints.

sparse_counts(molecules, num_threads=1) → list[SparseCountFingerprint | None]

Compute unfolded sparse count fingerprints in input order, retaining None entries.

sparse_fingerprints(molecules, num_threads=1) → list[SparseBitFingerprint | None]

Compute sparse bit fingerprints in input order, retaining None entries.

to_json() → str

Serialize the generator configuration in its native JSON format.

class cosmolkit.TopologicalTorsionFingerprintParams(*, torsion_atom_count=Ellipsis, only_shortest_paths=Ellipsis, include_chirality=Ellipsis, count_simulation=Ellipsis, count_bounds=Ellipsis, fp_size=Ellipsis, bits_per_feature=Ellipsis, from_atoms=Ellipsis, ignore_atoms=Ellipsis, custom_atom_invariants=Ellipsis, custom_bond_invariants=Ellipsis, atom_invariants_generator=Ellipsis, use_legacy_stereo_perception=Ellipsis)

Complete reusable fingerprint call configuration, including generator settings and atom selections.

Members (13)
atom_invariants_generator: AtomPairAtomInvariantsGenerator | None

Optional native atom-invariant provider; None uses the generator default.

bits_per_feature: int

Number of hash-derived positions generated for each torsion feature.

count_bounds: tuple[int, ...]

Occurrence thresholds used by count simulation.

count_simulation: bool

Encode occurrence-count thresholds as bits in bit fingerprints.

custom_atom_invariants: tuple[int, ...] | None

Optional per-atom invariant overrides in atom-index order.

custom_bond_invariants: tuple[int, ...] | None

Optional per-bond invariant overrides in bond-index order.

fp_size: int

Number of positions in folded fingerprints.

from_atoms: tuple[int, ...] | None

Optional zero-based atom indices restricting fingerprint contributions.

ignore_atoms: tuple[int, ...] | None

Optional zero-based atom indices excluded from fingerprint generation.

include_chirality: bool

Include atom chirality in torsion identifiers.

only_shortest_paths: bool

Keep only paths that are shortest paths between their endpoints.

torsion_atom_count: int

Number of atoms in each torsion path, normally four.

use_legacy_stereo_perception: bool

Use legacy stereochemistry perception when preparing the fingerprint input.

class cosmolkit.TopologicalTorsionGeneratorParams(*, torsion_atom_count=Ellipsis, only_shortest_paths=Ellipsis, include_chirality=Ellipsis, count_simulation=Ellipsis, count_bounds=Ellipsis, fp_size=Ellipsis, bits_per_feature=Ellipsis)

Topological-torsion fingerprint settings for atom paths and count encoding.

Members (10)
bits_per_feature: int

Number of hash-derived positions generated for each torsion feature.

count_bounds: tuple[int, ...]

Occurrence thresholds used by count simulation.

count_simulation: bool

Encode occurrence-count thresholds as bits in bit fingerprints.

fp_size: int

Number of positions in folded fingerprints.

include_chirality: bool

Include atom chirality in torsion identifiers.

info_string() → str

Return the native human-readable fingerprint generator settings summary.

only_shortest_paths: bool

Keep only paths that are shortest paths between their endpoints.

to_json() → str

Serialize generator parameters with the native JSON format.

torsion_atom_count: int

Number of atoms in each torsion path, normally four.

with_json(json) → TopologicalTorsionGeneratorParams

Return an independent configuration updated by the native JSON parser.

exception cosmolkit.TopologicalTorsionPathScoreError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TopologicalTorsionPathScoreError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (10)
property actual: int | None

Observed count or value. Present for TopologicalTorsionPathScoreError.ShortPath, TopologicalTorsionPathScoreError.ShortAtomCodes; None when unavailable.

property atom_count: int | None

Readonly atom_count payload of the AtomIndexOutOfRange error variant; None for other variants.

property code: int | None

Readonly code payload of the AtomCodeUnderflow error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Index associated with the failure. Present for TopologicalTorsionPathScoreError.AtomIndexOutOfRange, TopologicalTorsionPathScoreError.AtomCodeUnderflow; None when unavailable.

property required: int | None

Required size for the operation. Present for TopologicalTorsionPathScoreError.ShortPath, TopologicalTorsionPathScoreError.ShortAtomCodes; None when unavailable.

property source: TopologyValidationError | AtomCodeError | FingerprintError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property subtract: int | None

Readonly subtract payload of the AtomCodeUnderflow error variant; None for other variants.

property variant: TopologicalTorsionPathScoreErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TopologicalTorsionPathScoreErrorKind(value)

Discriminants of TopologicalTorsionPathScoreErrorKind.

Members: ZeroSize, ShortPath, ShortAtomCodes, AtomIndexOutOfRange, AtomCodeUnderflow, InvalidTopology, AtomCode, PackedCode, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (11)
AtomCode = TopologicalTorsionPathScoreErrorKind.AtomCode
AtomCodeUnderflow = TopologicalTorsionPathScoreErrorKind.AtomCodeUnderflow
AtomIndexOutOfRange = TopologicalTorsionPathScoreErrorKind.AtomIndexOutOfRange
InvalidTopology = TopologicalTorsionPathScoreErrorKind.InvalidTopology
PackedCode = TopologicalTorsionPathScoreErrorKind.PackedCode
ShortAtomCodes = TopologicalTorsionPathScoreErrorKind.ShortAtomCodes
ShortPath = TopologicalTorsionPathScoreErrorKind.ShortPath
ZeroSize = TopologicalTorsionPathScoreErrorKind.ZeroSize
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'ZeroSize': TopologicalTorsionPathScoreErrorKind.ZeroSize, 'ShortPath': TopologicalTorsionPathScoreErrorKind.ShortPath, 'ShortAtomCodes': TopologicalTorsionPathScoreErrorKind.ShortAtomCodes, 'AtomIndexOutOfRange': TopologicalTorsionPathScoreErrorKind.AtomIndexOutOfRange, 'AtomCodeUnderflow': TopologicalTorsionPathScoreErrorKind.AtomCodeUnderflow, 'InvalidTopology': TopologicalTorsionPathScoreErrorKind.InvalidTopology, 'AtomCode': TopologicalTorsionPathScoreErrorKind.AtomCode, 'PackedCode': TopologicalTorsionPathScoreErrorKind.PackedCode})
values = mappingproxy({0: TopologicalTorsionPathScoreErrorKind.ZeroSize, 1: TopologicalTorsionPathScoreErrorKind.ShortPath, 2: TopologicalTorsionPathScoreErrorKind.ShortAtomCodes, 3: TopologicalTorsionPathScoreErrorKind.AtomIndexOutOfRange, 4: TopologicalTorsionPathScoreErrorKind.AtomCodeUnderflow, 5: TopologicalTorsionPathScoreErrorKind.InvalidTopology, 6: TopologicalTorsionPathScoreErrorKind.AtomCode, 7: TopologicalTorsionPathScoreErrorKind.PackedCode})
exception cosmolkit.TopologicalTorsionReadError(*args, **kwargs)

Failure in the fingerprint domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TopologicalTorsionReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: FingerprintPreparationError | TopologicalTorsionError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: TopologicalTorsionReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TopologicalTorsionReadErrorKind(value)

Discriminants of TopologicalTorsionReadErrorKind.

Members: Preparation, Generator, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Generator = TopologicalTorsionReadErrorKind.Generator
Preparation = TopologicalTorsionReadErrorKind.Preparation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Preparation': TopologicalTorsionReadErrorKind.Preparation, 'Generator': TopologicalTorsionReadErrorKind.Generator})
values = mappingproxy({0: TopologicalTorsionReadErrorKind.Preparation, 1: TopologicalTorsionReadErrorKind.Generator})
class cosmolkit.TopologicalTorsionSettings

Live view of generator configuration. Property assignments update the owning generator.

Members (15)
bits_per_feature: int

Number of bits generated per feature.

count_bounds: list[int]

Occurrence thresholds used for count simulation.

count_simulation: bool

Encode occurrence thresholds as count-simulation bits.

fp_size: int

Number of bits in folded bit fingerprints.

include_chirality: bool

Include stereochemistry in atom invariants.

only_shortest_paths: bool

Include only paths whose length is the shortest distance between their endpoints.

params: TopologicalTorsionGeneratorParams

Independent snapshot of the generator parameters; editing it does not change this generator.

set_bits_per_feature(value) → None

Update the generator’s bits_per_feature setting; see the corresponding property for its meaning.

set_count_bounds(value) → None

Update the generator’s count_bounds setting; see the corresponding property for its meaning.

set_count_simulation(value) → None

Update the generator’s count_simulation setting; see the corresponding property for its meaning.

set_fp_size(value) → None

Update the generator’s fp_size setting; see the corresponding property for its meaning.

set_include_chirality(value) → None

Update the generator’s include_chirality setting; see the corresponding property for its meaning.

set_only_shortest_paths(value) → None

Update the generator’s only_shortest_paths setting; see the corresponding property for its meaning.

set_torsion_atom_count(value) → None

Update the generator’s torsion_atom_count setting; see the corresponding property for its meaning.

torsion_atom_count: int

Number of atoms in each torsion path.

class cosmolkit.TopologyBlock

Read-only topology view retaining the molecule’s COW storage. Requested row lists are detached copies.

Members (3)
atoms: list[Atom]

Independent detached atom rows in stored order.

bonds: list[Bond]

Independent detached bond rows in stored order.

substance_groups: list[SubstanceGroup]

Independent copies of the stored substance groups.

exception cosmolkit.TopologyEditError(*args, **kwargs)

Failure in the topology_edit domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TopologyEditError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (22)
property actual: int | None

Readonly actual payload of the PermutationLength error variant; None for other variants.

property atom: int | None

Atom identifier implicated in the failure. Applies to TopologyEditError.AtomOutOfRange, TopologyEditError.PermutationAtomOutOfRange, TopologyEditError.PermutationDuplicateAtom. None when this payload is absent.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to TopologyEditError.AtomOutOfRange, TopologyEditError.PermutationAtomOutOfRange. None when this payload is absent.

property begin: int | None

Readonly begin payload of the DuplicateBond error variant; None for other variants.

property bond: int | None

Bond identifier implicated in the failure. Applies to TopologyEditError.BondOutOfRange, TopologyEditError.BondEndPointsParse. None when this payload is absent.

property bond_count: int | None

Readonly bond_count payload of the BondOutOfRange error variant; None for other variants.

property carrier: int | None

Readonly carrier payload of the TemplateAttachmentRemap error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the DuplicateBond error variant; None for other variants.

property expected: int | None

Readonly expected payload of the PermutationLength error variant; None for other variants.

property group: int | None

Readonly group payload of the SourceGroupParentCycle error variant; None for other variants.

property invalid_bond: BondValueError | None

“error_payload”} Structured BondValueError payload of TopologyEditError.InvalidBond; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property invalid_mapping: MappingValidationError | None

“error_payload”} Structured MappingValidationError payload of TopologyEditError.InvalidMapping; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property invalid_result: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of TopologyEditError.InvalidResult; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property invalid_source: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of TopologyEditError.InvalidSource; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property kind: BondEndPointsParseErrorKind | None

“error_payload”} Native failure-specific category or value kind. Applies to TopologyEditError.BondEndPointsParse. None when this payload is absent.

Type:

{“role”

property position: int | None

Position reported by the native failure. Applies to TopologyEditError.PermutationAtomOutOfRange, TopologyEditError.PermutationDuplicateAtom. None when this payload is absent.

property source: StereoGroupError | CoordinateValidationError | MoleculePropertyError | AtomPropertyError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property token: str | None

Input token rejected by the parser. Applies to TopologyEditError.BondEndPointsParse. None when this payload is absent.

property token_index: int | None

Readonly token_index payload of the BondEndPointsParse error variant; None for other variants.

property variant: TopologyEditErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TopologyEditErrorKind(value)

Discriminants of TopologyEditErrorKind.

