Crate cosmolkit

Expand description

Rust-native cheminformatics and structural biology toolkit.

COSMolKit provides molecular graph operations, SMILES/SMARTS processing, molecular file IO, fingerprints and descriptors, 2D depiction, native 3D conformer generation, UFF/MMFF optimization, InChI, substructure search, batch workflows, and protein structure APIs.

For supported cheminformatics operations, RDKit-compatible behavior is treated as the correctness floor and validated through explicit parity tests.

This crate is the public Rust facade that re-exports COSMolKit core modules.

§Examples

use cosmolkit::Molecule;

let mol = Molecule::from_smiles("CCO").unwrap();
let with_hydrogens = mol.with_hydrogens().unwrap();

assert_eq!(mol.num_atoms(), 3);
assert!(with_hydrogens.num_atoms() > mol.num_atoms());

use cosmolkit::Molecule;

let mut mol = Molecule::from_smiles("CCO").unwrap();
mol.add_hydrogens_().unwrap();
mol.compute_2d_coordinates_().unwrap();

assert!(mol.num_atoms() > 3);
assert_eq!(mol.coordinates_2d().unwrap().len(), mol.num_atoms());

Residue codes use stable source names for parsing, display, and serde; their numeric table indexes are not a persistence format:

use cosmolkit::{ResidueCode, ResidueIdentity};

let mse: ResidueCode = "MSE".parse().unwrap();
assert_eq!(mse.to_string(), "MSE");
assert_eq!(mse.info().parent_standard_code(), Some(ResidueCode::MET));

let unknown = ResidueIdentity::new("MY_COMPONENT");
assert_eq!(unknown.name(), "MY_COMPONENT");
assert_eq!(unknown.code(), ResidueCode::UNKNOWN);

Elements are checked values over the dummy atom and the 118 real elements. Symbols are the stable display and serde representation:

use cosmolkit::{ELEMENTS, Element};

let chlorine: Element = "Cl".parse().unwrap();
assert_eq!(chlorine, Element::CL);
assert_eq!(chlorine.atomic_number(), 17);
assert_eq!(chlorine.info().symbol, "Cl");
assert_eq!(ELEMENTS.len(), 118);
assert!(Element::from_atomic_number(119).is_none());

Re-exports§

pub use cosmolkit_core as core;

Modules§

bio: Biomolecular structure primitives.
chemistry: Chemistry algorithms over the core molecule model.
confseq
inchi: COSMolKit Molecule bridge for the toolkit-neutral InChI source port.
io: IO pipelines.
model: Core molecule state model.
notation: Text notations and fragment/sequence construction.
operations: Registered mutation and finalization operations.
properties: Derived descriptors, rendering, hashing, serialization, and batch helpers.
search: Query, SMARTS, and substructure search.
support

