What is the RDKit skill for Claude Code used for?

It provides specialized guidance and implementation patterns for using the RDKit library to perform molecular analysis, property calculation, and structural manipulation.

How does this help with drug discovery tasks?

It enables automated screening for drug-likeness, calculating properties like lipophilicity (LogP) and polar surface area (TPSA), and performing similarity searches against compound libraries.

Does it support common chemical file formats?

Absolutely. The skill provides patterns for reading and writing SMILES strings, SDF files, Mol blocks, and InChI identifiers, including batch processing via suppliers.

When should I use RDKit over simpler wrappers like datamol?

Use the RDKit skill when you require advanced control, custom sanitization logic, specialized algorithms, or fine-grained manipulation of the molecular graph.

Can this skill handle 3D molecular modeling?

Yes, it includes guidance for generating 3D coordinates, conformer generation, and geometry optimization using force fields like UFF and MMFF94.

RDKit Cheminformatics

Name: RDKit Cheminformatics
Author: Zehong-Wang

byZehong-Wang

0•

数据科学与机器学习

Provides specialized guidance for molecular analysis, structural manipulation, and chemical property calculation using the RDKit library.

The RDKit skill equips Claude with deep expertise in cheminformatics, enabling precise control over molecular data structures and chemical information. It offers comprehensive implementation patterns for reading and writing common formats like SMILES and SDF, calculating essential chemical descriptors such as LogP and TPSA, and performing complex substructure searches using SMARTS. This skill is indispensable for researchers and developers working in drug discovery, computational chemistry, or bioinformatics who need to automate the processing and analysis of chemical libraries.

主要功能

010 GitHub stars

02Chemical descriptor calculation including MW, LogP, TPSA, and HBD/HBA

03Molecular fingerprinting and Tanimoto similarity analysis

042D and 3D coordinate generation with conformer optimization

05Advanced substructure searching and SMARTS pattern matching

06Molecular parsing and conversion for SMILES, SDF, InChI, and Mol blocks

使用场景

01Building high-throughput chemical database filtering and search pipelines

02Automating drug-likeness screening and Lipinski's Rule of Five validation

03Generating publication-quality 2D/3D molecular visualizations and depictions

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos rdkit

For use in Claude.ai and ChatGPT

Download Skill