Members: StereoGroup, Coordinate, MoleculeProperty, AtomProperty, SourceGroupParentCycle, InvalidSource, AtomOutOfRange, BondOutOfRange, BondEndPointsParse, IncompleteSourceBatchMasks, NullBondAtom, DuplicateBond, InvalidBond, PermutationLength, PermutationAtomOutOfRange, PermutationDuplicateAtom, InvalidMapping, TemplateAttachmentRemap, InvalidResult, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (22)
AtomOutOfRange = TopologyEditErrorKind.AtomOutOfRange
AtomProperty = TopologyEditErrorKind.AtomProperty
BondEndPointsParse = TopologyEditErrorKind.BondEndPointsParse
BondOutOfRange = TopologyEditErrorKind.BondOutOfRange
Coordinate = TopologyEditErrorKind.Coordinate
DuplicateBond = TopologyEditErrorKind.DuplicateBond
IncompleteSourceBatchMasks = TopologyEditErrorKind.IncompleteSourceBatchMasks
InvalidBond = TopologyEditErrorKind.InvalidBond
InvalidMapping = TopologyEditErrorKind.InvalidMapping
InvalidResult = TopologyEditErrorKind.InvalidResult
InvalidSource = TopologyEditErrorKind.InvalidSource
MoleculeProperty = TopologyEditErrorKind.MoleculeProperty
NullBondAtom = TopologyEditErrorKind.NullBondAtom
PermutationAtomOutOfRange = TopologyEditErrorKind.PermutationAtomOutOfRange
PermutationDuplicateAtom = TopologyEditErrorKind.PermutationDuplicateAtom
PermutationLength = TopologyEditErrorKind.PermutationLength
SourceGroupParentCycle = TopologyEditErrorKind.SourceGroupParentCycle
StereoGroup = TopologyEditErrorKind.StereoGroup
TemplateAttachmentRemap = TopologyEditErrorKind.TemplateAttachmentRemap
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': TopologyEditErrorKind.StereoGroup, 'Coordinate': TopologyEditErrorKind.Coordinate, 'MoleculeProperty': TopologyEditErrorKind.MoleculeProperty, 'AtomProperty': TopologyEditErrorKind.AtomProperty, 'SourceGroupParentCycle': TopologyEditErrorKind.SourceGroupParentCycle, 'InvalidSource': TopologyEditErrorKind.InvalidSource, 'AtomOutOfRange': TopologyEditErrorKind.AtomOutOfRange, 'BondOutOfRange': TopologyEditErrorKind.BondOutOfRange, 'BondEndPointsParse': TopologyEditErrorKind.BondEndPointsParse, 'IncompleteSourceBatchMasks': TopologyEditErrorKind.IncompleteSourceBatchMasks, 'NullBondAtom': TopologyEditErrorKind.NullBondAtom, 'DuplicateBond': TopologyEditErrorKind.DuplicateBond, 'InvalidBond': TopologyEditErrorKind.InvalidBond, 'PermutationLength': TopologyEditErrorKind.PermutationLength, 'PermutationAtomOutOfRange': TopologyEditErrorKind.PermutationAtomOutOfRange, 'PermutationDuplicateAtom': TopologyEditErrorKind.PermutationDuplicateAtom, 'InvalidMapping': TopologyEditErrorKind.InvalidMapping, 'TemplateAttachmentRemap': TopologyEditErrorKind.TemplateAttachmentRemap, 'InvalidResult': TopologyEditErrorKind.InvalidResult})
values = mappingproxy({0: TopologyEditErrorKind.StereoGroup, 1: TopologyEditErrorKind.Coordinate, 2: TopologyEditErrorKind.MoleculeProperty, 3: TopologyEditErrorKind.AtomProperty, 4: TopologyEditErrorKind.SourceGroupParentCycle, 5: TopologyEditErrorKind.InvalidSource, 6: TopologyEditErrorKind.AtomOutOfRange, 7: TopologyEditErrorKind.BondOutOfRange, 8: TopologyEditErrorKind.BondEndPointsParse, 9: TopologyEditErrorKind.IncompleteSourceBatchMasks, 10: TopologyEditErrorKind.NullBondAtom, 11: TopologyEditErrorKind.DuplicateBond, 12: TopologyEditErrorKind.InvalidBond, 13: TopologyEditErrorKind.PermutationLength, 14: TopologyEditErrorKind.PermutationAtomOutOfRange, 15: TopologyEditErrorKind.PermutationDuplicateAtom, 16: TopologyEditErrorKind.InvalidMapping, 17: TopologyEditErrorKind.TemplateAttachmentRemap, 18: TopologyEditErrorKind.InvalidResult})
exception cosmolkit.TopologyValidationError(*args, **kwargs)

Failure in the model domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TopologyValidationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (16)
property atom: int | None

Atom index involved in the failure. Present for TopologyValidationError.TemplateAttachmentOrder, TopologyValidationError.BondEndpointOutOfRange, TopologyValidationError.SelfLoopBond, TopologyValidationError.StereoReferenceOutOfRange, TopologyValidationError.SubstanceGroupAtomOutOfRange, TopologyValidationError.StereoGroupAtomOutOfRange; None when unavailable.

property atom_count: int | None

Number of atoms available to the operation. Present for TopologyValidationError.BondEndpointOutOfRange, TopologyValidationError.StereoAtomOutOfRange, TopologyValidationError.StereoReferenceOutOfRange, TopologyValidationError.SubstanceGroupAtomOutOfRange, TopologyValidationError.StereoGroupAtomOutOfRange; None when unavailable.

property begin: int | None

Readonly begin payload of the StereoAtomOutOfRange error variant; None for other variants.

property bond: int | None

Bond index involved in the failure. Present for TopologyValidationError.BondEndpointOutOfRange, TopologyValidationError.SelfLoopBond, TopologyValidationError.StereoAtomOutOfRange, TopologyValidationError.StereoReferenceOutOfRange, TopologyValidationError.StereoAtomsRequired, TopologyValidationError.SubstanceGroupBondOutOfRange, TopologyValidationError.StereoGroupBondOutOfRange; None when unavailable.

property bond_count: int | None

Number of bonds available to the operation. Present for TopologyValidationError.SubstanceGroupBondOutOfRange, TopologyValidationError.StereoGroupBondOutOfRange; None when unavailable.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the StereoAtomOutOfRange error variant; None for other variants.

property endpoint: str | None

Readonly endpoint payload of the BondEndpointOutOfRange error variant; None for other variants.

property id: int | None

Identifier associated with the failed validation. Present for TopologyValidationError.AtomIdMismatch, TopologyValidationError.BondIdMismatch, TopologyValidationError.SubstanceGroupIdMismatch; None when unavailable.

property parent: int | None

Readonly parent payload of the SubstanceGroupParentOutOfRange error variant; None for other variants.

property position: int | None

Position of the offending entry. Present for TopologyValidationError.AtomIdMismatch, TopologyValidationError.BondIdMismatch, TopologyValidationError.SubstanceGroupIdMismatch; None when unavailable.

property sgroup: int | None

Substance-group identifier associated with the failure. Present for TopologyValidationError.SubstanceGroupAtomOutOfRange, TopologyValidationError.SubstanceGroupBondOutOfRange, TopologyValidationError.SubstanceGroupParentOutOfRange; None when unavailable.

property source: StereoGroupError | TemplateAttachmentOrderError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property stereo: BondStereo | None

Readonly stereo payload of the StereoAtomsRequired error variant; None for other variants.

property variant: TopologyValidationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TopologyValidationErrorKind(value)

Discriminants of TopologyValidationErrorKind.

Members: StereoGroup, AtomIdMismatch, TemplateAttachmentOrder, BondIdMismatch, BondEndpointOutOfRange, SelfLoopBond, StereoAtomOutOfRange, StereoReferenceOutOfRange, StereoAtomsRequired, SubstanceGroupIdMismatch, SubstanceGroupAtomOutOfRange, SubstanceGroupBondOutOfRange, SubstanceGroupParentOutOfRange, StereoGroupAtomOutOfRange, StereoGroupBondOutOfRange, AdjacencyMismatch, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (19)
AdjacencyMismatch = TopologyValidationErrorKind.AdjacencyMismatch
AtomIdMismatch = TopologyValidationErrorKind.AtomIdMismatch
BondEndpointOutOfRange = TopologyValidationErrorKind.BondEndpointOutOfRange
BondIdMismatch = TopologyValidationErrorKind.BondIdMismatch
SelfLoopBond = TopologyValidationErrorKind.SelfLoopBond
StereoAtomOutOfRange = TopologyValidationErrorKind.StereoAtomOutOfRange
StereoAtomsRequired = TopologyValidationErrorKind.StereoAtomsRequired
StereoGroup = TopologyValidationErrorKind.StereoGroup
StereoGroupAtomOutOfRange = TopologyValidationErrorKind.StereoGroupAtomOutOfRange
StereoGroupBondOutOfRange = TopologyValidationErrorKind.StereoGroupBondOutOfRange
StereoReferenceOutOfRange = TopologyValidationErrorKind.StereoReferenceOutOfRange
SubstanceGroupAtomOutOfRange = TopologyValidationErrorKind.SubstanceGroupAtomOutOfRange
SubstanceGroupBondOutOfRange = TopologyValidationErrorKind.SubstanceGroupBondOutOfRange
SubstanceGroupIdMismatch = TopologyValidationErrorKind.SubstanceGroupIdMismatch
SubstanceGroupParentOutOfRange = TopologyValidationErrorKind.SubstanceGroupParentOutOfRange
TemplateAttachmentOrder = TopologyValidationErrorKind.TemplateAttachmentOrder
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'StereoGroup': TopologyValidationErrorKind.StereoGroup, 'AtomIdMismatch': TopologyValidationErrorKind.AtomIdMismatch, 'TemplateAttachmentOrder': TopologyValidationErrorKind.TemplateAttachmentOrder, 'BondIdMismatch': TopologyValidationErrorKind.BondIdMismatch, 'BondEndpointOutOfRange': TopologyValidationErrorKind.BondEndpointOutOfRange, 'SelfLoopBond': TopologyValidationErrorKind.SelfLoopBond, 'StereoAtomOutOfRange': TopologyValidationErrorKind.StereoAtomOutOfRange, 'StereoReferenceOutOfRange': TopologyValidationErrorKind.StereoReferenceOutOfRange, 'StereoAtomsRequired': TopologyValidationErrorKind.StereoAtomsRequired, 'SubstanceGroupIdMismatch': TopologyValidationErrorKind.SubstanceGroupIdMismatch, 'SubstanceGroupAtomOutOfRange': TopologyValidationErrorKind.SubstanceGroupAtomOutOfRange, 'SubstanceGroupBondOutOfRange': TopologyValidationErrorKind.SubstanceGroupBondOutOfRange, 'SubstanceGroupParentOutOfRange': TopologyValidationErrorKind.SubstanceGroupParentOutOfRange, 'StereoGroupAtomOutOfRange': TopologyValidationErrorKind.StereoGroupAtomOutOfRange, 'StereoGroupBondOutOfRange': TopologyValidationErrorKind.StereoGroupBondOutOfRange, 'AdjacencyMismatch': TopologyValidationErrorKind.AdjacencyMismatch})
values = mappingproxy({0: TopologyValidationErrorKind.StereoGroup, 1: TopologyValidationErrorKind.AtomIdMismatch, 2: TopologyValidationErrorKind.TemplateAttachmentOrder, 3: TopologyValidationErrorKind.BondIdMismatch, 4: TopologyValidationErrorKind.BondEndpointOutOfRange, 5: TopologyValidationErrorKind.SelfLoopBond, 6: TopologyValidationErrorKind.StereoAtomOutOfRange, 7: TopologyValidationErrorKind.StereoReferenceOutOfRange, 8: TopologyValidationErrorKind.StereoAtomsRequired, 9: TopologyValidationErrorKind.SubstanceGroupIdMismatch, 10: TopologyValidationErrorKind.SubstanceGroupAtomOutOfRange, 11: TopologyValidationErrorKind.SubstanceGroupBondOutOfRange, 12: TopologyValidationErrorKind.SubstanceGroupParentOutOfRange, 13: TopologyValidationErrorKind.StereoGroupAtomOutOfRange, 14: TopologyValidationErrorKind.StereoGroupBondOutOfRange, 15: TopologyValidationErrorKind.AdjacencyMismatch})
exception cosmolkit.TransformError(*args, **kwargs)

Failure in the coordinates domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

TransformError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (23)
property actual: int | None

Readonly actual payload of the WeightCount error variant; None for other variants.

property atom: int | None

Atom index involved in the failure. Present for TransformError.AtomOutOfRange, TransformError.NonFiniteWeight; None when unavailable.

property atom_count: int | None

Readonly atom_count payload of the AtomOutOfRange error variant; None for other variants.

property axis: str | None

Readonly axis payload of the NonFinitePoint error variant; None for other variants.

property bond: int | None

Readonly bond payload of the RingBondNotMovable error variant; None for other variants.

property column: int | None

Readonly column payload of the NonFiniteTransform error variant; None for other variants.

property conformer_id: int | None

Readonly conformer_id payload of the ConformerNotFound error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property first: int | None

Index of the first atom in a disconnected or coincident pair; None otherwise.

property first_bond: int | None

Readonly first_bond payload of the BothAngleBondsInRing error variant; None for other variants.

property first_role: str | None

Role of the first atom in a disconnected or coincident pair; None otherwise.

property quantity: str | None

Readonly quantity payload of the InvalidTargetValue error variant; None for other variants.

property required: int | None

Readonly required payload of the WeightCount error variant; None for other variants.

property role: str | None

Role of the affected reaction template or transformation participant. Present for TransformError.AtomOutOfRange, TransformError.NonFinitePoint; None when unavailable.

property row: int | None

Readonly row payload of the NonFiniteTransform error variant; None for other variants.

property second: int | None

Index of the second atom in a disconnected or coincident pair; None otherwise.

property second_bond: int | None

Readonly second_bond payload of the BothAngleBondsInRing error variant; None for other variants.

property second_role: str | None

Role of the second atom in a disconnected or coincident pair; None otherwise.

property source: TopologyValidationError | CoordinateValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property sum: float | None

Readonly sum payload of the InvalidWeightSum error variant; None for other variants.

property value: float | None

Original value rejected by the operation. Present for TransformError.NonFiniteWeight, TransformError.InvalidTargetValue; None when unavailable.

property variant: TransformErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.TransformErrorKind(value)

Discriminants of TransformErrorKind.

