Does it support standard chemical file formats?

Yes, it fully supports reading and writing SMILES, SDF, MOL, MOL2, and InChI formats, including batch processing for large datasets.

What is the RDKit skill used for in Claude Code?

It allows Claude to autonomously perform chemical informatics tasks such as parsing molecular structures, calculating physical properties, and performing substructure searches.

Can I generate 3D structures from SMILES strings?

Yes, this skill provides guidance on using RDKit's ETKDG method for 3D coordinate generation and force field optimization (UFF/MMFF94).

Can I calculate drug-likeness with this skill?

Absolutely. It includes functions for Lipinski's Rule of Five, calculating molecular weight, LogP, H-bond donors/acceptors, and TPSA.

How does this skill handle chemical reactions?

It uses Reaction SMARTS to define transformations, allowing Claude to simulate chemical reactions and predict products based on reactant inputs.

RDKit Cheminformatics Toolkit

Name: RDKit Cheminformatics Toolkit
Author: jimmc414

byjimmc414

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324

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Data Science & ML

Provides comprehensive cheminformatics capabilities for molecular analysis, manipulation, and property calculation within Claude Code.

This skill integrates the industry-standard RDKit library into the Claude Code environment, enabling autonomous execution of advanced cheminformatics workflows. It offers fine-grained control over molecular data, including SMILES/SDF parsing, Lipinski descriptor calculations, fingerprinting for similarity searching, and SMARTS-based substructure matching. Designed for drug discovery and computational chemistry, it allows Claude to handle complex tasks like 3D coordinate generation, conformer optimization, and chemical reaction modeling with scientific precision.

Key Features

01Comprehensive descriptor calculation including MW, LogP, and TPSA

02Molecular I/O and conversion for SMILES, SDF, MOL, and InChI formats

032D and 3D coordinate generation with force field optimization

04324 GitHub stars

05Molecular fingerprinting and Tanimoto similarity analysis

06Advanced substructure searching using SMARTS patterns

Use Cases

01Automating the generation and visualization of 3D chemical structures

02Identifying and clustering similar compounds within a chemical dataset

03Filtering large molecular libraries for drug-likeness and lead optimization

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos rdkit

For use in Claude.ai and ChatGPT