RDKit Cheminformatics

About

This skill integrates RDKit's powerful cheminformatics capabilities into Claude, enabling precise control over molecular structures. It facilitates complex tasks such as SMILES/SDF parsing, molecular property calculation (LogP, TPSA, MW), fingerprint generation for similarity searching, and 2D/3D coordinate generation. Designed for researchers and developers in drug discovery and chemical informatics, it provides standardized patterns for molecular sanitization, substructure searching using SMARTS, and chemical reaction modeling.

Key Features

• 2D depiction and 3D conformer generation with force field optimization
• Advanced molecular descriptor calculation including LogP, MW, and TPSA
• Comprehensive Molecular I/O for SMILES, SDF, MOL, and InChI formats
• 1 GitHub stars
• Molecular fingerprinting and Tanimoto similarity for chemical clustering
• Substructure searching and pattern matching using SMARTS

Use Cases

• Predicting chemical reaction products and modeling transformation rules
• Automating drug-likeness screening and Lipinski’s Rule of Five validation
• Building chemical libraries with similarity-based diversity analysis