What is the RDKit skill for Claude Code?

It is a specialized capability that provides Claude with the domain knowledge and code patterns needed to use the RDKit library for chemical data analysis and molecular manipulation.

Can I use this for 3D molecular modeling?

Yes, the skill includes guidance for 3D coordinate generation, conformer embedding, and geometry optimization using force fields like UFF and MMFF94.

Does it support batch processing of chemical files?

Yes, it provides patterns for using SDMolSupplier and MultithreadedSDMolSupplier to efficiently process large SDF and SMILES datasets.

Can I visualize molecules with this skill?

Yes, it includes instructions for generating molecular images, grid views, and highlighting substructures for visual analysis.

How does it handle chemical sanitization?

The skill enforces standard RDKit sanitization steps, including valence checking and aromaticity perception, to ensure molecular structures are chemically valid.

RDKit Cheminformatics

Name: RDKit Cheminformatics
Author: ljchg12-hue

byljchg12-hue

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Data Science & ML

Enables advanced molecular analysis, chemical property calculation, and 3D coordinate generation using the RDKit toolkit.

The RDKit Cheminformatics skill equips Claude Code with the specialized knowledge required for sophisticated molecular modeling and chemical data manipulation. It provides implementation patterns for parsing SMILES and SDF formats, calculating essential descriptors like LogP and TPSA, performing high-performance substructure searches using SMARTS, and generating 3D conformers. Designed for researchers and developers in drug discovery and computational chemistry, this skill ensures best practices for molecular sanitization, fingerprinting, and chemical reaction modeling within an AI-assisted development workflow.

Key Features

01Comprehensive molecular I/O for SMILES, SDF, InChI, and MOL formats

021 GitHub stars

03Substructure searching and chemical reaction SMARTS patterns

04Advanced descriptor calculations including LogP, TPSA, and molecular weight

052D and 3D coordinate generation with force field optimization

06Molecular visualization and similarity clustering techniques

Use Cases

01Performing batch processing and sanitization of large chemical datasets

02Automating drug discovery pipelines and molecular screening tasks

03Generating 3D conformers and calculating molecular fingerprints for ML models

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ljchg12-hue/dotfiles scientific-skills

For use in Claude.ai and ChatGPT

Download Skill