COSMolKit 0.6 — Rust-native cheminformatics toolkit

COSMolKit is a Rust-native cheminformatics and structural biology toolkit with first-class Python and JavaScript/TypeScript bindings. It provides molecular graph operations, SMILES/SMARTS and molecular file workflows, 2D depiction, native 3D conformer generation, UFF/MMFF optimization, fingerprints, molecular descriptors, InChI, batch processing, and protein structure APIs. Selected workflows are also available directly in the browser through the COSMolKit Web Tools.

Chemistry implementations follow pinned upstream source semantics. Reference versions, comparison rules and completed results are recorded in VALIDATION.md.

COSMolKit combines a native Rust API with Python interfaces for scientific and machine-learning workflows and JavaScript/TypeScript interfaces for browser applications. Molecular graphs, coordinates, fingerprints, bounds matrices, and structural data integrate with NumPy, PyTorch and JavaScript typed arrays.

Features

The current chemistry reference is RDKit 2026.09.1 (Python distribution 2026.9.1). See the upstream-diff audit for the exact revision and upstream-diff scope.

• Modular Rust architecture: separate crates own model values and domain algorithms; cosmolkit remains the public entry point and molecule runtime.
• Cargo features: select functionality such as core, bio, fingerprints, or reaction; prerequisites are included. Default is full; see the Rust feature guide.
• WebAssembly support: run the same Rust chemistry engine in the browser through JavaScript bindings, without a separate algorithm implementation.
• One API, three languages: shared operations, defaults, results, and error categories, with idiomatic names for Rust, Python, and JavaScript. See Public API Design for cross-language naming rules and shared API contracts.

Each public API is one logical entry with three projections:

Logical name	Rust	Python	JavaScript
from_smiles	Molecule::from_smiles("CCO")?	ck.mol_from_smiles("CCO")	ck.molFromSmiles("CCO")
molecular_weight	mol.molecular_weight()	mol.molecular_weight()	mol.molecularWeight()
to_smiles	mol.to_smiles()	mol.to_smiles()	mol.toSmiles()
with_hydrogens	mol.with_hydrogens()	mol.with_hydrogens()	mol.withHydrogens()
tpsa	mol.tpsa()	mol.tpsa()	mol.tpsa()

Learn once, then move between Python notebooks, native Rust applications, and browser-based JavaScript without relearning the chemistry API.

Documentation

• Python documentation: https://kit.cosmol.org/python
• JavaScript documentation: https://kit.cosmol.org/javascript
• Rust documentation: https://docs.rs/cosmolkit/latest/cosmolkit/
• Interactive Web Tools: https://tools.cosmol.org/tools

Installation

# Rust
cargo add cosmolkit

# Python
pip install cosmolkit

# JavaScript/TypeScript (browser or bundler)
npm install @cosmol-studio/cosmolkit

Core Concepts

• Value-style molecules: methods such as with_hydrogens(), without_hydrogens(), with_kekulized_bonds(), and with_2d_coordinates() return new molecule values, keeping topology-changing operations explicit and preventing derived chemistry state from being silently invalidated.
• Explicit mutation: in-place Molecule operations always end with _. The trailing underscore has no other public Molecule meaning.
• Explicit errors: invalid input and unsupported behavior are surfaced as errors instead of silent fallbacks.
• Batch-native processing: MoleculeBatch keeps input order, supports structured per-record failures, and can run batch transforms and exports with configurable parallelism.
• Array-friendly data access: coordinates, bounds matrices, fingerprints, and graph features are exposed through NumPy and JavaScript typed arrays.
• Source-backed 3D workflows: conformer generation and UFF/MMFF optimization are available through the Python and JavaScript APIs, and atom chiral tags can be assigned from a selected 3D conformer with pinned-RDKit parity.

Value-Style Transformations

Normal molecule operations return new objects and do not mutate their inputs. This follows the same explicit-dataflow direction as modern dataframe libraries: users can reason about each transformation as a new value while COSMolKit can share unchanged internal storage efficiently.

import cosmolkit as ck

mol = ck.mol_from_smiles("CCO")
mol_h = mol.with_hydrogens()

assert mol is not mol_h

Python Quick Start

import cosmolkit as ck

mol = ck.mol_from_smiles("c1ccccc1O")
mol_2d = mol.with_2d_coordinates()

print(mol_2d.to_smiles())
print(mol_2d.coordinates_2d)

mol_3d = mol.with_hydrogens().with_3d_conformer()
print(mol_3d.coordinates_3d())

svg = mol_2d.to_svg(width=400, height=300)
mol_2d.write_png("phenol.png", width=400, height=300)

fp = mol.fingerprint_morgan()
print(fp.on_bits)

array = fp.to_numpy()  # uint8, one entry per bit

batch = (
    ck.mols_from_smiles_list(
        ["CCO", "c1ccccc1", "CC(=O)O"],
    )
    .with_parallel_jobs(8)
    .with_progress_bar(False)
)

prepared = batch.with_hydrogens().with_2d_coordinates()
print(prepared.valid_mask)
print(prepared.to_smiles())

prepared.write_images("molecule_images")

JavaScript Quick Start

Importing the package initializes WASM automatically. Value-style transforms leave their input unchanged; call free() when WASM objects are no longer needed.

import * as ck from "@cosmol-studio/cosmolkit";

const mol = ck.Molecule.fromSmiles("c1ccccc1O");
const mol2d = mol.with2dCoordinates();
const fp = mol.fingerprintMorgan();
const batch = ck.MoleculeBatch.fromSmilesList(["CCO", "c1ccccc1", "CC(=O)O"]);

console.log(mol.toSmiles(), mol.molecularWeight());
console.log(mol2d.toSvg(400, 300));
console.log(fp.onBits);
console.log(batch.toSmiles());

batch.free();
fp.free();
mol2d.free();
mol.free();

See the JavaScript guide for installation options and more examples.