Members: InvalidTopology, InvalidCoordinates, AtomOutOfRange, WeightCount, NonFiniteWeight, InvalidWeightSum, NoSelectedAtoms, NonFinitePoint, NonFiniteTransform, EigenDecompositionDidNotConverge, No3dConformer, ConformerNotFound, AtomsNotBonded, RingBondNotMovable, BothAngleBondsInRing, CoincidentCoordinates, UndefinedRotationAxis, InvalidTargetValue, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (21)
AtomOutOfRange = TransformErrorKind.AtomOutOfRange
AtomsNotBonded = TransformErrorKind.AtomsNotBonded
BothAngleBondsInRing = TransformErrorKind.BothAngleBondsInRing
CoincidentCoordinates = TransformErrorKind.CoincidentCoordinates
ConformerNotFound = TransformErrorKind.ConformerNotFound
EigenDecompositionDidNotConverge = TransformErrorKind.EigenDecompositionDidNotConverge
InvalidCoordinates = TransformErrorKind.InvalidCoordinates
InvalidTargetValue = TransformErrorKind.InvalidTargetValue
InvalidTopology = TransformErrorKind.InvalidTopology
InvalidWeightSum = TransformErrorKind.InvalidWeightSum
No3dConformer = TransformErrorKind.No3dConformer
NoSelectedAtoms = TransformErrorKind.NoSelectedAtoms
NonFinitePoint = TransformErrorKind.NonFinitePoint
NonFiniteTransform = TransformErrorKind.NonFiniteTransform
NonFiniteWeight = TransformErrorKind.NonFiniteWeight
RingBondNotMovable = TransformErrorKind.RingBondNotMovable
UndefinedRotationAxis = TransformErrorKind.UndefinedRotationAxis
WeightCount = TransformErrorKind.WeightCount
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidTopology': TransformErrorKind.InvalidTopology, 'InvalidCoordinates': TransformErrorKind.InvalidCoordinates, 'AtomOutOfRange': TransformErrorKind.AtomOutOfRange, 'WeightCount': TransformErrorKind.WeightCount, 'NonFiniteWeight': TransformErrorKind.NonFiniteWeight, 'InvalidWeightSum': TransformErrorKind.InvalidWeightSum, 'NoSelectedAtoms': TransformErrorKind.NoSelectedAtoms, 'NonFinitePoint': TransformErrorKind.NonFinitePoint, 'NonFiniteTransform': TransformErrorKind.NonFiniteTransform, 'EigenDecompositionDidNotConverge': TransformErrorKind.EigenDecompositionDidNotConverge, 'No3dConformer': TransformErrorKind.No3dConformer, 'ConformerNotFound': TransformErrorKind.ConformerNotFound, 'AtomsNotBonded': TransformErrorKind.AtomsNotBonded, 'RingBondNotMovable': TransformErrorKind.RingBondNotMovable, 'BothAngleBondsInRing': TransformErrorKind.BothAngleBondsInRing, 'CoincidentCoordinates': TransformErrorKind.CoincidentCoordinates, 'UndefinedRotationAxis': TransformErrorKind.UndefinedRotationAxis, 'InvalidTargetValue': TransformErrorKind.InvalidTargetValue})
values = mappingproxy({0: TransformErrorKind.InvalidTopology, 1: TransformErrorKind.InvalidCoordinates, 2: TransformErrorKind.AtomOutOfRange, 3: TransformErrorKind.WeightCount, 4: TransformErrorKind.NonFiniteWeight, 5: TransformErrorKind.InvalidWeightSum, 6: TransformErrorKind.NoSelectedAtoms, 7: TransformErrorKind.NonFinitePoint, 8: TransformErrorKind.NonFiniteTransform, 9: TransformErrorKind.EigenDecompositionDidNotConverge, 10: TransformErrorKind.No3dConformer, 11: TransformErrorKind.ConformerNotFound, 12: TransformErrorKind.AtomsNotBonded, 13: TransformErrorKind.RingBondNotMovable, 14: TransformErrorKind.BothAngleBondsInRing, 15: TransformErrorKind.CoincidentCoordinates, 16: TransformErrorKind.UndefinedRotationAxis, 17: TransformErrorKind.InvalidTargetValue})
exception cosmolkit.TryReserveError(*args, **kwargs)

TryReserveError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (1)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

exception cosmolkit.UffBondMathError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffBondMathError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property bond_order: float | None

Readonly bond_order payload of the InvalidBondOrder error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UffBondMathErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffBondMathErrorKind(value)

Discriminants of UffBondMathErrorKind.

Members: InvalidBondOrder, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
InvalidBondOrder = UffBondMathErrorKind.InvalidBondOrder
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidBondOrder': UffBondMathErrorKind.InvalidBondOrder})
values = mappingproxy({0: UffBondMathErrorKind.InvalidBondOrder})
class cosmolkit.UffBoundsCause

Structured cause of UFF bounds construction failure.

Members (7)
actual: int | None

Observed count or value. Present for UffBoundsCause.AssignmentLength; None when unavailable.

bond_math: UffBondMathError | None

Structured native error payload. Present for UffBoundsCause.BondMath; None when unavailable.

bond_order: ValenceError | None

Structured native error payload. Present for UffBoundsCause.BondOrder; None when unavailable.

expected: int | None

Expected count or value. Present for UffBoundsCause.AssignmentLength; None when unavailable.

field: str | None

Input field associated with the failure. Present for UffBoundsCause.AssignmentLength; None when unavailable.

parameter: UffParameterError | None

Structured native error payload. Present for UffBoundsCause.Parameter; None when unavailable.

variant: UffBoundsCauseKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.UffBoundsCauseKind(value)

Discriminants of UffBoundsCauseKind.

Members: Parameter, BondOrder, BondMath, AssignmentLength, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
AssignmentLength = UffBoundsCauseKind.AssignmentLength
BondMath = UffBoundsCauseKind.BondMath
BondOrder = UffBoundsCauseKind.BondOrder
Parameter = UffBoundsCauseKind.Parameter
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Parameter': UffBoundsCauseKind.Parameter, 'BondOrder': UffBoundsCauseKind.BondOrder, 'BondMath': UffBoundsCauseKind.BondMath, 'AssignmentLength': UffBoundsCauseKind.AssignmentLength})
values = mappingproxy({0: UffBoundsCauseKind.Parameter, 1: UffBoundsCauseKind.BondOrder, 2: UffBoundsCauseKind.BondMath, 3: UffBoundsCauseKind.AssignmentLength})
exception cosmolkit.UffBoundsError(*args, **kwargs)

UffBoundsError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property cause: UffBoundsCause

“error_payload”} Structured UFF bounds-construction failure details.

Type:

{“role”

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: UffParameterError | ValenceError | UffBondMathError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.UffBuilderError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffBuilderError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (25)
property actual: int | Hybridization | None

“error_payload”} Observed value reported by the native check. Applies to UffBuilderError.ValenceAssignmentLengthMismatch, UffBuilderError.SourceTbpHybridizationPrecondition. None when this payload is absent.

Type:

{“role”

property actual_degree: int | None

Readonly actual_degree payload of the SourceTbpDegreePrecondition error variant; None for other variants.

property atom_id: int | None

Atom identifier implicated in the failure. Applies to UffBuilderError.SourceValencePrecondition, UffBuilderError.SourceValenceOutOfRange. None when this payload is absent.

property atom_index: int | None

Atom index involved in the native failure. Applies to UffBuilderError.SourceBondIndexOverflow, UffBuilderError.SourceTorsionIndexOverflow, UffBuilderError.SourceAngleIndexOverflow, UffBuilderError.SourceInversionIndexOverflow. None when this payload is absent.

property atoms: int | None

Atom identifiers implicated in the failure. Applies to UffBuilderError.ParamsLengthMismatch, UffBuilderError.SelectedConformerCoordinateCountMismatch. None when this payload is absent.

property byte_count: int | None

Readonly byte_count payload of the NeighborMatrixAllocationFailed error variant; None for other variants.

property byte_index: int | None

Readonly byte_index payload of the NeighborMatrixStorageOutOfRange error variant; None for other variants.

property center_atom_index: int | None

Atom index of the failing stereochemical center. Applies to UffBuilderError.SourceDirectionVectorBelowTolerance, UffBuilderError.SourceTbpAtomPrecondition, UffBuilderError.SourceTbpHybridizationPrecondition, UffBuilderError.SourceTbpDegreePrecondition, UffBuilderError.SourceTbpAxialBondNotFound, UffBuilderError.SourceTbpEquatorialBondNotFound, UffBuilderError.SourceTbpCenterParamsMissing. None when this payload is absent.

property conformer_id: int | None

Conformer identifier implicated in the failure. Applies to UffBuilderError.SelectedThreeDimensionalConformerNotFound, UffBuilderError.SelectedConformerCoordinateCountMismatch. None when this payload is absent.

property coordinates: int | None

Readonly coordinates payload of the SelectedConformerCoordinateCountMismatch error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the ValenceAssignmentLengthMismatch error variant; None for other variants.

property field: UffPreparedValenceField | None

“error_payload”} Field whose content or type caused the failure. Applies to UffBuilderError.ValenceAssignmentLengthMismatch, UffBuilderError.SourceValencePrecondition, UffBuilderError.SourceValenceOutOfRange. None when this payload is absent.

Type:

{“role”

property i: int | None

Readonly i payload of the NeighborMatrixIndexOutOfRange error variant; None for other variants.

property j: int | None

Readonly j payload of the NeighborMatrixIndexOutOfRange error variant; None for other variants.

property n_atoms: int | None

Atom count used by the failed structural check. Applies to UffBuilderError.NeighborMatrixIndexOutOfRange, UffBuilderError.NeighborMatrixIndexOverflow. None when this payload is absent.

property neighbor_atom_index: int | None

Readonly neighbor_atom_index payload of the SourceDirectionVectorBelowTolerance error variant; None for other variants.

property params: int | None

Readonly params payload of the ParamsLengthMismatch error variant; None for other variants.

property position: int | None

Position reported by the native failure. Applies to UffBuilderError.NeighborMatrixCellPositionOverflow, UffBuilderError.NeighborMatrixStorageOutOfRange. None when this payload is absent.

property role: int | None

Readonly role payload of the SourceTbpEquatorialBondNotFound error variant; None for other variants.

property source: UffTorsionBondQueryError | UffInversionContributionError | ValenceError | ForceFieldKernelError | TopologyValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property storage_len: int | None

Readonly storage_len payload of the NeighborMatrixStorageOutOfRange error variant; None for other variants.

property value: int | None

Value rejected or reported by the native operation. Applies to UffBuilderError.SourceValencePrecondition, UffBuilderError.SourceValenceOutOfRange. None when this payload is absent.

property variant: UffBuilderErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffBuilderErrorKind(value)

Discriminants of UffBuilderErrorKind.

