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

Guides coding agents through cheminformatics tasks in Python, including SMILES parsing, descriptor calculations, and 3D coordinate generation.

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

What rdkit does

This skill guides agents through Python cheminformatics. It covers parsing SMILES and SDF formats, validating structures, and computing properties such as LogP and TPSA.

The reference covers Morgan fingerprints and SMARTS queries. It also details ETKDG 3D coordinate embedding. Checking the return code of EmbedMolecule is critical. A value of -1 indicates embedding failure. Sending a failed conformer to force-field optimization breaks the run.

Workflows require the rdkit Python package. It was tested on version 2026.03.6 with Python 3.13. No network access or API credentials are required after setup. Mixing conda and pip installs causes binary extension conflicts.

What it helps with

  • parse and sanitize molecular structures from SMILES and SDF files
  • calculate molecular descriptors including LogP, TPSA, and molecular weight
  • execute substructure searches using SMARTS query patterns
  • generate 3D conformers with ETKDG and optimize geometries

Example prompts for the agent

  • Calculate LogP, TPSA, and molecular weight for these SMILES strings using RDKit
  • Generate 3D coordinates for this molecule using ETKDG and check for embedding failures
  • Search this SDF file for substructures matching the specified SMARTS pattern

How to install rdkit

1Skills CLI (Vercel)

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

2Manually: put the files in place

~/.claude/skills/rdkit/SKILL.md

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

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Questions about rdkit

How to install rdkit in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill rdkit -a claude-code in your terminal. You can also install it manually by saving the skill to ~/.claude/skills/rdkit/SKILL.md.

What does the rdkit skill do?

It provides patterns and instructions for Python cheminformatics. The agent handles descriptor calculation, SMARTS substructure matching, fingerprint generation, and 3D coordinates.

What prerequisites are required?

You need Python with the rdkit package installed. The skill operates locally and does not require API keys or internet access.

See also

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