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datamol

k-dense-ai/scie…t-skills

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

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安装命令

npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill datamol

SKILL.md

Datamol Cheminformatics Skill

Overview

Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify 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.

Verified target: datamol 0.13.0, released September 9, 2026. Local checks used Python 3.13 and RDKit 2026.03.6. Python 3.11+ and RDKit 2024.09+ are required. The 0.13 distribution includes SELFIES, visualization, cloud, Excel and Parquet runtime dependencies. Current API examples and verification limits are recorded in references/review.md. Pin the environment: RDKit upgrades can change canonical representations and retained conformers. Compare chemical invariants, not a fixed conformer count or an exact version-dependent canonical string.

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