Skip to main content

Crate cosmolkit

Crate cosmolkit

Expand description

Facade crate 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());

Re-exports§

pub use cosmolkit_core as core;

Modules§

bio: Biomolecular structure primitives.
chemistry: Chemistry algorithms over the core molecule model.
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
AdjacencyList
AltLocLabel: Single-char altloc label (e.g. b’A’, b’B’).
AngleConstraintContrib
AngleConstraintContribs
AngleConstraintContribsParams
AromaticityAssignment
Atom: Immutable atom record owned by Molecule.
AtomId: Stable atom table index.
AtomMapping
AtomName: Up to 4-char atom name (e.g. “ CA “, “ N “).
AtomPdbResidueInfo: Typed atom-level PDB residue metadata.
AtomRow
AtomSourceIds
AtomSpec: Atom construction payload.
BatchExportReport
BatchProgressBar
BatchRecordError
BatchValidationError
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
Conformer2D
Conformer3D
ConformerStore
CoordinateBlock: 3D coordinates for all atoms, indexed by AtomId. Invariant: len() == atoms.len() in the owning BioStructure.
CrystalCell
CrystalInfo
CxSmilesFields
DerivedState: Derived state invalidated by molecule operations.
DihedralOutput
DistanceConstraintContrib
DistanceConstraintContribs
DistanceConstraintContribsParams
Element: Minimal element identity for the core.
EmbedMoleculeResult
EmbedMultipleConfsResult
EmbedParameters
EntityRow
EntitySourceIds
FeatureSpec
Fingerprint
ForceField
ForceFieldSnapshot
ForceFieldVec3
InvariantCheckSet
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
Molecule: Immutable molecule value.
MoleculeBatch
MoleculeBuilder: One-shot molecule construction API.
MoleculeCapabilities
MoleculeOpSpec
MoleculeProperties
MorganAdditionalOutput
MorganBondInvariantsGenerator
MorganFingerprintOutput
MorganFingerprintParams
NeighborRef
OperationInvariantEntry
OperationTrace
ParityMatrixEntry
PositionConstraintContrib
PropertyStore
Protein
ProteinAtomRef
ProteinChainRef
ProteinResidueRef
ProteinSelectionSummary
RdkitPdbMolProfile
RemoveHsParams
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
SmilesWriteParams
StereoGroup
SubstanceGroup
SubstanceGroupId: Substance-group identity inside a molecule.
SubstructMatchParams: Parameters controlling substructure matching behaviour.
SubstructMatchResult: Result of a single substructure match.
SupportMatrixEntry
TetrahedralStereo
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§

Constants§

Traits§

ForceFieldContrib

Functions§

assign_double_bond_stereo_from_directions
assign_radicals
assign_stereochemistryDeprecated
assign_valence
assign_valence_with_options
atom_has_valence_violation
batch_progress_bar
bio_structure_to_rdkit_pdb_molecule
calc_torsion_energy
calc_torsion_energy_m6
classify_residue_name
compute_dihedral_from_flat
compute_dihedral_from_points
compute_dihedral_from_position_vec
detect_chemistry_problems
embed_molecule
embed_molecule_result
embed_multiple_confs
embed_multiple_confs_result
embed_multiple_confs_return_vector
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_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_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.
mmff_has_all_molecule_params
mmff_optimize_molecule
mmff_optimize_molecule_confs
mmff_sanitize_ops
mol_from_binary: Deserialize a Molecule from binary data produced by mol_to_binary.
mol_from_mol2_block_like_rdkit
mol_from_mol2_data_stream_like_rdkit
mol_from_mol2_file_like_rdkit
mol_to_binary: Serialize a Molecule to a compact binary format.
mol_to_random_smiles_vect
molecule_from_mmcif_block_with_options
molecule_from_pdb_block_with_options
normalize_angle_deg
perceive_stereochemistry: RDKit❗✔️: assignStereochemistry — main stereochemistry perception entry point
rdkit_valence_list
read_mmcif_atom_site_subset_from_str: 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
set_aromaticity
symmetrize_sssr
uff_has_all_molecule_params
uff_optimize_molecule
uff_optimize_molecule_confs
version: Returns the crate version at compile time.

Type Aliases§

BatchProgress