Rdkit

If you need to manipulate molecular structures at a granular level, this is the canonical cheminformatics library. It handles SMILES and SDF parsing, calculates descriptors like molecular weight and LogP, generates fingerprints for similarity searches, and manages 2D/3D coordinate generation. The skill documentation covers sanitization control (RDKit runs 13 validation steps by default), stereochemistry assignment, and the modern fingerprint generator API for Morgan and RDKit topological fingerprints. Worth noting that the maintainers recommend using datamol for standard workflows since it wraps RDKit with a simpler interface. Reach for this when you need custom sanitization logic, specialized substructure algorithms, or direct control over molecular validation steps that higher-level tools abstract away.

skills.sh installs: 2K
GitHub stars: 56.6K
last updated: Aug 21, 2026

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Install

$ npx -y skills add k-dense-ai/scientific-agent-skills --skill rdkit --agent claude-code

Installs into .claude/skills of the current project.

Files

RDKit Cheminformatics Toolkit

Overview

RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for reading/writing molecular structures, calculating descriptors, fingerprinting, substructure searching, chemical reactions, 2D/3D coordinate generation, and molecular visualization. Use this skill for drug discovery, computational chemistry, and cheminformatics research tasks.

Tested stable baseline (reviewed 2026-10-01): RDKit 2026.03.6, distributed as rdkit==2026.3.6 on PyPI; this is the current stable GitHub/PyPI release. Official installation docs continue to recommend conda-forge for most users, while cross-platform PyPI wheels are published under the rdkit package name. rdkit-pypi is the old PyPI package name and should only appear when maintaining legacy environments.