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.

Installation and Setup

Use uv when installing into an existing Python environment:

uv pip install "rdkit==2026.3.6"

For reproducible chemistry environments, especially when mixing compiled scientific packages, conda-forge remains the upstream recommendation: