alterlab-rdkit
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.
Version: install with uv pip install rdkit (current release 2026.03.6 as of 2026-09; examples assume ≥ 2024.09). In 2026.03 the legacy fingerprint helpers (AllChem.GetMorganFingerprintAsBitVect, rdkit.Chem.AtomPairs.Pairs.*, Torsions.*) and Atom.GetImplicitValence() / GetExplicitValence() still run but log DEPRECATION WARNINGs — use the rdFingerprintGenerator API and atom.GetValence(Chem.ValenceType.IMPLICIT | EXPLICIT) in new code.
When to Use This Skill
Reach for this skill when you need fine-grained molecular control: custom sanitization, specialized fingerprints or descriptors, reaction enumeration, conformer generation, or programmatic drawing. For standard, high-level workflows with a simpler interface, prefer datamol (a wrapper around RDKit).