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datamol

Python cheminformatics library (RDKit wrapper). Input: SMILES strings you already possess. Output: computed molecular properties, fingerprints, conformers, clustering. Does NOT retrieve compounds from any database — querying by topic name returns only a metadata stub. Use pubchem or chembl to obtain SMILES first, then pass those SMILES here.

skills/datamol/SKILL.md

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# Datamol Cheminformatics Skill

## ⚠<U+FE0F> When NOT To Use This Skill

**Do NOT invoke datamol** if you want to:
- Look up compounds related to a research topic (e.g. "KRAS covalent inhibitors") → use **pubchem** or **chembl**
- Find binding affinities or IC50 data → use **chembl** or **tdc**
- Search for compounds by mechanism or target → use **pubchem** or **pubmed**

**datamol requires SMILES strings you already have.** It performs computations on those structures — it does not retrieve structures from any database. Invoking `demo.py` without a SMILES input returns only a metadata confirmation that the library is available.

**Correct agent workflow:**
1. Get SMILES from pubchem/chembl (e.g. sotorasib: `CC1=CN=C(C=C1)NC(=O)C2=CC(=CC=C2)F`)
2. Pass those SMILES to datamol for property calculation, fingerprinting, clustering, etc.