Structs§

AddHsParams
AdditionalOutput: RDKit-style scratch container for optional fingerprint provenance outputs.
AdjacencyList
AlignmentAtomMap
AlignmentParameters
AlignmentResult
AlignmentTransform
AllConformerRmsdParameters
AltLocLabel: Single-char altloc label (e.g. b’A’, b’B’).
AngleConstraintContrib
AngleConstraintContribs
AngleConstraintContribsParams
AromaticityAssignment
Atom: Immutable atom record owned by Molecule.
AtomCoordsMatchFunctor
AtomId: Stable atom table index.
AtomMapping
AtomName: Up to 4-char atom name (e.g. “ CA “, “ N “).
AtomPairFingerprintGenerator
AtomPairFingerprintOutput: Explicit-bit AtomPair fingerprint together with optional provenance.
AtomPairFingerprintParams: Parameters for the project-native AtomPair fingerprint API.
AtomPdbResidueInfo: Typed atom-level PDB residue metadata.
AtomRow
AtomSourceIds
AtomSpec: Atom construction payload.
AvalonFingerprintFlags: Avalon feature flags from the source ssmatch.h definitions.
AvalonFingerprintParams: Parameters for the source-backed Avalon bit-vector API.
BatchExportReport
BatchProgressBar
BatchRecordError
BatchValidationError
BestAlignmentParameters
BioAssembly
BioAtomId
BioBlockSet
BioChainId
BioCisPep
BioConnection
BioDerivedState
BioEntityId
BioMetadata
BioModRes
BioModelId
BioNcsOperator
BioPdbReadParams
BioResidueId
BioRowMapping
BioStateSet
BioStructure: Flat-row biomolecular structure.
BioStructureMapping
BioStructureOpSpec
BioTransform
BlockAccess
BlockSet
Bond: Immutable bond record owned by Molecule.
BondId: Stable bond table index.
BondMapping
BondSpec: Bond construction payload. Builders assign BondId.
ChainRow
ChainSourceIds
CipLabelOptions: Options for modern molecular-context CIP assignment.
ConfSeqBatchDecodeResult
ConfSeqDecodeOptions
Conformer2D
Conformer3D
ConformerAlignmentParameters
ConformerAlignmentReport
ConformerRmsd
ConformerStore
CoordinateBlock: 3D coordinates for all atoms, indexed by AtomId. Invariant: len() == atoms.len() in the owning BioStructure.
CoordinateRmsdParameters
CrippenDescriptorValues
CrystalCell
CrystalInfo
CxSmilesFields
DerivedState: Derived state invalidated by molecule operations.
DihedralOutput
DistanceConstraintContrib
DistanceConstraintContribs
DistanceConstraintContribsParams
Element: Stable chemical-element identity.
ElementInfo: Source-aligned periodic-table metadata for an Element.
ElementParseError: Error returned when a string is not a source-recognized element symbol.
EmbedMoleculeResult
EmbedMultipleConfsResult
EmbedParameters
EntityRow
EntitySourceIds
FeatureSpec
Fingerprint
FingerprintArguments: RDKit-style common fingerprint arguments shared by Morgan/MACCS wrappers.
FingerprintFuncArguments
ForceField
ForceFieldSnapshot
ForceFieldVec3
HallKierAlphaValues: Hall-Kier alpha and its atom-index-aligned contributions.
InchiApiParitySpec: Exact-parity contract for one public scalar InChI API.
InchiDiagnostic
InchiError: Structured failure from one of the four scalar InChI operations.
InchiReturnValues: Return fields written by the official InChI generation or parsing API.
InchiToInchiKeyOutput: Output of inchi_to_inchi_key.
InvariantCheckSet
LabuteAsaContributions: Labute ASA and its atom-index-aligned source contributions.
LayeredFingerprintLayers: Source layer flags for RDKit’s experimental Layered fingerprint algorithm.
LayeredFingerprintParams: Parameters for the source-backed Layered fingerprint API.
LayeredFingerprintResult
MaccsFingerprintParams: Parameters for MACCS key generation.
MmcifOutputGroups
MmcifWriteOptions: Options for canonical Gemmi-aligned mmCIF output.
MmffAngle: MMFF angle-bending parameter.
MmffAngleCollection: MMFF angle-bending parameter collection.
MmffAtomProperties
MmffBond: MMFF bond-stretching parameter.
MmffBondCollection: MMFF bond-stretching parameter collection.
MmffChg: MMFF bond-charge-increment parameter.
MmffChgCollection: MMFF bond-charge-increment collection.
MmffDef: MMFF atom type equivalence levels.
MmffDefCollection: MMFF atom type equivalence definition collection.
MmffDfsbCollection: MMFF default stretch-bend parameter collection.
MmffMolProperties
MmffOop: MMFF out-of-plane bending parameter.
MmffOopCollection: MMFF out-of-plane bending parameter collection.
MmffOptimizeMoleculeConfResult
MmffOptimizeMoleculeConfsResult
MmffOptimizeMoleculeResult
MmffPbci: MMFF partial bond charge increments.
MmffPbciCollection: MMFF partial bond charge increment collection.
