datamol

Wraps RDKit through the datamol Python library (import datamol as dm) for molecular cheminformatics, returning native rdkit.Chem.Mol objects. Covers SMILES/SELFIES/InChI conversion, sanitization and standardization, descriptors, fingerprints and similarity, Butina clustering and diverse subset picking, Bemis-Murcko scaffolds, BRICS/RECAP fragmentation, 3D conformers, reactions, SDF/CSV/Excel I/O including cloud paths, and parallel batch processing. Use when parsing or standardizing SMILES from external sources, computing descriptors or fingerprints for a compound library, clustering or selecting diverse molecules, making scaffold-based train/test splits, or generating conformers. Use when running a molecule-processing pipeline with n_jobs. For fine-grained control or custom parameters, use RDKit directly instead.

Version

1.2

License

Apache-2.0 license

Compatibility

Requires Python 3.8+ and datamol (uv pip install). RDKit is installed automatically as a datamol dependency (since 0.12.2). Optional s3fs/gcsfs for cloud I/O via fsspec.