rdkit - Advanced molecular analysis with RDKit
Provides Python-based molecular parsing, validation, descriptors, fingerprints, similarity, substructure search, reactions, coordinate generation, and visualization.
Tags
Updated: 2026-10-08Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Parse molecular structures
- Write molecular representations
- Sanitize molecular structures
- Validate chemistry problems
- Calculate molecular descriptors
- Generate molecular fingerprints
- Compare molecular similarity
- Search molecular substructures
- Run chemical reactions
- Generate 2D and 3D coordinates
- Analyze molecular fragments
- Visualize molecular structures
Inputs
- Molecular structure strings
- Molecular structure files
- Molecule datasets
- SMARTS query patterns
- Reaction SMARTS patterns
- Processing parameters
Outputs
- Parsed molecular structures
- Molecular representations
- Descriptor values
- Molecular fingerprints
- Similarity scores
- Substructure matches
- Reaction products
- 2D and 3D coordinates
- Molecular visualizations
- Validation errors
Requirements
- Python environment
- RDKit library