Agent skill · research science · aiskillstore
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
Why this skill is useful
Provides advanced cheminformatics capabilities and domain-specific knowledge for molecular analysis that the AI wouldn't reliably generate on its own.
What it needs
Requires rdkit installed locally. About 9k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
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: Writing Molecules: Convert molecules to text representations: Batch Processing: For processing multiple molecules, use Supplier/Writer objects: Important Notes: All MolFrom functions return None on failure with error messages Always check for None before processing molecules Molecules are automatically sanitized on import (validates valence, perceives aromaticity) 2. Molecular Sanitization and Validation RDKit automatically sanitizes molecules during parsing, executing 13 steps including valence checking, aromaticity perception, and chirality assignment. Sanitization Control: Common Sanitization Issues: Atoms with explicit valence exceeding maximum allowed will raise exceptions Invalid aromatic rings will cause kekulization errors Radical electrons may not be properly assigned without explicit specification 3. Molecular Analysis and Properties Accessing Molecular Structure: Stereochemistry: Fragment Analysis: 4. Molecular Descriptors and Properties Basic Descriptors: Batch Descriptor Calculation: Lipinski's Rule of Five: 5. Fingerprints and Molecular Similarity Fingerprint Types: Similarity Calculation: Clustering and Diversity: 6. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/rdkit--f4682d