RDKit Cheminformatics Skill

Claude skill providing Python recipes for the full RDKit cheminformatics stack — molecular I/O, descriptor calculation, fingerprinting, substructure matching, reaction handling, and 3D coordinate generation.

   
Type Claude Skill
Supplier K-Dense Inc. (community OSS)
Availability GA — actively maintained 2025–2026
Pricing Free / OSS (BSD-3-Clause skill; MIT repo)
Capabilities Read/Write — Claude executes RDKit via the Bash/Python tool

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/structural-biology-drug-discovery/rdkit-cheminformatics into ~/.claude/skills/). Install via the Skills CLI (recommended): npx skills add K-Dense-AI/scientific-agent-skills, then enable the rdkit skill. Or clone the repo manually:
git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/rdkit ~/.claude/skills/
pip install rdkit

Project-scoped alternative: copy into .claude/skills/ instead of ~/.claude/skills/.

What it does

SKILL.md with recipes for:

  • SMILES / SDF / MOL parsing and standardization
  • Descriptors (MW, LogP, TPSA) and Lipinski rules
  • Morgan / RDKit / MACCS fingerprints and similarity
  • Substructure matching and SMARTS queries
  • 2D depiction and 3D embedding (ETKDG)
  • Reaction templates and enumeration

Primary use cases: SMILES parsing and standardization for ML pipelines, descriptor calculation, substructure / similarity search, reaction enumeration.

Notes

Skill is documentation plus Python recipes — Claude executes RDKit locally via Bash/Python. Sibling skills in the same repo (datamol, molfeat, medchem, deepchem) cover higher-level workflows.

Sources

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