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:

conda create -c conda-forge -n my-rdkit-env rdkit
conda activate my-rdkit-env

Avoid installing both conda rdkit and PyPI rdkit/rdkit-pypi into the same environment unless you are deliberately debugging packaging behavior. Mixed installs can make it unclear which binary extension is being imported.

Core Capabilities

Twelve capability areas, each with worked code, are documented in references/core_capabilities.md:

Worked workflows and the performance, thread-safety, and version-sensitivity notes are in references/workflows_and_best_practices.md.

Prefer portable exchange formats (SMILES, SDF) for shared data; for local caches RDKit's binary molecule representation avoids generic pickle.

Preserve chemical meaning

Canonical isomeric SMILES records one molecular graph under a particular RDKit version. It does not merge tautomers, choose a pH-dependent protonation state, remove salts, or resolve unspecified stereo. Preserve the original structure and source ID before any explicit standardization policy. Similarity 1.0 is not an identity test: fingerprints collide and the bundled search ignores chirality unless --chirality is selected. See the tested identity/standardization example in references/workflows_and_best_practices.md.

The helpers retain one-based source IDs through invalid-record filtering, reject empty molecules, and perform no implicit salt stripping or neutralization. SMILES files have no header; RDKit parses a SMILES/CXSMILES structure followed by an optional name. Text outputs retain enhanced stereo groups as CXSMILES;

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