Members: NeighborMatrixIndexOutOfRange, NeighborMatrixIndexOverflow, NeighborMatrixAllocationFailed, NeighborMatrixCellPositionOverflow, NeighborMatrixStorageOutOfRange, ValenceAssignmentLengthMismatch, SourceValencePrecondition, SourceValenceOutOfRange, ParamsLengthMismatch, SelectedThreeDimensionalConformerNotFound, SelectedConformerCoordinateCountMismatch, SourceBondIndexOverflow, SourceTorsionIndexOverflow, SourceAngleIndexOverflow, SourceInversionIndexOverflow, SourceDirectionVectorBelowTolerance, SourceTbpAtomPrecondition, SourceTbpHybridizationPrecondition, SourceTbpDegreePrecondition, SourceTbpAxialBondNotFound, SourceTbpEquatorialBondNotFound, SourceTbpCenterParamsMissing, TorsionBondQuery, InversionContribution, Valence, ForceFieldKernel, TopologyValidation, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (30)
ForceFieldKernel = UffBuilderErrorKind.ForceFieldKernel
InversionContribution = UffBuilderErrorKind.InversionContribution
NeighborMatrixAllocationFailed = UffBuilderErrorKind.NeighborMatrixAllocationFailed
NeighborMatrixCellPositionOverflow = UffBuilderErrorKind.NeighborMatrixCellPositionOverflow
NeighborMatrixIndexOutOfRange = UffBuilderErrorKind.NeighborMatrixIndexOutOfRange
NeighborMatrixIndexOverflow = UffBuilderErrorKind.NeighborMatrixIndexOverflow
NeighborMatrixStorageOutOfRange = UffBuilderErrorKind.NeighborMatrixStorageOutOfRange
ParamsLengthMismatch = UffBuilderErrorKind.ParamsLengthMismatch
SelectedConformerCoordinateCountMismatch = UffBuilderErrorKind.SelectedConformerCoordinateCountMismatch
SelectedThreeDimensionalConformerNotFound = UffBuilderErrorKind.SelectedThreeDimensionalConformerNotFound
SourceAngleIndexOverflow = UffBuilderErrorKind.SourceAngleIndexOverflow
SourceBondIndexOverflow = UffBuilderErrorKind.SourceBondIndexOverflow
SourceDirectionVectorBelowTolerance = UffBuilderErrorKind.SourceDirectionVectorBelowTolerance
SourceInversionIndexOverflow = UffBuilderErrorKind.SourceInversionIndexOverflow
SourceTbpAtomPrecondition = UffBuilderErrorKind.SourceTbpAtomPrecondition
SourceTbpAxialBondNotFound = UffBuilderErrorKind.SourceTbpAxialBondNotFound
SourceTbpCenterParamsMissing = UffBuilderErrorKind.SourceTbpCenterParamsMissing
SourceTbpDegreePrecondition = UffBuilderErrorKind.SourceTbpDegreePrecondition
SourceTbpEquatorialBondNotFound = UffBuilderErrorKind.SourceTbpEquatorialBondNotFound
SourceTbpHybridizationPrecondition = UffBuilderErrorKind.SourceTbpHybridizationPrecondition
SourceTorsionIndexOverflow = UffBuilderErrorKind.SourceTorsionIndexOverflow
SourceValenceOutOfRange = UffBuilderErrorKind.SourceValenceOutOfRange
SourceValencePrecondition = UffBuilderErrorKind.SourceValencePrecondition
TopologyValidation = UffBuilderErrorKind.TopologyValidation
TorsionBondQuery = UffBuilderErrorKind.TorsionBondQuery
Valence = UffBuilderErrorKind.Valence
ValenceAssignmentLengthMismatch = UffBuilderErrorKind.ValenceAssignmentLengthMismatch
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'NeighborMatrixIndexOutOfRange': UffBuilderErrorKind.NeighborMatrixIndexOutOfRange, 'NeighborMatrixIndexOverflow': UffBuilderErrorKind.NeighborMatrixIndexOverflow, 'NeighborMatrixAllocationFailed': UffBuilderErrorKind.NeighborMatrixAllocationFailed, 'NeighborMatrixCellPositionOverflow': UffBuilderErrorKind.NeighborMatrixCellPositionOverflow, 'NeighborMatrixStorageOutOfRange': UffBuilderErrorKind.NeighborMatrixStorageOutOfRange, 'ValenceAssignmentLengthMismatch': UffBuilderErrorKind.ValenceAssignmentLengthMismatch, 'SourceValencePrecondition': UffBuilderErrorKind.SourceValencePrecondition, 'SourceValenceOutOfRange': UffBuilderErrorKind.SourceValenceOutOfRange, 'ParamsLengthMismatch': UffBuilderErrorKind.ParamsLengthMismatch, 'SelectedThreeDimensionalConformerNotFound': UffBuilderErrorKind.SelectedThreeDimensionalConformerNotFound, 'SelectedConformerCoordinateCountMismatch': UffBuilderErrorKind.SelectedConformerCoordinateCountMismatch, 'SourceBondIndexOverflow': UffBuilderErrorKind.SourceBondIndexOverflow, 'SourceTorsionIndexOverflow': UffBuilderErrorKind.SourceTorsionIndexOverflow, 'SourceAngleIndexOverflow': UffBuilderErrorKind.SourceAngleIndexOverflow, 'SourceInversionIndexOverflow': UffBuilderErrorKind.SourceInversionIndexOverflow, 'SourceDirectionVectorBelowTolerance': UffBuilderErrorKind.SourceDirectionVectorBelowTolerance, 'SourceTbpAtomPrecondition': UffBuilderErrorKind.SourceTbpAtomPrecondition, 'SourceTbpHybridizationPrecondition': UffBuilderErrorKind.SourceTbpHybridizationPrecondition, 'SourceTbpDegreePrecondition': UffBuilderErrorKind.SourceTbpDegreePrecondition, 'SourceTbpAxialBondNotFound': UffBuilderErrorKind.SourceTbpAxialBondNotFound, 'SourceTbpEquatorialBondNotFound': UffBuilderErrorKind.SourceTbpEquatorialBondNotFound, 'SourceTbpCenterParamsMissing': UffBuilderErrorKind.SourceTbpCenterParamsMissing, 'TorsionBondQuery': UffBuilderErrorKind.TorsionBondQuery, 'InversionContribution': UffBuilderErrorKind.InversionContribution, 'Valence': UffBuilderErrorKind.Valence, 'ForceFieldKernel': UffBuilderErrorKind.ForceFieldKernel, 'TopologyValidation': UffBuilderErrorKind.TopologyValidation})
values = mappingproxy({0: UffBuilderErrorKind.NeighborMatrixIndexOutOfRange, 1: UffBuilderErrorKind.NeighborMatrixIndexOverflow, 2: UffBuilderErrorKind.NeighborMatrixAllocationFailed, 3: UffBuilderErrorKind.NeighborMatrixCellPositionOverflow, 4: UffBuilderErrorKind.NeighborMatrixStorageOutOfRange, 5: UffBuilderErrorKind.ValenceAssignmentLengthMismatch, 6: UffBuilderErrorKind.SourceValencePrecondition, 7: UffBuilderErrorKind.SourceValenceOutOfRange, 8: UffBuilderErrorKind.ParamsLengthMismatch, 9: UffBuilderErrorKind.SelectedThreeDimensionalConformerNotFound, 10: UffBuilderErrorKind.SelectedConformerCoordinateCountMismatch, 11: UffBuilderErrorKind.SourceBondIndexOverflow, 12: UffBuilderErrorKind.SourceTorsionIndexOverflow, 13: UffBuilderErrorKind.SourceAngleIndexOverflow, 14: UffBuilderErrorKind.SourceInversionIndexOverflow, 15: UffBuilderErrorKind.SourceDirectionVectorBelowTolerance, 16: UffBuilderErrorKind.SourceTbpAtomPrecondition, 17: UffBuilderErrorKind.SourceTbpHybridizationPrecondition, 18: UffBuilderErrorKind.SourceTbpDegreePrecondition, 19: UffBuilderErrorKind.SourceTbpAxialBondNotFound, 20: UffBuilderErrorKind.SourceTbpEquatorialBondNotFound, 21: UffBuilderErrorKind.SourceTbpCenterParamsMissing, 22: UffBuilderErrorKind.TorsionBondQuery, 23: UffBuilderErrorKind.InversionContribution, 24: UffBuilderErrorKind.Valence, 25: UffBuilderErrorKind.ForceFieldKernel, 26: UffBuilderErrorKind.TopologyValidation})
exception cosmolkit.UffConformerError(*args, **kwargs)

UffConformerError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: UffPreparedOptimizationError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.UffConformerOptimizationParams(*, num_threads=Ellipsis, max_iterations=Ellipsis, vdw_threshold=Ellipsis, ignore_interfragment_interactions=Ellipsis)

Options for source-ordered optimization of every stored 3D conformer.

Members (4)
ignore_interfragment_interactions: bool

Omit non-bonded interactions between disconnected molecular fragments.

max_iterations: int

Maximum number of minimizer iterations.

num_threads: int

Native worker count for conformer optimization; zero requests the available hardware thread count.

vdw_threshold: float

Cutoff multiplier relative to the van der Waals contact distance for UFF non-bonded interactions.

class cosmolkit.UffConformerOptimizationResult(molecule, conformers)

UFF multi-conformer optimization result with the output molecule and ordered per-conformer outcomes.

Members (2)
conformer_results: list[UffConformerResult]

Independent list of per-conformer outcomes in native result order.

molecule: Molecule

Output molecule as a copy-on-write value; editing this value does not alter the result.

class cosmolkit.UffConformerResult(conformer_id, outcome)

UFF optimization outcome associated with one conformer identifier.

Members (5)
conformer_id: int

Identifier of the conformer associated with this outcome.

energy: float | None

Evaluated force-field energy; optimization outcomes without parameters return None.

needs_more: bool

Whether the native outcome reports nonconvergence requiring further optimization.

outcome: OptimizationOutcome

Typed optimization outcome retaining both convergence status and optional energy.

status_code: int

Native optimization status code corresponding to the typed outcome.

exception cosmolkit.UffDefaultTorsionQueryError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffDefaultTorsionQueryError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: SmartsParseError | QueryCompileError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UffDefaultTorsionQueryErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffDefaultTorsionQueryErrorKind(value)

Discriminants of UffDefaultTorsionQueryErrorKind.

Members: Parse, Compile, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Compile = UffDefaultTorsionQueryErrorKind.Compile
Parse = UffDefaultTorsionQueryErrorKind.Parse
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Parse': UffDefaultTorsionQueryErrorKind.Parse, 'Compile': UffDefaultTorsionQueryErrorKind.Compile})
values = mappingproxy({0: UffDefaultTorsionQueryErrorKind.Parse, 1: UffDefaultTorsionQueryErrorKind.Compile})
class cosmolkit.UffEnergyGradient(energy, gradient)

Force-field energy and Cartesian gradient at the evaluated coordinates.

Members (2)
energy: float

Evaluated force-field energy; optimization outcomes without parameters return None.

gradient: list[float]

Flat Cartesian energy-gradient components in atom order (x, y, z per atom).

exception cosmolkit.UffEvaluationError(*args, **kwargs)

UffEvaluationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property failure: UffEvaluationFailure

“error_payload”} Structured native UFF evaluation failure.

Type:

{“role”

property source: UffParameterError | AutomaticForceFieldConstructionError | ForceFieldKernelError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.UffEvaluationFailure

Native UFF evaluation failure and variant-specific diagnostic data.

Members (5)
construction: AutomaticForceFieldConstructionError | None

Structured native error payload. Present for UffEvaluationFailure.Construction; None when unavailable.

kernel: ForceFieldKernelError | None

Structured native error payload. Present for UffEvaluationFailure.Kernel; None when unavailable.

preparation: UffParameterError | None

Structured native error payload. Present for UffEvaluationFailure.Preparation; None when unavailable.

requested: int | None

Requested conformer identifier. Present for UffEvaluationFailure.MissingConformer; None when unavailable.

variant: UffEvaluationFailureKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.UffEvaluationFailureKind(value)

Discriminants of UffEvaluationFailureKind.

Members: MissingConformer, Preparation, Construction, Kernel, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
Construction = UffEvaluationFailureKind.Construction
Kernel = UffEvaluationFailureKind.Kernel
MissingConformer = UffEvaluationFailureKind.MissingConformer
Preparation = UffEvaluationFailureKind.Preparation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingConformer': UffEvaluationFailureKind.MissingConformer, 'Preparation': UffEvaluationFailureKind.Preparation, 'Construction': UffEvaluationFailureKind.Construction, 'Kernel': UffEvaluationFailureKind.Kernel})
values = mappingproxy({0: UffEvaluationFailureKind.MissingConformer, 1: UffEvaluationFailureKind.Preparation, 2: UffEvaluationFailureKind.Construction, 3: UffEvaluationFailureKind.Kernel})
class cosmolkit.UffEvaluationParams(*, vdw_threshold=Ellipsis, conformer_id=Ellipsis, ignore_interfragment_interactions=Ellipsis)

UFF energy/gradient evaluation settings for a selected stored conformer.

Members (3)
conformer_id: int | None

Stored 3D conformer identifier, or None for the native default selection.

ignore_interfragment_interactions: bool

Omit non-bonded interactions between disconnected molecular fragments.

vdw_threshold: float

Cutoff multiplier relative to the van der Waals contact distance for UFF non-bonded interactions.

exception cosmolkit.UffForceFieldError(*args, **kwargs)

UffForceFieldError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property kind: MolecularForceFieldErrorKind

Typed native persistent-force-field failure category.

property requested: int | None

Requested conformer identifier when relevant, otherwise None.

property source: ForceFieldError | RingFindingError | OperationError | None

“error_source”} Actual underlying exception, identical to __cause__.

Type:

{“role”

class cosmolkit.UffForceFieldParams(*, conformer_id=Ellipsis, vdw_threshold=Ellipsis, ignore_interfragment_interactions=Ellipsis)

Configuration for constructing a persistent UFF force field over a selected conformer.

Members (3)
conformer_id: int | None

Stored 3D conformer identifier, or None for the native default selection.

ignore_interfragment_interactions: bool

Omit non-bonded interactions between disconnected molecular fragments.

vdw_threshold: float

Cutoff multiplier relative to the van der Waals contact distance for UFF non-bonded interactions.

exception cosmolkit.UffInversionContributionError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffInversionContributionError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (6)
property argument: UffInversionIndexArgument

“error_payload”} Which UFF inversion atom-index argument was out of bounds.

Type:

{“role”

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property index: int | None

Readonly index payload of the IndexOutOfRange error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property upper_bound: int | None

Readonly upper_bound payload of the IndexOutOfRange error variant; None for other variants.

property variant: UffInversionContributionErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffInversionContributionErrorKind(value)

Discriminants of UffInversionContributionErrorKind.

Members: IndexOutOfRange, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
IndexOutOfRange = UffInversionContributionErrorKind.IndexOutOfRange
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'IndexOutOfRange': UffInversionContributionErrorKind.IndexOutOfRange})
values = mappingproxy({0: UffInversionContributionErrorKind.IndexOutOfRange})
class cosmolkit.UffInversionIndexArgument(value)

Typed UffInversionIndexArgument values corresponding to the Rust enum.

Members: First, Second, Third, Fourth, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (7)
First = UffInversionIndexArgument.First
Fourth = UffInversionIndexArgument.Fourth
Second = UffInversionIndexArgument.Second
Third = UffInversionIndexArgument.Third
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'First': UffInversionIndexArgument.First, 'Second': UffInversionIndexArgument.Second, 'Third': UffInversionIndexArgument.Third, 'Fourth': UffInversionIndexArgument.Fourth})
values = mappingproxy({0: UffInversionIndexArgument.First, 1: UffInversionIndexArgument.Second, 2: UffInversionIndexArgument.Third, 3: UffInversionIndexArgument.Fourth})
exception cosmolkit.UffOptimizationError(*args, **kwargs)

UffOptimizationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property kind: UffOptimizationErrorKind

Native UFF optimization failure category.

property source: RingFindingError | UffSingleError | UffConformerError | UffEvaluationError | None

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.UffOptimizationErrorKind

UFF optimization failure category, including an optional requested conformer identifier.

Members (6)
ConformerOptimization = <cosmolkit.UffOptimizationErrorKind object>
Evaluation = <cosmolkit.UffOptimizationErrorKind object>
static MissingConformer(requested) → UffOptimizationErrorKind

Construct a missing-conformer category with the optional requested conformer ID.

Optimization = <cosmolkit.UffOptimizationErrorKind object>
Rings = <cosmolkit.UffOptimizationErrorKind object>
requested: int | None

Requested conformer ID for MissingConformer, or None for unspecified requests and other categories.

class cosmolkit.UffOptimizationParams(*, max_iterations=Ellipsis, vdw_threshold=Ellipsis, ignore_interfragment_interactions=Ellipsis, conformer_id=Ellipsis)

Options matching UFFOptimizeMolecule; None selects the first stored 3D row.

Members (4)
conformer_id: int | None

Stored 3D conformer identifier, or None for the native default selection.

ignore_interfragment_interactions: bool

Omit non-bonded interactions between disconnected molecular fragments.

max_iterations: int

Maximum number of minimizer iterations.

vdw_threshold: float

Cutoff multiplier relative to the van der Waals contact distance for UFF non-bonded interactions.

class cosmolkit.UffOptimizationResult(molecule, outcome)

UFF optimization result containing the output molecule and optimization outcome.

Members (5)
energy: float | None

Evaluated force-field energy; optimization outcomes without parameters return None.

molecule: Molecule

Output molecule as a copy-on-write value; editing this value does not alter the result.

needs_more: bool

Whether the native outcome reports nonconvergence requiring further optimization.

outcome: OptimizationOutcome

Typed optimization outcome retaining both convergence status and optional energy.

status_code: int

Native optimization status code corresponding to the typed outcome.

exception cosmolkit.UffParamError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffParamError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property column_count: int | None

Readonly column_count payload of the MalformedLine error variant; None for other variants.

property column_name: str | None

Readonly column_name payload of the ParseFloat error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property line_number: int

Source line number reported by the parser. Applies to UffParamError.EmptyLine, UffParamError.MalformedLine, UffParamError.ParseFloat.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Readonly value payload of the ParseFloat error variant; None for other variants.

property variant: UffParamErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffParamErrorKind(value)

Discriminants of UffParamErrorKind.

Members: EmptyLine, MalformedLine, ParseFloat, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
EmptyLine = UffParamErrorKind.EmptyLine
MalformedLine = UffParamErrorKind.MalformedLine
ParseFloat = UffParamErrorKind.ParseFloat
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyLine': UffParamErrorKind.EmptyLine, 'MalformedLine': UffParamErrorKind.MalformedLine, 'ParseFloat': UffParamErrorKind.ParseFloat})
values = mappingproxy({0: UffParamErrorKind.EmptyLine, 1: UffParamErrorKind.MalformedLine, 2: UffParamErrorKind.ParseFloat})
exception cosmolkit.UffParameterError(*args, **kwargs)

UffParameterError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property kind: UffParameterErrorKind

Native UFF parameter lookup error category.

property source: UffBuilderError | UffParamError | UffTypingError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

class cosmolkit.UffParameterErrorKind(value)

Typed UffParameterErrorKind values corresponding to the Rust enum.

Members: Preparation, ParameterTable, Typing, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
ParameterTable = UffParameterErrorKind.ParameterTable
Preparation = UffParameterErrorKind.Preparation
Typing = UffParameterErrorKind.Typing
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Preparation': UffParameterErrorKind.Preparation, 'ParameterTable': UffParameterErrorKind.ParameterTable, 'Typing': UffParameterErrorKind.Typing})
values = mappingproxy({0: UffParameterErrorKind.Preparation, 1: UffParameterErrorKind.ParameterTable, 2: UffParameterErrorKind.Typing})
exception cosmolkit.UffParameterQueryError(*args, **kwargs)

Failure in the forcefield domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffParameterQueryError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: OperationError | UffParameterError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UffParameterQueryErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffParameterQueryErrorKind(value)

Discriminants of UffParameterQueryErrorKind.

Members: Cache, Parameters, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Cache = UffParameterQueryErrorKind.Cache
Parameters = UffParameterQueryErrorKind.Parameters
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Cache': UffParameterQueryErrorKind.Cache, 'Parameters': UffParameterQueryErrorKind.Parameters})
values = mappingproxy({0: UffParameterQueryErrorKind.Cache, 1: UffParameterQueryErrorKind.Parameters})
exception cosmolkit.UffPreparedOptimizationError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffPreparedOptimizationError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: UffParameterError | SingleConformerOptimizationError | SerialUffOptimizationError | SerialConformerOptimizationError | DispatchedUffOptimizationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UffPreparedOptimizationErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffPreparedOptimizationErrorKind(value)

Discriminants of UffPreparedOptimizationErrorKind.

Members: Preparation, Single, Serial, ConformerStage, Dispatch, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (8)
ConformerStage = UffPreparedOptimizationErrorKind.ConformerStage
Dispatch = UffPreparedOptimizationErrorKind.Dispatch
Preparation = UffPreparedOptimizationErrorKind.Preparation
Serial = UffPreparedOptimizationErrorKind.Serial
Single = UffPreparedOptimizationErrorKind.Single
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Preparation': UffPreparedOptimizationErrorKind.Preparation, 'Single': UffPreparedOptimizationErrorKind.Single, 'Serial': UffPreparedOptimizationErrorKind.Serial, 'ConformerStage': UffPreparedOptimizationErrorKind.ConformerStage, 'Dispatch': UffPreparedOptimizationErrorKind.Dispatch})
values = mappingproxy({0: UffPreparedOptimizationErrorKind.Preparation, 1: UffPreparedOptimizationErrorKind.Single, 2: UffPreparedOptimizationErrorKind.Serial, 3: UffPreparedOptimizationErrorKind.ConformerStage, 4: UffPreparedOptimizationErrorKind.Dispatch})
class cosmolkit.UffPreparedValenceField(value)

Typed UffPreparedValenceField values corresponding to the Rust enum.

Members: Explicit, ImplicitHydrogen, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
Explicit = UffPreparedValenceField.Explicit
ImplicitHydrogen = UffPreparedValenceField.ImplicitHydrogen
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Explicit': UffPreparedValenceField.Explicit, 'ImplicitHydrogen': UffPreparedValenceField.ImplicitHydrogen})
values = mappingproxy({0: UffPreparedValenceField.Explicit, 1: UffPreparedValenceField.ImplicitHydrogen})
exception cosmolkit.UffSingleError(*args, **kwargs)

UffSingleError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (2)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property source: UffPreparedOptimizationError

“error_source”} Immediate native cause, also available as __cause__; None when the native error has no cause.

Type:

{“role”

exception cosmolkit.UffThreadCountError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffThreadCountError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UffThreadCountErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffThreadCountErrorKind(value)

Discriminants of UffThreadCountErrorKind.

Members: UndefinedSignedNegation, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (4)
UndefinedSignedNegation = UffThreadCountErrorKind.UndefinedSignedNegation
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'UndefinedSignedNegation': UffThreadCountErrorKind.UndefinedSignedNegation})
values = mappingproxy({0: UffThreadCountErrorKind.UndefinedSignedNegation})
exception cosmolkit.UffTorsionBondQueryError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffTorsionBondQueryError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (8)
property actual: int | None

Readonly actual payload of the MatchArity error variant; None for other variants.

property begin_atom_index: int | None

Readonly begin_atom_index payload of the MissingMatchedBond error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end_atom_index: int | None

Readonly end_atom_index payload of the MissingMatchedBond error variant; None for other variants.

property smarts: str | None

Readonly smarts payload of the MatchArity error variant; None for other variants.

property source: UffDefaultTorsionQueryError | SmartsParseError | QueryCompileError | MatchError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UffTorsionBondQueryErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffTorsionBondQueryErrorKind(value)

Discriminants of UffTorsionBondQueryErrorKind.