Protein Structures

Use BioStructure for complete PDB/mmCIF structural data, including modeled proteins, nucleic acids, ligands, waters, entities, models, and metadata. Use Protein only when an amino-acid-only projection is intended.

import cosmolkit as ck
from pathlib import Path

structure = ck.BioStructure.from_pdb(Path("complex.pdb").read_text())
print(structure.num_models, structure.num_chains, structure.num_atoms)

# Structural format conversion remains on the complete structural value.
mmcif_text = structure.to_mmcif()
roundtrip = ck.BioStructure.from_mmcif(mmcif_text)
print(roundtrip.num_atoms)

This example reads your complex.pdb file.

The protein projection is explicit and leaves the full structure available:

protein = structure.protein()

print(protein.num_chains)
print(protein.num_residues)
print(protein.num_atoms)

SDF and Dataset Workflows

SdfDataset builds a lightweight index of SDF record byte ranges, so individual records and chunks can be read without loading an entire file into memory. Molfile-only readers such as Molecule.read_mol() follow RDKit MolFromMolBlock boundaries: they stop after the first M END line and leave trailing SDF data fields to the SDF APIs.

import cosmolkit as ck

dataset = ck.SdfDataset.open("library.sdf")
print(len(dataset))

record = dataset[0]
mol = record.molecule

for batch in dataset.batches(size=1024, errors="keep", n_jobs=8):
    smiles = batch.to_smiles()

This example reads your library.sdf file.

Conformer Generation And Optimization

import cosmolkit as ck

mol = ck.mol_from_smiles("CC(=O)NC").with_hydrogens()

params = ck.EmbedParams(random_seed=0xF00D, num_threads=1)

embedded = mol.with_3d_conformer(params)
print(len(embedded.conformers_3d))
print(embedded.coordinates_3d())

multi = mol.with_3d_conformers(5, params)
print(len(multi.conformers_3d))

uff = embedded.uff_force_field()
print(uff.energy())
outcome = uff.minimize_(max_iterations=200)
print(uff.energy())

mmff = embedded.mmff_force_field()
print(mmff.energy())
outcome = mmff.minimize_(max_iterations=200)
print(mmff.energy())

with_3d_conformer() uses source-backed distance-geometry embedding for trusted molecular graphs: molecules without explicit hydrogens are embedded as heavy-atom-only conformers instead of failing or automatically adding hydrogens. Calling with_hydrogens() first is recommended for all-atom geometry, force-field optimization, and hydrogen-bond-sensitive workflows. Coordinate-only inputs such as XYZ blocks do not contain a bond topology and are not valid ETKDG inputs until a trusted graph has been constructed.

Feature Areas

• Molecular graph construction and inspection
• SMILES parsing and writing
• MOL/SDF reading and writing
• MOL2 reading with RDKit-style Mol2ParserParams
• XYZ block reading
• InChI/InChIKey conversion with structured diagnostics
• Source-backed 3D atom-chiral-tag assignment
• Typed potential-stereo analysis and lazy, source-ordered stereoisomer enumeration with exhaustive, bounded random, uniqueness, enhanced-group, and optional embedding controls
• Hydrogen transforms and Kekulization
• Sanitization and chemistry problem detection
• Source-backed Rust tautomer enumeration, canonical selection, scoring, callbacks, current and V1 transform catalogs, and ordered result provenance
• 2D coordinate generation and SVG/PNG depiction
• Native 3D conformer generation with DG/KDG/ETDG/ETKDG parameter presets
• Read-only molecular alignment/RMSD measurement and explicit value-style or trailing-underscore coordinate alignment
• UFF/MMFF optimization of generated or imported 3D conformers
• Morgan, MACCS, RDKit topological, Avalon, Pattern, AtomPair, and Topological Torsion fingerprints, including sparse/count forms, provenance, tautomer-aware Pattern hashing, 2D/3D AtomPair distances, and ordered batch execution
• Source-backed RDKit Layered fingerprint 0.7.0 with all six active layers, roots, masks, seeded atom counts, and ordered batch execution; this family retains upstream's experimental classification
• Distance-geometry bounds matrices
• Substructure matching and SMARTS parse metadata
• Ordered batch transforms and exports
• Python pickle round-tripping for Molecule
• Complete PDB/mmCIF BioStructure parsing, Gemmi-aligned mmCIF writing, protein projections, and explicit structure-to-molecule conversion
• Support-status metadata for public features

Design Principles

COSMolKit aims to be Python- and JavaScript-friendly, batch-friendly, and suitable for scientific and browser workflows.

• Correctness comes before breadth.
• Public transforms use value semantics.
• Mutation-capable workflows are explicit.
• Fail-closed capability boundaries: a separately named capability outside documented support returns a structured error rather than fabricated chemistry. This is an API design rule, not an accepted mismatch within a supported feature.
• RDKit-parity behavior is the correctness floor for supported cheminformatics features.
• High-throughput APIs should preserve input order and expose per-record failures.
• Reference semantics come before heuristic approximation; semantic debt is treated as a correctness risk.

Examples

Python examples live in python/examples/; JavaScript examples live in wasm/examples/vanilla/. For the current InChI interface, see python/examples/inchi_roundtrip.py.

Development

See dev/README.md for local checks and contribution rules, python/dev.md for Python builds, and wasm/dev.md for JavaScript/TypeScript builds.

Acknowledgments

COSMolKit includes Rust ports of code and algorithms from:

• RDKit
• Gemmi

License

COSMolKit is licensed under the MIT License. Vendored sources and externally derived test fixtures retain their upstream copyright and license terms as documented beside those files.