MmffProp: MMFF atom-type properties.
MmffPropCollection: MMFF atom-type property collection.
MmffStbn: MMFF stretch-bend parameter.
MmffStbnCollection: MMFF stretch-bend parameter collection.
MmffTor: MMFF torsion parameter.
MmffTorCollection: MMFF torsion parameter collection.
MmffVdw: MMFF non-bonded Van der Waals parameter.
MmffVdwCollection: MMFF non-bonded Van der Waals parameter collection.
MmffVdwRijstarEps: MMFF combined Van der Waals pair constants.
ModelRow
Mol2ReadParams
Mol2Record
MolFromInchiOutput: Result of parsing an InChI into a COSMolKit molecule.
MolToInchiKeyOutput: Output of mol_to_inchi_key.
MolToInchiOutput: Output of mol_to_inchi.
Molecule: Immutable molecule value.
MoleculeBatch
MoleculeBuilder: One-shot molecule construction API.
MoleculeCapabilities
MoleculeOpSpec
MoleculeProperties
MorganAdditionalOutput
MorganBitFingerprintOutput
MorganBondInvariantsGenerator
MorganFingerprintOutput
MorganFingerprintParams
MorganSparseFingerprintOutput
NeighborRef
OperationInvariantEntry
OperationTrace
ParityMatrixEntry
PatternFingerprintParams: Parameters for the source-compatible Pattern fingerprint.
PositionConstraintContrib
PotentialStereoAnalysis: Value-style result of potential-stereo analysis.
PotentialStereoOptions: Options for the single potential-stereo analysis engine.
PropertyStore
Protein
ProteinAtomRef
ProteinChainRef
ProteinResidueRef
ProteinSelectionSummary
RemoveHsParams
ResidueCodeParseError: Error returned when a name is not present in the source residue table.
ResidueIdentity: A residue name together with its table classification.
ResidueInfo
ResidueName: Up to 3-char residue name (e.g. “ALA”, “GLY”).
ResidueRow
RingInfo
RowSpan
SGroupAttachPoint
SGroupBracket
SGroupCState
SGroupData
SGroupDisplay
SanitizeError
SanitizeOps
SdfDataset
SdfPropertyList
SdfReadParams
SdfRecordMetadata
SemanticPreconditionSet
SmartsParseParams: 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✔️✔️: };
SmilesParseParams: Source-backed SMILES parser options.
SmilesWriteParams
SparseBitFingerprint
SparseCountFingerprint
StereoGroup
StereoInfo
StereoisomerIterator: Lazy iterator over source-ordered stereoisomers.
StereoisomerOptions: Options for lazy stereoisomer enumeration.
StructureMoleculeOptions
SubstanceGroup
SubstanceGroupId: Substance-group identity inside a molecule.
SubstructMatchParams
SubstructMatchResult: Result of a single substructure match.
SupportMatrixEntry
TautomerCatalog: An ordered collection of compiled tautomer transforms.
TautomerEnumeration: Ordered molecules and metadata produced by one tautomer-enumeration run.
TautomerEnumerator: Configured tautomer enumerator backed by one shared immutable catalog.
TautomerOptions: Source-compatible limits and stereochemistry policies for enumeration.
TautomerScore: Source-defined components of a tautomer canonicalization score.
TautomerScoreTerm: One named SMARTS contribution to tautomer canonicalization.
TautomerTransform: One compiled, source-ordered tautomer transformation.
TetrahedralStereo
TopologicalFingerprintOutput: Typed provenance returned by the source atomBits and bitInfo outputs.
TopologicalFingerprintOutputRequest: Typed request for the two legacy RDKFingerprintMol provenance outputs.
TopologicalFingerprintParams: Parameters for the source-backed RDKFingerprintMol boundary.
TopologicalFingerprintResult
TopologicalTorsionFingerprintGenerator: RDKit’s Topological Torsion generator is instantiated only with a 64-bit output type; Rust fixes the bit-id and sparse-vector domain to u64.
TopologicalTorsionFingerprintOutputRequest: Typed request for a Topological Torsion vector and shared provenance.
TopologicalTorsionFingerprintParams: Rust-native parameters for the RDKit Topological Torsion generator.
TopologicalTorsionFingerprintResult: Rust-native Topological Torsion result with optional shared provenance.
TopologicalTorsionLegacyParams: Rust-native parameters for the three deprecated RDKit compatibility paths.
TopologyMapping
TorsionAngleContribM6
TorsionAngleContribs
TorsionAngleContribsParams
TorsionConstraintContrib
UffAngle: UFF parameters for angle bending.
UffBond: UFF parameters for bond stretching.
UffInv: UFF parameters for inversions.
UffOptimizeMoleculeConfResult
UffOptimizeMoleculeConfsResult
UffOptimizeMoleculeResult
UffTor: UFF parameters for torsions.
UffVdw: UFF parameters for van der Waals interactions.
UnsupportedFeatureError
ValenceAssignment
With2DCoordinatesParams

