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.

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.

from rdkit import Chem
mol = Chem.MolFromSmiles('Cc1ccccc1')   # returns Mol or None
smiles = Chem.MolToSmiles(mol)          # canonical SMILES

Every MolFrom* function returns None on failure — always check before use. Molecules are auto-sanitized on import.

2. Molecular Sanitization and Validation

Parsing runs a 13-step sanitization (valence checks, aromaticity perception, chirality assignment). Control it with sanitize=False, SanitizeMol, partial sanitizeOps, and diagnose failures with DetectChemistryProblems.

mol = Chem.MolFromSmiles('C1=CC=CC=C1', sanitize=False)
problems = Chem.DetectChemistryProblems(mol)

Common failure modes: valence overflow, kekulization errors on invalid aromatic rings, and unassigned radicals.