Members: DefaultQuery, Parse, Compile, Match, MatchArity, MissingMatchedBond, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (9)
Compile = UffTorsionBondQueryErrorKind.Compile
DefaultQuery = UffTorsionBondQueryErrorKind.DefaultQuery
Match = UffTorsionBondQueryErrorKind.Match
MatchArity = UffTorsionBondQueryErrorKind.MatchArity
MissingMatchedBond = UffTorsionBondQueryErrorKind.MissingMatchedBond
Parse = UffTorsionBondQueryErrorKind.Parse
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'DefaultQuery': UffTorsionBondQueryErrorKind.DefaultQuery, 'Parse': UffTorsionBondQueryErrorKind.Parse, 'Compile': UffTorsionBondQueryErrorKind.Compile, 'Match': UffTorsionBondQueryErrorKind.Match, 'MatchArity': UffTorsionBondQueryErrorKind.MatchArity, 'MissingMatchedBond': UffTorsionBondQueryErrorKind.MissingMatchedBond})
values = mappingproxy({0: UffTorsionBondQueryErrorKind.DefaultQuery, 1: UffTorsionBondQueryErrorKind.Parse, 2: UffTorsionBondQueryErrorKind.Compile, 3: UffTorsionBondQueryErrorKind.Match, 4: UffTorsionBondQueryErrorKind.MatchArity, 5: UffTorsionBondQueryErrorKind.MissingMatchedBond})
exception cosmolkit.UffTypingError(*args, **kwargs)

Failure in the uff domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UffTypingError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (15)
property actual: int | None

Readonly actual payload of the PreparedStateLength error variant; None for other variants.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to UffTypingError.AtomIdOutOfBounds, UffTypingError.AtomIndexOutOfBounds. None when this payload is absent.

property atom_id: int | None

Readonly atom_id payload of the AtomIdOutOfBounds error variant; None for other variants.

property atom_index: int | None

Readonly atom_index payload of the CentralParameterSlotMissingAfterSourceSuccess error variant; None for other variants.

property bond_count: int | None

Readonly bond_count payload of the BondIdOutOfBounds error variant; None for other variants.

property bond_id: int | None

Readonly bond_id payload of the BondIdOutOfBounds error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property expected: int | None

Readonly expected payload of the PreparedStateLength error variant; None for other variants.

property idx2: int | None

Readonly idx2 payload of the CenterBondMissingAfterSourceSuccess error variant; None for other variants.

property idx3: int | None

Readonly idx3 payload of the CenterBondMissingAfterSourceSuccess error variant; None for other variants.

property index: int | None

Readonly index payload of the AtomIndexOutOfBounds error variant; None for other variants.

property input: UffTypingInput | None

“error_payload”} Input value rejected by the native parser. Applies to UffTypingError.PreparedStateLength. None when this payload is absent.

Type:

{“role”

property source: ValenceError | PropertyStringError | UffBondMathError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UffTypingErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UffTypingErrorKind(value)

Discriminants of UffTypingErrorKind.

Members: CoreValence, CorePropertyString, BondMath, PreparedStateLength, AtomIdOutOfBounds, AtomIndexOutOfBounds, BondIdOutOfBounds, CenterBondMissingAfterSourceSuccess, CentralParameterSlotMissingAfterSourceSuccess, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
AtomIdOutOfBounds = UffTypingErrorKind.AtomIdOutOfBounds
AtomIndexOutOfBounds = UffTypingErrorKind.AtomIndexOutOfBounds
BondIdOutOfBounds = UffTypingErrorKind.BondIdOutOfBounds
BondMath = UffTypingErrorKind.BondMath
CenterBondMissingAfterSourceSuccess = UffTypingErrorKind.CenterBondMissingAfterSourceSuccess
CentralParameterSlotMissingAfterSourceSuccess = UffTypingErrorKind.CentralParameterSlotMissingAfterSourceSuccess
CorePropertyString = UffTypingErrorKind.CorePropertyString
CoreValence = UffTypingErrorKind.CoreValence
PreparedStateLength = UffTypingErrorKind.PreparedStateLength
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'CoreValence': UffTypingErrorKind.CoreValence, 'CorePropertyString': UffTypingErrorKind.CorePropertyString, 'BondMath': UffTypingErrorKind.BondMath, 'PreparedStateLength': UffTypingErrorKind.PreparedStateLength, 'AtomIdOutOfBounds': UffTypingErrorKind.AtomIdOutOfBounds, 'AtomIndexOutOfBounds': UffTypingErrorKind.AtomIndexOutOfBounds, 'BondIdOutOfBounds': UffTypingErrorKind.BondIdOutOfBounds, 'CenterBondMissingAfterSourceSuccess': UffTypingErrorKind.CenterBondMissingAfterSourceSuccess, 'CentralParameterSlotMissingAfterSourceSuccess': UffTypingErrorKind.CentralParameterSlotMissingAfterSourceSuccess})
values = mappingproxy({0: UffTypingErrorKind.CoreValence, 1: UffTypingErrorKind.CorePropertyString, 2: UffTypingErrorKind.BondMath, 3: UffTypingErrorKind.PreparedStateLength, 4: UffTypingErrorKind.AtomIdOutOfBounds, 5: UffTypingErrorKind.AtomIndexOutOfBounds, 6: UffTypingErrorKind.BondIdOutOfBounds, 7: UffTypingErrorKind.CenterBondMissingAfterSourceSuccess, 8: UffTypingErrorKind.CentralParameterSlotMissingAfterSourceSuccess})
class cosmolkit.UffTypingInput(value)

Typed UffTypingInput values corresponding to the Rust enum.

Members: TotalValence, ConjugatedBondPresence, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (5)
ConjugatedBondPresence = UffTypingInput.ConjugatedBondPresence
TotalValence = UffTypingInput.TotalValence
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'TotalValence': UffTypingInput.TotalValence, 'ConjugatedBondPresence': UffTypingInput.ConjugatedBondPresence})
values = mappingproxy({0: UffTypingInput.TotalValence, 1: UffTypingInput.ConjugatedBondPresence})
exception cosmolkit.UIntLexicalReadError(*args, **kwargs)

Failure in the property domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UIntLexicalReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property byte: int | None

Readonly byte payload of the Character error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property position: int | None

Readonly position payload of the Character error variant; None for other variants.

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UIntLexicalReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UIntLexicalReadErrorKind(value)

Discriminants of UIntLexicalReadErrorKind.

Members: Empty, Character, Overflow, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (6)
Character = UIntLexicalReadErrorKind.Character
Empty = UIntLexicalReadErrorKind.Empty
Overflow = UIntLexicalReadErrorKind.Overflow
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Empty': UIntLexicalReadErrorKind.Empty, 'Character': UIntLexicalReadErrorKind.Character, 'Overflow': UIntLexicalReadErrorKind.Overflow})
values = mappingproxy({0: UIntLexicalReadErrorKind.Empty, 1: UIntLexicalReadErrorKind.Character, 2: UIntLexicalReadErrorKind.Overflow})
exception cosmolkit.UnsignedStreamArrayError(*args, **kwargs)

Failure in the property domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

UnsignedStreamArrayError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (4)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property source: TryReserveError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: UnsignedStreamArrayErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.UnsignedStreamArrayErrorKind(value)

Discriminants of UnsignedStreamArrayErrorKind.

Members: MissingFirstValue, Allocation, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (5)
Allocation = UnsignedStreamArrayErrorKind.Allocation
MissingFirstValue = UnsignedStreamArrayErrorKind.MissingFirstValue
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'MissingFirstValue': UnsignedStreamArrayErrorKind.MissingFirstValue, 'Allocation': UnsignedStreamArrayErrorKind.Allocation})
values = mappingproxy({0: UnsignedStreamArrayErrorKind.MissingFirstValue, 1: UnsignedStreamArrayErrorKind.Allocation})
class cosmolkit.UnsupportedFeatureError

Read-only feature identifier and explanation retained by an unsupported operation.

Members (2)
feature: str

Name of the unsupported capability.

reason: str

Explanation of why the capability is unavailable for this operation.

exception cosmolkit.Utf8Error(*args, **kwargs)

Utf8Error is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (3)
property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property error_len: int | None

Length of the invalid byte sequence; None indicates an incomplete final sequence.

property valid_up_to: int

Number of valid UTF-8 bytes before the first invalid sequence.

exception cosmolkit.ValenceError(*args, **kwargs)

Failure in the valence domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

ValenceError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (25)
property atom: int | None

Atom index involved in the failure. Present for ValenceError.PiElectronExplicitValenceCacheNotInitialized, ValenceError.PiElectronInvariant, ValenceError.InvalidValence, ValenceError.AtomOutOfRange, ValenceError.AdjacencyAtomOutOfRange, ValenceError.AdjacencyBondOutOfRange, ValenceError.AdjacencyEndpointMismatch, ValenceError.InvalidExplicitValenceInput, ValenceError.ExplicitValenceCacheNotInitialized, ValenceError.ImplicitValenceCacheNotInitialized, ValenceError.HydrogenCountOverflow; None when unavailable.

property atom_count: int | None

Atom count used when validating the reported atom reference. Applies to ValenceError.AtomOutOfRange, ValenceError.AdjacencyAtomOutOfRange. None when this payload is absent.

property atomic_number: int | None

Atomic number involved in the failed chemistry operation. Applies to ValenceError.InvalidValence, ValenceError.PeriodicTableLookup. None when this payload is absent.

property begin: int | None

Readonly begin payload of the AdjacencyEndpointMismatch error variant; None for other variants.

property bond: int | None

Bond identifier implicated in the failure. Applies to ValenceError.AdjacencyBondOutOfRange, ValenceError.AdjacencyEndpointMismatch, ValenceError.BadBondType. None when this payload is absent.

property bond_count: int | None

Readonly bond_count payload of the AdjacencyBondOutOfRange error variant; None for other variants.

property calculated: int | None

Readonly calculated payload of the InvalidValence error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property end: int | None

Readonly end payload of the AdjacencyEndpointMismatch error variant; None for other variants.

property explicit: int | None

Readonly explicit payload of the HydrogenCountOverflow error variant; None for other variants.

property explicit_valence: int | None

Readonly explicit_valence payload of the PiElectronInvariant error variant; None for other variants.

property field: str | None

Readonly field payload of the PeriodicTableLookup error variant; None for other variants.

property formal_charge: int | None

Readonly formal_charge payload of the InvalidValence error variant; None for other variants.

property implicit: int | None

Readonly implicit payload of the HydrogenCountOverflow error variant; None for other variants.

property message: str | None

Readonly message payload of the InvalidValence error variant; None for other variants.

property neighbor_atom: int | None

Neighbor atom implicated in the failed topology check. Applies to ValenceError.AdjacencyAtomOutOfRange, ValenceError.AdjacencyEndpointMismatch. None when this payload is absent.

property neighbor_hydrogens: int | None

Readonly neighbor_hydrogens payload of the HydrogenCountOverflow error variant; None for other variants.

property order: BondOrder | None

Readonly order payload of the BadBondType error variant; None for other variants.

property phase: ValencePhase | None

“error_payload”} Processing stage in which the failure occurred. Applies to ValenceError.InvalidValence. None when this payload is absent.

Type:

{“role”

property physical_bonds: int | None

Readonly physical_bonds payload of the PiElectronInvariant error variant; None for other variants.

property reason: str | None

Readonly reason payload of the InvalidValence error variant; None for other variants.

property source: TopologyValidationError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: int | None

Readonly value payload of the InvalidExplicitValenceInput error variant; None for other variants.

property variant: ValenceErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.ValenceErrorKind(value)

Discriminants of ValenceErrorKind.