Enums§

AddHydrogensError
AdjacencyError
AlignmentError
AromaticityError
AromaticityModel
AtomQueryPredicate: Atom-level SMARTS / MolFile query predicates.
BatchErrorMode
BatchRecord
BioConnectionType
BioCoorFormat
BioEditKind
BioOpDomain
BioOpKind
BioOperationError
BioParityPolicy
BioReadError
BioWriteError
BondDirection
BondOrder: COSMolKit core bond order.
BondQueryPredicate: Bond-level query predicates.
BondStereo
ChainKind
ChiralTag
CipDescriptor: A descriptor emitted by the supported modern CIP assignment dispatcher.
CipDescriptorError: Error returned when persisted _CIPCode state is not a descriptor emitted by the supported modern assignment dispatcher.
CipLabelerError: Structured failures from the modern source-backed CIP labeler.
CipStatePolicy: Source-defined lifecycle of modern CIP observable state for an operation.
ConfSeqDecodeError
ConfSeqFastGeometryError
ConfSeqTemplateBackend
ControllingAtom: One ordered controlling-atom slot in a potential-stereo record.
CoordinateDimension
DescriptorError
DgBoundsError
DoubleBondStereo: RDKit❗✔️: E/Z bond stereo information
EmbedFailureCause
EntityKind
EnumerationError
FeatureCategory
FingerprintError
Hybridization
InchiDiagnosticLevel
InchiErrorKind: Stable category for failures at the toolkit-neutral InChI boundary.
InvariantError
KekulizeError
LigandRef
MappingRequirement
MmffMolPropertiesError
MmffParamError
MmffPublicApiError
MmffVariant
Mol2ReadError
Mol2Type
MoleculeBuildError
MoleculeOpKind
MoleculeOpOutput: Number of molecule values produced by a registered operation wrapper.
MorganAtomInvariantsGenerator
NumRotatableBondsOptions
OperationDomain
OperationError
ParityPolicy
PickleError
PolymerKind
PotentialStereoError
QueryNode: A recursive Boolean query tree over a predicate type T.
RemoveHydrogensError
ResidueCode
ResidueInfoKind
ResidueInfoSequenceError
ResidueKind
RestoreBondDirOption
RingFindType
RingFindingError
SGroupBondRole
SGroupBracketStyle
SGroupConnection
SanitizeStep
SdfCoordinateMode
SdfPropertyListTarget
SemanticPrecondition
SmartsParseError: Errors produced by SMARTS parsing.
SmartsWriteError
SmilesParseError
SmilesWriteError
StereoCenter: Typed location of a potential stereochemical element.
StereoDescriptor
StereoError
StereoGroupKind
StereoSpecified
StereoType
StructureMoleculeConversionError
SubstanceGroupKind
SubstructMatchError
SubstructMatchOverload
SubstructMatchParamsJsonError
SupportStatus
SvgDrawError: Errors returned by SVG / PNG drawing routines.
TautomerCanonicalizationError
TautomerCatalogError
TautomerEnumerationError
TautomerEnumerationStatus: Completion state of a tautomer-enumeration run.
TautomerRunError: Structured failures produced while executing a tautomer-enumeration run.
TautomerScoreError
TautomerTransformError: A structurally invalid tautomer transform.
TopologicalTorsionFingerprintValue: One of the four source-supported Topological Torsion vector forms.
TopologicalTorsionFingerprintVector: Vector form requested from topological_torsion_fingerprint_with_output.
TopologicalTorsionLegacyKind: Legacy compatibility form selected by TopologicalTorsionLegacyParams.
TopologicalTorsionLegacyResult
TopologyEditKind
TopologyTrust
UffPublicApiError
ValenceError
ValenceModel
XyzReadError

