Rdkit

This is the go-to cheminformatics library when you need fine-grained control over molecular operations. You get SMILES and SDF parsing, descriptor calculations like molecular weight and LogP, fingerprinting for similarity searches, substructure matching, and 2D/3D coordinate generation. It auto-sanitizes molecules on import with valence checking and aromaticity perception, which is great until you need to override it for edge cases. The skill documentation covers batch processing with suppliers, Morgan and MACCS fingerprints, Tanimoto similarity, and Butina clustering. If you just need standard workflows, use datamol instead since it wraps this with a simpler interface. Pick rdkit when you're doing custom sanitization or need specialized algorithms that higher-level tools don't expose.

skills.sh installs: 297
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill rdkit --agent claude-code

Installs into .claude/skills of the current project.

Files

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.

Core Capabilities

1. Molecular I/O and Creation

Reading Molecules:

Read molecular structures from various formats:

from rdkit import Chem

# From SMILES strings
mol = Chem.MolFromSmiles('Cc1ccccc1')  # Returns Mol object or None

# From MOL files
mol = Chem.MolFromMolFile('path/to/file.mol')

# From MOL blocks (string data)
mol = Chem.MolFromMolBlock(mol_block_string)

# From InChI
mol = Chem.MolFromInchi('InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')

Writing Molecules:

Convert molecules to text representations:

# To canonical SMILES
smiles = Chem.MolToSmiles(mol)

# To MOL block
mol_block = Chem.MolToMolBlock(mol)

# To InChI
inchi = Chem.MolToInchi(mol)

Batch Processing:

SKILL.md on GitHub

Details

Repository: github.com/davila7/claude-code-templates
Category: Data Science & ML
First seen: Jun 3, 2026