Members: PiElectronExplicitValenceCacheNotInitialized, PiElectronInvariant, InvalidValence, InvalidTopology, AtomOutOfRange, AdjacencyAtomOutOfRange, AdjacencyBondOutOfRange, AdjacencyEndpointMismatch, InvalidExplicitValenceInput, PeriodicTableLookup, ExplicitValenceCacheNotInitialized, ImplicitValenceCacheNotInitialized, HydrogenCountOverflow, BadBondType, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (17)
AdjacencyAtomOutOfRange = ValenceErrorKind.AdjacencyAtomOutOfRange
AdjacencyBondOutOfRange = ValenceErrorKind.AdjacencyBondOutOfRange
AdjacencyEndpointMismatch = ValenceErrorKind.AdjacencyEndpointMismatch
AtomOutOfRange = ValenceErrorKind.AtomOutOfRange
BadBondType = ValenceErrorKind.BadBondType
ExplicitValenceCacheNotInitialized = ValenceErrorKind.ExplicitValenceCacheNotInitialized
HydrogenCountOverflow = ValenceErrorKind.HydrogenCountOverflow
ImplicitValenceCacheNotInitialized = ValenceErrorKind.ImplicitValenceCacheNotInitialized
InvalidExplicitValenceInput = ValenceErrorKind.InvalidExplicitValenceInput
InvalidTopology = ValenceErrorKind.InvalidTopology
InvalidValence = ValenceErrorKind.InvalidValence
PeriodicTableLookup = ValenceErrorKind.PeriodicTableLookup
PiElectronExplicitValenceCacheNotInitialized = ValenceErrorKind.PiElectronExplicitValenceCacheNotInitialized
PiElectronInvariant = ValenceErrorKind.PiElectronInvariant
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'PiElectronExplicitValenceCacheNotInitialized': ValenceErrorKind.PiElectronExplicitValenceCacheNotInitialized, 'PiElectronInvariant': ValenceErrorKind.PiElectronInvariant, 'InvalidValence': ValenceErrorKind.InvalidValence, 'InvalidTopology': ValenceErrorKind.InvalidTopology, 'AtomOutOfRange': ValenceErrorKind.AtomOutOfRange, 'AdjacencyAtomOutOfRange': ValenceErrorKind.AdjacencyAtomOutOfRange, 'AdjacencyBondOutOfRange': ValenceErrorKind.AdjacencyBondOutOfRange, 'AdjacencyEndpointMismatch': ValenceErrorKind.AdjacencyEndpointMismatch, 'InvalidExplicitValenceInput': ValenceErrorKind.InvalidExplicitValenceInput, 'PeriodicTableLookup': ValenceErrorKind.PeriodicTableLookup, 'ExplicitValenceCacheNotInitialized': ValenceErrorKind.ExplicitValenceCacheNotInitialized, 'ImplicitValenceCacheNotInitialized': ValenceErrorKind.ImplicitValenceCacheNotInitialized, 'HydrogenCountOverflow': ValenceErrorKind.HydrogenCountOverflow, 'BadBondType': ValenceErrorKind.BadBondType})
values = mappingproxy({0: ValenceErrorKind.PiElectronExplicitValenceCacheNotInitialized, 1: ValenceErrorKind.PiElectronInvariant, 2: ValenceErrorKind.InvalidValence, 3: ValenceErrorKind.InvalidTopology, 4: ValenceErrorKind.AtomOutOfRange, 5: ValenceErrorKind.AdjacencyAtomOutOfRange, 6: ValenceErrorKind.AdjacencyBondOutOfRange, 7: ValenceErrorKind.AdjacencyEndpointMismatch, 8: ValenceErrorKind.InvalidExplicitValenceInput, 9: ValenceErrorKind.PeriodicTableLookup, 10: ValenceErrorKind.ExplicitValenceCacheNotInitialized, 11: ValenceErrorKind.ImplicitValenceCacheNotInitialized, 12: ValenceErrorKind.HydrogenCountOverflow, 13: ValenceErrorKind.BadBondType})
class cosmolkit.ValenceModel(value)

Typed ValenceModel values corresponding to the Rust enum.

Members: RdkitLike, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (4)
RdkitLike = ValenceModel.RdkitLike
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'RdkitLike': ValenceModel.RdkitLike})
values = mappingproxy({0: ValenceModel.RdkitLike})
class cosmolkit.ValenceParams(*, model=Ellipsis, strict=Ellipsis)

Valence-assignment model and strictness settings.

Members (2)
model: ValenceModel

Valence-assignment model to use.

strict: bool

Reject invalid valence states according to the native strict valence rules.

class cosmolkit.ValencePhase(value)

Typed ValencePhase values corresponding to the Rust enum.

Members: EffectiveAtomicNumber, Explicit, Implicit, Compare members by value. names and values provide readonly lookups; pickle preserves the type and value. Use the declared constructor signature rather than relying on implicit string conversion.

Members (6)
EffectiveAtomicNumber = ValencePhase.EffectiveAtomicNumber
Explicit = ValencePhase.Explicit
Implicit = ValencePhase.Implicit
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EffectiveAtomicNumber': ValencePhase.EffectiveAtomicNumber, 'Explicit': ValencePhase.Explicit, 'Implicit': ValencePhase.Implicit})
values = mappingproxy({0: ValencePhase.EffectiveAtomicNumber, 1: ValencePhase.Explicit, 2: ValencePhase.Implicit})
exception cosmolkit.WedgeError(*args, **kwargs)

Failure in the stereo domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

WedgeError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (24)
property atom: int | None

Atom identifier implicated in the failure. Applies to WedgeError.SourceSignedScoreOverflow, WedgeError.UnsignedRankOverflow, WedgeError.InvalidStereoRank, WedgeError.InvalidStereoRankType. None when this payload is absent.

property atropisomer: AtropisomerError | None

“error_payload”} Structured AtropisomerError payload of WedgeError.Atropisomer; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property bond: int | None

Bond identifier implicated in the failure. Applies to WedgeError.BondOutOfRange, WedgeError.NonSingleBond, WedgeError.CenterNotIncident. None when this payload is absent.

property bond_count: int | None

Readonly bond_count payload of the BondOutOfRange error variant; None for other variants.

property center: int | None

Stereochemical center reported by the native check. Applies to WedgeError.CenterNotIncident, WedgeError.UnsupportedCenterTag. None when this payload is absent.

property coordinates: CoordinateValidationError | None

“error_payload”} Structured CoordinateValidationError payload of WedgeError.Coordinates; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property count: int | None

Readonly count payload of the SourceStateIndex error variant; None for other variants.

property domain: str

Domain that reported this failure; this does not replace the typed variant.

property geometry: StereoError | None

“error_payload”} Structured StereoError payload of WedgeError.Geometry; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property index: int | None

Index reported by the failing native check. Applies to WedgeError.SourceStateIndex, WedgeError.SourceIndexWidth. None when this payload is absent.

property kind: PropertyValueKind | None

“error_payload”} Native failure-specific category or value kind. Applies to WedgeError.InvalidStereoRankType. None when this payload is absent.

Type:

{“role”

property message: str | None

Readonly message payload of the SourcePrecondition error variant; None for other variants.

property operation: str | None

Readonly operation payload of the SourceSignedScoreOverflow error variant; None for other variants.

property potential_stereo: PotentialStereoError | None

“error_payload”} Structured PotentialStereoError payload of WedgeError.PotentialStereo; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property property: str | None

Property name involved in the failure. Applies to WedgeError.UnsignedRankOverflow, WedgeError.InvalidStereoRank, WedgeError.InvalidStereoRankType. None when this payload is absent.

property ring_finding: RingFindingError | None

“error_payload”} Structured RingFindingError payload of WedgeError.RingFinding; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property source: StereoGroupError | ValenceError | ConjugationError | HybridizationError | RingFindingError | TopologyValidationError | CoordinateValidationError | BondValueError | StereoOrderError | AtomPropertyError | PropertyIntReadError | CanonicalRankError | DoubleBondStereoError | MoleculePropertyError | TemplateAttachmentOrderError | PropertyUIntReadError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property state: str | None

Native wedge-assignment state whose index failed validation; None otherwise.

property stereo_order: StereoOrderError | None

“error_payload”} Structured StereoOrderError payload of WedgeError.StereoOrder; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property tag: ChiralTag | None

Readonly tag payload of the UnsupportedCenterTag error variant; None for other variants.

property topology: TopologyValidationError | None

“error_payload”} Structured TopologyValidationError payload of WedgeError.Topology; None for other variants. Inspect __cause__ separately for the actual exception chain.

Type:

{“role”

property value: int | str | None

Value rejected or reported by the native operation. Applies to WedgeError.UnsignedRankOverflow, WedgeError.InvalidStereoRank. None when this payload is absent.

property variant: WedgeErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.WedgeErrorKind(value)

Discriminants of WedgeErrorKind.

Members: SourcePrecondition, SourceStateIndex, SourceIndexWidth, SourceSignedScoreOverflow, UnsignedRankOverflow, Topology, Coordinates, BondOutOfRange, NonSingleBond, CenterNotIncident, UnsupportedCenterTag, Geometry, StereoOrder, PotentialStereo, RingFinding, Atropisomer, InvalidStereoRank, InvalidStereoRankType, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (21)
Atropisomer = WedgeErrorKind.Atropisomer
BondOutOfRange = WedgeErrorKind.BondOutOfRange
CenterNotIncident = WedgeErrorKind.CenterNotIncident
Coordinates = WedgeErrorKind.Coordinates
Geometry = WedgeErrorKind.Geometry
InvalidStereoRank = WedgeErrorKind.InvalidStereoRank
InvalidStereoRankType = WedgeErrorKind.InvalidStereoRankType
NonSingleBond = WedgeErrorKind.NonSingleBond
PotentialStereo = WedgeErrorKind.PotentialStereo
RingFinding = WedgeErrorKind.RingFinding
SourceIndexWidth = WedgeErrorKind.SourceIndexWidth
SourcePrecondition = WedgeErrorKind.SourcePrecondition
SourceSignedScoreOverflow = WedgeErrorKind.SourceSignedScoreOverflow
SourceStateIndex = WedgeErrorKind.SourceStateIndex
StereoOrder = WedgeErrorKind.StereoOrder
Topology = WedgeErrorKind.Topology
UnsignedRankOverflow = WedgeErrorKind.UnsignedRankOverflow
UnsupportedCenterTag = WedgeErrorKind.UnsupportedCenterTag
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'SourcePrecondition': WedgeErrorKind.SourcePrecondition, 'SourceStateIndex': WedgeErrorKind.SourceStateIndex, 'SourceIndexWidth': WedgeErrorKind.SourceIndexWidth, 'SourceSignedScoreOverflow': WedgeErrorKind.SourceSignedScoreOverflow, 'UnsignedRankOverflow': WedgeErrorKind.UnsignedRankOverflow, 'Topology': WedgeErrorKind.Topology, 'Coordinates': WedgeErrorKind.Coordinates, 'BondOutOfRange': WedgeErrorKind.BondOutOfRange, 'NonSingleBond': WedgeErrorKind.NonSingleBond, 'CenterNotIncident': WedgeErrorKind.CenterNotIncident, 'UnsupportedCenterTag': WedgeErrorKind.UnsupportedCenterTag, 'Geometry': WedgeErrorKind.Geometry, 'StereoOrder': WedgeErrorKind.StereoOrder, 'PotentialStereo': WedgeErrorKind.PotentialStereo, 'RingFinding': WedgeErrorKind.RingFinding, 'Atropisomer': WedgeErrorKind.Atropisomer, 'InvalidStereoRank': WedgeErrorKind.InvalidStereoRank, 'InvalidStereoRankType': WedgeErrorKind.InvalidStereoRankType})
values = mappingproxy({0: WedgeErrorKind.SourcePrecondition, 1: WedgeErrorKind.SourceStateIndex, 2: WedgeErrorKind.SourceIndexWidth, 3: WedgeErrorKind.SourceSignedScoreOverflow, 4: WedgeErrorKind.UnsignedRankOverflow, 5: WedgeErrorKind.Topology, 6: WedgeErrorKind.Coordinates, 7: WedgeErrorKind.BondOutOfRange, 8: WedgeErrorKind.NonSingleBond, 9: WedgeErrorKind.CenterNotIncident, 10: WedgeErrorKind.UnsupportedCenterTag, 11: WedgeErrorKind.Geometry, 12: WedgeErrorKind.StereoOrder, 13: WedgeErrorKind.PotentialStereo, 14: WedgeErrorKind.RingFinding, 15: WedgeErrorKind.Atropisomer, 16: WedgeErrorKind.InvalidStereoRank, 17: WedgeErrorKind.InvalidStereoRankType})
exception cosmolkit.XmlParseError(*args, **kwargs)

XmlParseError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (11)
property actual: int | str | None

Observed value reported by the native check. Applies to XmlParseError.UnexpectedCloseTag, XmlParseError.InvalidChar, XmlParseError.InvalidChar2. None when this payload is absent.

property attribute: str | None

XML attribute involved in the parsing failure. Applies to XmlParseError.DuplicatedAttribute. None when this payload is absent.

property character: str | None

Character rejected by the parser. Applies to XmlParseError.NonXmlChar. None when this payload is absent.

property domain: str

Native subsystem reporting this failure, preserved independently of the human-readable message.

property entity: str | None

Structural entity involved in the failure. Applies to XmlParseError.UnknownEntityReference. None when this payload is absent.

property expected: int | str | None

Required value reported by the native check. Applies to XmlParseError.UnexpectedCloseTag, XmlParseError.InvalidChar, XmlParseError.InvalidChar2, XmlParseError.InvalidString. None when this payload is absent.

property message: str | None

Detailed native diagnostic message. Applies to XmlParseError.EntityResolver. None when this payload is absent.

property namespace: str | None

XML namespace involved in the parsing failure. Applies to XmlParseError.DuplicatedNamespace. None when this payload is absent.

property position: XmlTextPos

“error_payload”} Text position reported by the XML parser.

Type:

{“role”

property prefix: str | None

XML prefix involved in the parsing failure. Applies to XmlParseError.UnknownNamespace. None when this payload is absent.

property variant: XmlParseErrorKind

Exact native error category. Variant-specific payload fields are None when that variant is not active.

class cosmolkit.XmlParseErrorKind(value)

Discriminants of XmlParseErrorKind.