Constants§

AROMATICITY_FEATURE
ASSIGNED_AROMATICITY_SPEC
ASSIGNED_RINGS_SPEC
ASSIGNED_RING_FAMILIES_SPEC
ASSIGNED_VALENCE_SPEC
ATOM_PAIRS_VERSION
ATOM_PAIR_ATOM_NUMBER_TYPES
ATOM_PAIR_CODE_SIZE
ATOM_PAIR_FINGERPRINT_FEATURE
ATOM_PAIR_MAX_NUM_BRANCHES
ATOM_PAIR_MAX_NUM_PI
ATOM_PAIR_MAX_PATH_LENGTH
ATOM_PAIR_NUM_BRANCH_BITS
ATOM_PAIR_NUM_CHIRAL_BITS
ATOM_PAIR_NUM_FINGERPRINT_BITS
ATOM_PAIR_NUM_PATH_BITS
ATOM_PAIR_NUM_PI_BITS
ATOM_PAIR_NUM_TYPE_BITS
AVALON_FINGERPRINT_FEATURE
BATCH_FEATURE
BIO_MMCIF_ATOM_SITE_SUBSET_READ_FEATUREDeprecated
BIO_MMCIF_READ_FEATURE
BIO_MMCIF_WRITE_FEATURE
BIO_PDB_COORDINATE_SUBSET_READ_FEATUREDeprecated
BIO_PDB_READ_FEATURE
BIO_SELECTION_FEATURE
BIO_STRUCTURE_FEATURE
CIP_LABELER_FEATURE
CONFORMER_GENERATION_FEATURE
COORDINATE_2D_FEATURE
COORDINATE_EDIT_FEATURE
DESCRIPTORS_FEATURE
DG_BOUNDS_FEATURE
DRAWING_FEATURE
ENUMERATE_TAUTOMERS_WITH_OPTIONS_SPEC
FINGERPRINT_FEATURE
HYDROGENS_FEATURE
INCHI_API_PARITY_MATRIX: Structured parity matrix for the complete public InChI surface.
INCHI_FEATURE
KEKULIZE_FEATURE
LAYERED_FINGERPRINT_FEATURE
LAYERED_FINGERPRINT_MAX_LAYERS
LAYERED_FINGERPRINT_SUBSTRUCTURE_LAYERS
LAYERED_FINGERPRINT_VERSION
MMFF_MOL_PROPERTIES_FEATURE
MOLALIGN_FEATURE
MOLBLOCK_IO_FEATURE
MOLECULE_OPS
OPERATION_INVARIANT_MATRIX
PARITY_MATRIX
PATTERN_FINGERPRINT_FEATURE
PATTERN_FINGERPRINT_VERSION
PUBLIC_FEATURES
RESIDUE_INFO_TABLE
RINGS_FEATURE
SANITIZE_FEATURE
SANITIZE_SPEC
SMILES_PARSE_FEATURE
SMILES_WRITE_FEATURE
STEREOISOMER_ENUMERATION_FEATURE
STEREO_FEATURE
SUBSTRUCTURE_FEATURE
SUPPORT_MATRIX
TAUTOMER_ENUMERATION_FEATURE
TOPOLOGICAL_TORSION_FINGERPRINT_FEATURE
UNKNOWN_TABULATED_RESIDUE_IDX
VALENCE_FEATURE
WITHOUT_HYDROGENS_SPEC
WITHOUT_HYDROGENS_WITH_PARAMS_SPEC
WITH_2D_COORDINATES_SPEC
WITH_3D_CONFORMERS_SPEC
WITH_3D_CONFORMER_SPEC
WITH_ADDED_3D_CONFORMER_SPEC
WITH_CLEARED_3D_CONFORMERS_SPEC
WITH_HYDROGENS_SPEC
WITH_KEKULIZED_BONDS_SPEC
WITH_ONLY_3D_CONFORMER_SPEC

Statics§

ELEMENTS: All 118 real elements in ascending atomic-number order (H through Og).
ELEMENTS_WITH_DUMMY: The dummy atom followed by all real elements in atomic-number order.

Traits§

ForceFieldContrib
TautomerEnumerationCallback: Borrowed cancellation hook evaluated at the source callback point.

