cosmolkit 0.1.1

Python bindings for COSMolKit

COSMolKit Python

COSMolKit is a Python package for molecule graph workflows, SMILES/SDF IO, coordinate access, Morgan fingerprints, molecule depiction, and high-throughput batch processing.

Current Python documentation: https://kit.cosmol.org/

API Model: Copy-On-Write (COW) Molecule Values

COSMolKit's Python API uses copy-on-write (COW) value semantics for molecule transforms. Methods such as with_hydrogens(), without_hydrogens(), with_kekulized_bonds(), and with_2d_coords() return a new Molecule; they do not mutate the original object in place.

This is intentionally different from common RDKit Python workflows, where many operations mutate an RWMol or update a molecule object directly. In COSMolKit, keep the returned value:

mol = Molecule.from_smiles("CCO")
mol_h = mol.with_hydrogens()

assert mol is not mol_h
print(mol.to_smiles())
print(mol_h.to_smiles())

Installation

pip install cosmolkit

Quick Start

from cosmolkit import Molecule

mol = Molecule.from_smiles("c1ccccc1O")
drawn = mol.with_2d_coords()

print(mol.to_smiles())
print(drawn.atoms()[0])

drawn.write_png("phenol.png", width=400, height=300)

Morgan fingerprints are exposed as RDKit-style sparse bit vectors. The on_bits() output is a list of bit indexes set to 1 inside a fixed-length binary vector, not a dense neural embedding:

fp = mol.fingerprint_morgan(radius=2, n_bits=2048)

print(fp.n_bits())
print(fp.on_bits())
print(fp.tanimoto(Molecule.from_smiles("c1ccccc1").fingerprint_morgan()))

Additional output mirrors RDKit's Morgan provenance helpers:

result = mol.fingerprint_morgan_with_output(radius=2, n_bits=2048)
info = result.additional_output()

print(result.fingerprint().on_bits())
print(info.atom_counts())
print(info.bit_info_map())

Chiral tags are available directly on atoms, so code that works with the SMILES/RDKit-style CW and CCW path does not need to switch to the ordered tetrahedral view:

chiral = Molecule.from_smiles("F[C@H](Cl)Br")

print(chiral.to_smiles())
print(chiral.to_smiles(isomeric_smiles=False))

for atom in chiral.atoms():
    if atom.chiral_tag() != "CHI_UNSPECIFIED":
        print(atom.idx(), atom.chiral_tag())

Use Molecule.edit() when you want an explicit editing workflow:

editor = mol.edit()
cl = editor.add_atom("Cl")
editor.add_bond(0, cl, order="single")
mol2 = editor.commit()

Batch Workflows

from cosmolkit import MoleculeBatch

smiles = ["CCO", "c1ccccc1", "not-smiles"]
batch = MoleculeBatch.from_smiles_list(smiles, errors="keep")

prepared = batch.add_hydrogens(errors="keep").compute_2d_coords(errors="keep")
report = prepared.to_images("molecule_images", format="png", errors="skip")
fingerprints = prepared.fingerprint_morgan_list(n_bits=2048, n_jobs=8)

print(prepared.valid_mask())
print(prepared.errors())
print([fp.on_bits() if fp is not None else None for fp in fingerprints])
print(report)

The errors option controls invalid records:

• errors="raise" raises on the first batch validation failure.
• errors="keep" preserves failed records and exposes structured errors.
• errors="skip" omits failed records from the returned result or export.

Batch SMILES output accepts formatting options:

canonical = prepared.to_smiles_list(canonical=True)
explicit = prepared.to_smiles_list(
    all_bonds_explicit=True,
    all_hs_explicit=True,
)
without_maps = prepared.to_smiles_list(ignore_atom_map_numbers=True)

SDF and Arrays

mol = Molecule.from_smiles("CCO").with_2d_coords()

sdf_text = mol.to_sdf_string(format="v2000")
restored = Molecule.read_sdf_record_from_str(sdf_text, coordinate_dim="2d")

coords = restored.coords_2d()
bounds = restored.dg_bounds_matrix()

print(coords.shape)
print(bounds.shape)

Main Features

• SMILES parsing and writing with Molecule.from_smiles() and to_smiles()
• copy-on-write molecule value semantics for transforms
• SDF file and string IO
• atom and bond feature inspection
• hydrogen add/remove transforms
• Kekule bond representation
• CW/CCW chiral tags, chiral centers, and tetrahedral stereo inspection
• 2D coordinate generation and NumPy coordinate arrays
• distance-geometry bounds matrix export
• Morgan fingerprint bit vectors, Tanimoto similarity, and AdditionalOutput
• SVG and PNG molecule depictions
• ordered batch construction, transformation, filtering, and export
• batch Morgan fingerprint generation with Rust-side parallel scheduling
• explicit molecule editing with Molecule.edit()