datamol

SUMMARY

What it does

Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. It simplifies complex molecular operations with sensible defaults, efficient parallelization, and modern I/O capabilities. All molecular objects are native rdkit.Chem.Mol instances, ensuring full compatibility with the RDKit ecosystem. The skill covers molecular format conversion (SMILES, SELFIES, InChI), structure standardization and sanitization, molecular descriptors and fingerprints, 3D conformer generation and analysis, clustering and diversity selection, scaffold and fragment analysis, chemical reaction application, visualization and alignment, batch processing with parallelization, and cloud storage support via fsspec. It requires Python 3.8+ and datamol (installed via uv pip install), with RDKit installed automatically as a dependency since datamol 0.12.2. Optional s3fs/gcsfs for cloud I/O. The skill is part of Scientific Agent Skills by K-Dense and is licensed under Apache-2.0 (as stated in the source SKILL.md frontmatter).