Functions§

analyze_potential_stereo: Analyze potential stereochemistry on an isolated molecule value.
assign_radicals
assign_stereochemistryDeprecated
assign_valence
assign_valence_with_options
atom_has_valence_violation
atom_pair_fingerprint: Generate the explicit-bit AtomPair result without mutating the molecule.
atom_pair_fingerprint_with_output: Generate an explicit-bit AtomPair fingerprint and, when requested, all source-supported provenance containers.
batch_progress_bar
bio_structure_to_rdkit_pdb_moleculeDeprecated
cached_valence_assignment: Returns the molecule’s current atom property-cache valence, when present.
calc_chi_0
calc_chi_0n
calc_chi_0v
calc_chi_1
calc_chi_1n
calc_chi_1v
calc_chi_2n
calc_chi_2v
calc_chi_3n
calc_chi_3v
calc_chi_4n
calc_chi_4v
calc_chi_nn
calc_chi_nv
calc_crippen_descriptors
calc_exact_mol_wt
calc_fraction_csp3
calc_hall_kier_alpha
calc_hall_kier_alpha_with_contributions
calc_kappa_1
calc_kappa_2
calc_kappa_3
calc_labute_asa
calc_labute_asa_contributions
calc_lipinski_hba
calc_lipinski_hbd
calc_mol_formula
calc_mol_wt
calc_mqns
calc_num_aliphatic_carbocycles
calc_num_aliphatic_heterocycles
calc_num_aliphatic_rings
calc_num_amide_bonds
calc_num_aromatic_carbocycles
calc_num_aromatic_heterocycles
calc_num_aromatic_rings
calc_num_atom_stereo_centers
calc_num_atoms
calc_num_bridgehead_atoms
calc_num_hba
calc_num_hbd
calc_num_heavy_atoms
calc_num_heteroatoms
calc_num_heterocycles
calc_num_rings
calc_num_rotatable_bonds
calc_num_saturated_carbocycles
calc_num_saturated_heterocycles
calc_num_saturated_rings
calc_num_spiro_atoms
calc_num_unspecified_atom_stereo_centers
calc_phi
calc_qed
calc_slogp_vsa
calc_slogp_vsa_1
calc_slogp_vsa_2
calc_slogp_vsa_3
calc_slogp_vsa_4
calc_slogp_vsa_5
calc_slogp_vsa_6
calc_slogp_vsa_7
calc_slogp_vsa_8
calc_slogp_vsa_9
calc_slogp_vsa_10
calc_slogp_vsa_11
calc_slogp_vsa_12
calc_slogp_vsa_with_bins
calc_smr_vsa
calc_smr_vsa_1
calc_smr_vsa_2
calc_smr_vsa_3
calc_smr_vsa_4
calc_smr_vsa_5
calc_smr_vsa_6
calc_smr_vsa_7
calc_smr_vsa_8
calc_smr_vsa_9
calc_smr_vsa_10
calc_smr_vsa_with_bins
calc_torsion_energy
calc_torsion_energy_m6
calc_tpsa
check_substruct_match_overload_support
classify_residue_name
compute_dihedral_from_flat
compute_dihedral_from_points
compute_dihedral_from_position_vec
decode_confseq
decode_confseq_batch
decode_confseq_batch_with_options
decode_confseq_record
decode_confseq_record_batch
decode_confseq_record_batch_with_options
decode_confseq_record_with_options
decode_confseq_with_options
default_tautomer_score_terms
detect_chemistry_problems
embed_molecule
embed_molecule_result
embed_multiple_confs
embed_multiple_confs_result
embed_multiple_confs_return_vector
enumerate_stereoisomers: Create a lazy source-ordered stereoisomer iterator.
enumerate_stereoisomers_with_random_bits: Create a lazy stereoisomer iterator using a source-compatible random-bit callback when the option boundary selects bounded random enumeration.
expand_one_letter
expand_one_letter_sequence
expand_protein_one_letter
expand_protein_one_letter_string
fast_find_rings
find_ring_families
find_sssr
find_tabulated_residue
find_tabulated_residue_idx
get_atom_code
get_atom_smarts
get_bond_smarts
get_residue_info
get_residue_info_checked
get_substruct_match: Get the first substructure match, if any.
get_substruct_matches: Get all substructure matches with default parameters.
get_substruct_matches_with_params: Get all substructure matches with custom parameters.
get_topological_torsion_code
get_topological_torsion_hash
get_uff_angle_bend_params
get_uff_bond_stretch_params
get_uff_inversion_params
get_uff_torsion_params
get_uff_vdw_params
has_substruct_match: Check if a molecule contains a substructure match for the given query.
