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datamol — Claude Code skill: what it does, how to install

Guides an agent through molecular data work with datamol and RDKit, from SMILES parsing to descriptors, clustering, and 3D conformers.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill datamol -a claude-code
Open on GitHub

What datamol does

This skill guides an agent using datamol, a Python layer over RDKit for molecular work. It covers format conversion, structure cleanup, descriptors, fingerprints, similarity work, clustering, and scaffold analysis. Molecules remain rdkit.Chem.Mol objects, so they can move into RDKit code.

The documented workflows include SDF, SMILES, CSV, and Excel files, plus conformer generation, visual output, fragmentation, and SMARTS reactions. Batch operations can use n_jobs and progress reporting. Remote file access is handled through fsspec.

It requires Python 3.11+, datamol 0.13.0, and RDKit 2024.09+. Remote I/O also needs credentials for the chosen provider. Set a positive batch_size for parallel descriptor batches: the tested stack sends None to joblib and raises an error, so leaving that value implicit is risky.

What it helps with

  • parse SMILES into RDKit molecules
  • standardize molecular structures
  • calculate descriptors for compound sets
  • cluster molecules by similarity
  • generate and select 3D conformers

Example prompts for the agent

  • Parse the SMILES column with datamol and keep rejected rows separately.
  • Calculate descriptors for this SDF with `n_jobs=-1` and a positive `batch_size`.
  • Cluster these molecules from their fingerprints and select cluster representatives.

How to install datamol

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill datamol -a claude-code

2Manually: put the files in place

~/.claude/skills/datamol/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/datamol/

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Questions about datamol

How do I install datamol in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill datamol -a claude-code, then run npx skills add K-Dense-AI/scientific-agent-skills --skill datamol -a claude-code again. The skill file is at ~/.claude/skills/datamol/SKILL.md.

What does the datamol skill do?

It gives an agent guidance for using datamol with RDKit to handle molecular structures, descriptors, fingerprints, clustering, and 3D conformers.

What is needed for parallel descriptor calculations?

The skill requires Python 3.11+, datamol 0.13.0, and RDKit 2024.09+. Parallel descriptor batches need a positive batch_size.

See also

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