Crate cosmolkit 

Facade crate that re-exports COSMolKit core modules.

Re-exports

pub use cosmolkit_core as core;

Modules

adjacency

atom

batch

bio

Biomolecular structure primitives and traversal helpers.

bond

canon_smiles

distgeom

draw

RDKit MolDraw2D-compatible drawing entry points.

fingerprint

hydrogens

io

File format I/O entry points for chemistry and biomolecular data.

kekulize

molecule

query

sanitize

smiles_write

stereo

valence

Structs

AdjacencyList

Graph adjacency list indexed by atom index.

Atom

Atom record in a molecule graph.

BatchExportReport

BatchProgressBar

Terminal progress bar for Rust batch workflows.

BatchRecordError

BatchValidationError

Bond

Bond record in a molecule graph.

ConformerStore

Coordinate storage owned separately from topology.

Fingerprint

Molecule

Molecular graph with split owned topology, coordinate, and metadata blocks.

MoleculeBatch

MorganAdditionalOutput

MorganBondInvariantsGenerator

MorganFingerprintOutput

MorganFingerprintParams

NeighborRef

Adjacency entry: neighboring atom and corresponding bond index.

PreparedDrawAtom

Atom snapshot after the RDKit PrepareMolForDrawing() preparation boundary.

PreparedDrawBond

Bond snapshot after the RDKit PrepareMolForDrawing() preparation boundary.

PreparedDrawMolecule

Molecule snapshot after the RDKit PrepareMolForDrawing() preparation boundary.

PropertyStore

Molecule-level metadata storage.

SanitizeError

SanitizeOps

SmilesWriteParams

TetrahedralStereo

Ordered tetrahedral stereochemistry for one atom center.

TopologyData

Persistent topology storage owned by a molecule value.

ValenceAssignment

Per-atom valence assignment result.

Enums

AddHydrogensError

AtomQueryPredicate

BatchErrorMode

BatchRecord

BondDirection

RDKit-style directional single-bond marker used for SMILES cis/trans stereo.

BondOrder

Bond order for chemical edges.

BondQueryPredicate

BondStereo

RDKit-style double-bond stereo assignment.

ChiralTag

CoordinateDimension

DgBoundsError

FingerprintError

LigandRef

A ligand participating in a tetrahedral stereocenter.

MorganAtomInvariantsGenerator

QueryNode

RemoveHydrogensError

SanitizeStep

SmilesParseError

Errors returned by SMILES parsing routines.

SmilesWriteError

SvgDrawError

Errors returned by SVG drawing routines.

ValenceError

Valence handling errors.

ValenceModel

Valence model selector for future compatibility modes.

Functions

add_hydrogens_in_place

assign_double_bond_stereo_from_directions

Assign double-bond stereochemistry from stored directional single bonds.

assign_radicals_rdkit_2025

RDKit 2026.03.1 MolOps::assignRadicals parity helper.

assign_valence

Compute explicit valence and implicit hydrogen assignment.

batch_progress_bar

Create a progress bar when enabled is true and total is non-zero.

rdkit_valence_list

Returns the RDKit 2026.03.1 valence list for an atomic number.

remove_hydrogens_in_place

version

Returns the crate version at compile time.

Type Aliases

BatchProgress

Optional per-record progress callback used by parallel batch operations.