Members: InvalidXmlPrefixUri, UnexpectedXmlUri, UnexpectedXmlnsUri, InvalidElementNamePrefix, DuplicatedNamespace, UnknownNamespace, UnexpectedCloseTag, UnexpectedEntityCloseTag, UnknownEntityReference, MalformedEntityReference, EntityReferenceLoop, InvalidAttributeValue, DuplicatedAttribute, NoRootNode, UnclosedRootNode, UnexpectedDeclaration, DtdDetected, NodesLimitReached, AttributesLimitReached, NamespacesLimitReached, InvalidName, NonXmlChar, InvalidChar, InvalidChar2, InvalidString, InvalidExternalID, EntityResolver, InvalidComment, InvalidCharacterData, UnknownToken, UnexpectedEndOfStream, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (34)
AttributesLimitReached = XmlParseErrorKind.AttributesLimitReached
DtdDetected = XmlParseErrorKind.DtdDetected
DuplicatedAttribute = XmlParseErrorKind.DuplicatedAttribute
DuplicatedNamespace = XmlParseErrorKind.DuplicatedNamespace
EntityReferenceLoop = XmlParseErrorKind.EntityReferenceLoop
EntityResolver = XmlParseErrorKind.EntityResolver
InvalidAttributeValue = XmlParseErrorKind.InvalidAttributeValue
InvalidChar = XmlParseErrorKind.InvalidChar
InvalidChar2 = XmlParseErrorKind.InvalidChar2
InvalidCharacterData = XmlParseErrorKind.InvalidCharacterData
InvalidComment = XmlParseErrorKind.InvalidComment
InvalidElementNamePrefix = XmlParseErrorKind.InvalidElementNamePrefix
InvalidExternalID = XmlParseErrorKind.InvalidExternalID
InvalidName = XmlParseErrorKind.InvalidName
InvalidString = XmlParseErrorKind.InvalidString
InvalidXmlPrefixUri = XmlParseErrorKind.InvalidXmlPrefixUri
MalformedEntityReference = XmlParseErrorKind.MalformedEntityReference
NamespacesLimitReached = XmlParseErrorKind.NamespacesLimitReached
NoRootNode = XmlParseErrorKind.NoRootNode
NodesLimitReached = XmlParseErrorKind.NodesLimitReached
NonXmlChar = XmlParseErrorKind.NonXmlChar
UnclosedRootNode = XmlParseErrorKind.UnclosedRootNode
UnexpectedCloseTag = XmlParseErrorKind.UnexpectedCloseTag
UnexpectedDeclaration = XmlParseErrorKind.UnexpectedDeclaration
UnexpectedEndOfStream = XmlParseErrorKind.UnexpectedEndOfStream
UnexpectedEntityCloseTag = XmlParseErrorKind.UnexpectedEntityCloseTag
UnexpectedXmlUri = XmlParseErrorKind.UnexpectedXmlUri
UnexpectedXmlnsUri = XmlParseErrorKind.UnexpectedXmlnsUri
UnknownEntityReference = XmlParseErrorKind.UnknownEntityReference
UnknownNamespace = XmlParseErrorKind.UnknownNamespace
UnknownToken = XmlParseErrorKind.UnknownToken
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'InvalidXmlPrefixUri': XmlParseErrorKind.InvalidXmlPrefixUri, 'UnexpectedXmlUri': XmlParseErrorKind.UnexpectedXmlUri, 'UnexpectedXmlnsUri': XmlParseErrorKind.UnexpectedXmlnsUri, 'InvalidElementNamePrefix': XmlParseErrorKind.InvalidElementNamePrefix, 'DuplicatedNamespace': XmlParseErrorKind.DuplicatedNamespace, 'UnknownNamespace': XmlParseErrorKind.UnknownNamespace, 'UnexpectedCloseTag': XmlParseErrorKind.UnexpectedCloseTag, 'UnexpectedEntityCloseTag': XmlParseErrorKind.UnexpectedEntityCloseTag, 'UnknownEntityReference': XmlParseErrorKind.UnknownEntityReference, 'MalformedEntityReference': XmlParseErrorKind.MalformedEntityReference, 'EntityReferenceLoop': XmlParseErrorKind.EntityReferenceLoop, 'InvalidAttributeValue': XmlParseErrorKind.InvalidAttributeValue, 'DuplicatedAttribute': XmlParseErrorKind.DuplicatedAttribute, 'NoRootNode': XmlParseErrorKind.NoRootNode, 'UnclosedRootNode': XmlParseErrorKind.UnclosedRootNode, 'UnexpectedDeclaration': XmlParseErrorKind.UnexpectedDeclaration, 'DtdDetected': XmlParseErrorKind.DtdDetected, 'NodesLimitReached': XmlParseErrorKind.NodesLimitReached, 'AttributesLimitReached': XmlParseErrorKind.AttributesLimitReached, 'NamespacesLimitReached': XmlParseErrorKind.NamespacesLimitReached, 'InvalidName': XmlParseErrorKind.InvalidName, 'NonXmlChar': XmlParseErrorKind.NonXmlChar, 'InvalidChar': XmlParseErrorKind.InvalidChar, 'InvalidChar2': XmlParseErrorKind.InvalidChar2, 'InvalidString': XmlParseErrorKind.InvalidString, 'InvalidExternalID': XmlParseErrorKind.InvalidExternalID, 'EntityResolver': XmlParseErrorKind.EntityResolver, 'InvalidComment': XmlParseErrorKind.InvalidComment, 'InvalidCharacterData': XmlParseErrorKind.InvalidCharacterData, 'UnknownToken': XmlParseErrorKind.UnknownToken, 'UnexpectedEndOfStream': XmlParseErrorKind.UnexpectedEndOfStream})
values = mappingproxy({0: XmlParseErrorKind.InvalidXmlPrefixUri, 1: XmlParseErrorKind.UnexpectedXmlUri, 2: XmlParseErrorKind.UnexpectedXmlnsUri, 3: XmlParseErrorKind.InvalidElementNamePrefix, 4: XmlParseErrorKind.DuplicatedNamespace, 5: XmlParseErrorKind.UnknownNamespace, 6: XmlParseErrorKind.UnexpectedCloseTag, 7: XmlParseErrorKind.UnexpectedEntityCloseTag, 8: XmlParseErrorKind.UnknownEntityReference, 9: XmlParseErrorKind.MalformedEntityReference, 10: XmlParseErrorKind.EntityReferenceLoop, 11: XmlParseErrorKind.InvalidAttributeValue, 12: XmlParseErrorKind.DuplicatedAttribute, 13: XmlParseErrorKind.NoRootNode, 14: XmlParseErrorKind.UnclosedRootNode, 15: XmlParseErrorKind.UnexpectedDeclaration, 16: XmlParseErrorKind.DtdDetected, 17: XmlParseErrorKind.NodesLimitReached, 18: XmlParseErrorKind.AttributesLimitReached, 19: XmlParseErrorKind.NamespacesLimitReached, 20: XmlParseErrorKind.InvalidName, 21: XmlParseErrorKind.NonXmlChar, 22: XmlParseErrorKind.InvalidChar, 23: XmlParseErrorKind.InvalidChar2, 24: XmlParseErrorKind.InvalidString, 25: XmlParseErrorKind.InvalidExternalID, 26: XmlParseErrorKind.EntityResolver, 27: XmlParseErrorKind.InvalidComment, 28: XmlParseErrorKind.InvalidCharacterData, 29: XmlParseErrorKind.UnknownToken, 30: XmlParseErrorKind.UnexpectedEndOfStream})
class cosmolkit.XmlTextPos

One-based row and column in XML text.

Members (2)
col: int

One-based XML column number.

row: int

One-based XML row number.

exception cosmolkit.XyzReadError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

XyzReadError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (7)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property line: int | None

Source line associated with the failure. Present for XyzReadError.MissingCoordinates, XyzReadError.Coordinate; None when unavailable.

property message: str | None

Readonly message payload of the AtomSymbol error variant; None for other variants.

property source: ParseFloatError | TopologyValidationError | CoordinateValidationError | MoleculePropertyError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property value: str | None

Original value rejected by the operation. Present for XyzReadError.AtomCount, XyzReadError.Coordinate; None when unavailable.

property variant: XyzReadErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.XyzReadErrorKind(value)

Discriminants of XyzReadErrorKind.

Members: EmptyBlock, AtomCount, UnexpectedEof, MissingCoordinates, Coordinate, AtomSymbol, Topology, Coordinates, MoleculeProperty, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (12)
AtomCount = XyzReadErrorKind.AtomCount
AtomSymbol = XyzReadErrorKind.AtomSymbol
Coordinate = XyzReadErrorKind.Coordinate
Coordinates = XyzReadErrorKind.Coordinates
EmptyBlock = XyzReadErrorKind.EmptyBlock
MissingCoordinates = XyzReadErrorKind.MissingCoordinates
MoleculeProperty = XyzReadErrorKind.MoleculeProperty
Topology = XyzReadErrorKind.Topology
UnexpectedEof = XyzReadErrorKind.UnexpectedEof
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'EmptyBlock': XyzReadErrorKind.EmptyBlock, 'AtomCount': XyzReadErrorKind.AtomCount, 'UnexpectedEof': XyzReadErrorKind.UnexpectedEof, 'MissingCoordinates': XyzReadErrorKind.MissingCoordinates, 'Coordinate': XyzReadErrorKind.Coordinate, 'AtomSymbol': XyzReadErrorKind.AtomSymbol, 'Topology': XyzReadErrorKind.Topology, 'Coordinates': XyzReadErrorKind.Coordinates, 'MoleculeProperty': XyzReadErrorKind.MoleculeProperty})
values = mappingproxy({0: XyzReadErrorKind.EmptyBlock, 1: XyzReadErrorKind.AtomCount, 2: XyzReadErrorKind.UnexpectedEof, 3: XyzReadErrorKind.MissingCoordinates, 4: XyzReadErrorKind.Coordinate, 5: XyzReadErrorKind.AtomSymbol, 6: XyzReadErrorKind.Topology, 7: XyzReadErrorKind.Coordinates, 8: XyzReadErrorKind.MoleculeProperty})
exception cosmolkit.XyzWriteError(*args, **kwargs)

Failure in the io domain.

The readonly variant identifies the Rust error case. Payload fields are present only for their documented variant and otherwise return None. str(error) preserves the native message; __cause__ retains the underlying exception when one exists.

XyzWriteError is a structured native exception. Its readonly fields retain the Rust failure data. Use str(error) for the message and __cause__ for the underlying failure, when present. Instances are raised by operations, not constructed directly.

Members (5)
property domain: str

Domain that reported this failure; this does not replace the typed variant.

property id: int | None

Readonly id payload of the ConformerNotFound error variant; None for other variants.

property source: TopologyValidationError | CoordinateValidationError | PropertyStringError | None

“error_source”} The actual underlying exception, identical to __cause__, or None.

Type:

{“role”

property source_message: str | None

Message of the immediate underlying cause, or None when there is no cause.

property variant: XyzWriteErrorKind

Exact Rust error variant, independent of the human-readable message.

class cosmolkit.XyzWriteErrorKind(value)

Discriminants of XyzWriteErrorKind.

Members: Topology, Coordinates, ConformerNotFound, Property, Compare members by value. names and values are readonly lookup mappings; pickle preserves the enum type and value.

Members (7)
ConformerNotFound = XyzWriteErrorKind.ConformerNotFound
Coordinates = XyzWriteErrorKind.Coordinates
Property = XyzWriteErrorKind.Property
Topology = XyzWriteErrorKind.Topology
name: str

Canonical member name; aliases of the same value share this name.

names = mappingproxy({'Topology': XyzWriteErrorKind.Topology, 'Coordinates': XyzWriteErrorKind.Coordinates, 'ConformerNotFound': XyzWriteErrorKind.ConformerNotFound, 'Property': XyzWriteErrorKind.Property})
values = mappingproxy({0: XyzWriteErrorKind.Topology, 1: XyzWriteErrorKind.Coordinates, 2: XyzWriteErrorKind.ConformerNotFound, 3: XyzWriteErrorKind.Property})
class cosmolkit.XyzWriteParams(*, conformer_id=Ellipsis, precision=Ellipsis)

Controls RDKit-aligned XYZ conformer selection and coordinate precision.

Members (2)
conformer_id: int | None

Select a conformer by id. None uses the first available conformer.

precision: int

Number of digits after the decimal point.