inchi_to_inchi_key: Generates an InChIKey directly from an InChI byte string.
layered_fingerprint
layered_fingerprint_with_output: Compute a source-backed Layered fingerprint and optional atom counts.
maccs_fingerprint
maccs_get_fingerprint_as_bit_vect
mmff_has_all_molecule_params
mmff_optimize_molecule
mmff_optimize_molecule_confs
mmff_sanitize_ops
mol_fragment_to_cx_smarts
mol_fragment_to_smarts
mol_from_binary: Deserialize a Molecule from binary data produced by mol_to_binary.
mol_from_inchi: Parses an InChI into a COSMolKit molecule through the source-backed bridge.
mol_from_mol2_block_like_rdkit
mol_from_mol2_data_stream_like_rdkit
mol_from_mol2_file_like_rdkit
mol_from_smarts
mol_to_binary: Serialize a Molecule to a compact binary format.
mol_to_cx_smarts
mol_to_inchi: Generates an InChI from a COSMolKit molecule without mutating it.
mol_to_inchi_key: Generates an InChIKey from a COSMolKit molecule without mutating it.
mol_to_random_smiles_vect
mol_to_smarts
molecule_from_mmcif_block_with_optionsDeprecated
molecule_from_pdb_block_with_optionsDeprecated
morgan_get_fingerprint
morgan_get_fingerprint_as_bit_vect
morgan_get_hashed_fingerprint
normalize_angle_deg
pattern_fingerprint: Computes an explicit Pattern fingerprint without mutating molecule.
perceive_stereochemistry: RDKit❗✔️: assignStereochemistry — main stereochemistry perception entry point
rdkit_atomic_number_from_symbol
rdkit_element_symbol
rdkit_valence_list
read_mmcif_atom_site_subset_from_strDeprecated: Reads the Gemmi-aligned mmCIF structural reader surface into a BioStructure.
read_mol2_file
read_mol2_file_with_params
read_mol2_from_str
read_mol2_from_str_with_params
read_xyz_from_str
residue_code_from_name
sanitize_mmff_mol
score_tautomer: Compute the source tautomer score using the pinned default SMARTS terms.
score_tautomer_hetero_hydrogens: Penalize hydrogens attached to phosphorus, sulfur, selenium, and tellurium.
score_tautomer_rings: Score aromatic rings using RDKit’s tautomer-canonicalization weights.
score_tautomer_substructures: Score every match of the supplied source-ordered tautomer SMARTS terms.
score_tautomer_with_terms: Compute all source tautomer score components and their signed aggregate.
set_aromaticity
stereoisomer_count: Return RDKit Python’s upper-bound stereoisomer count for molecule.
substruct_match_params_to_json
symmetrize_sssr
topological_fingerprint_with_output
topological_torsion_count_fingerprint
topological_torsion_fingerprint
topological_torsion_fingerprint_with_output: Generate any source-supported Topological Torsion vector form and the requested shared provenance without mutating molecule.
topological_torsion_generator: Construct the public Rust Topological Torsion generator over the sole shared fingerprint-generator core.
topological_torsion_legacy_fingerprint: Call one of the three source-compatible legacy adapters. This function is a naming/typing layer only and does not contain a second chemistry path.
topological_torsion_sparse_count_fingerprint
topological_torsion_sparse_fingerprint
try_get_substruct_matches_with_params: Get all substructure matches with custom parameters and structured unsupported-feature errors for source-porting callers.
uff_has_all_molecule_params
uff_optimize_molecule
uff_optimize_molecule_confs
update_substruct_match_params_from_json
version: Returns the crate version at compile time.

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BatchProgress
DescriptorResult
ExtraAtomCheck: Parameters controlling substructure matching behaviour.
ExtraBondCheck
ExtraFinalCheck
PdbMoleculeConversionErrorDeprecated
RdkitPdbMolProfileDeprecated

Crate cosmolkit

Crate cosmolkit Copy item path

§Examples

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Crate cosmolkit