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.

When to Use

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).

Core Capabilities

RDKit exposes twelve capability areas. Each is summarized below with the single most common call; complete, runnable recipes for every area live in references/code_recipes.md.

1. Molecular I/O and Creation

Read and write molecules across SMILES, MOL/SDF, MOL2, PDB, and InChI. Batch-process with Supplier/Writer objects, including ForwardSDMolSupplier and MultithreadedSDMolSupplier for large or gzipped files.