alterlab-rdkit - Advanced RDKit cheminformatics toolkit
Provides Python guidance for molecular structure handling, analysis, descriptors, fingerprints, substructure searches, reactions, coordinates, and visualization with RDKit.
Tags
Updated: 2026-10-07Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Read molecular structures
- Write molecular representations
- Sanitize molecular structures
- Validate chemistry problems
- Calculate molecular descriptors
- Generate molecular fingerprints
- Calculate molecular similarity
- Cluster molecular compounds
- Search molecular substructures
- Run chemical reactions
- Generate 2D coordinates
- Generate 3D coordinates
- Visualize molecular structures
Inputs
- SMILES strings
- SDF files
- MOL files
- MOL blocks
- InChI strings
- SMARTS patterns
- Molecular objects
- Reaction SMARTS
- Molecular datasets
Outputs
- Molecular objects
- SMILES strings
- MOL blocks
- InChI strings
- Sanitization results
- Molecular descriptors
- Fingerprint data
- Similarity scores
- Cluster assignments
- Substructure matches
- Reaction products
- 2D coordinates
- 3D coordinates
- Molecular visualizations
Requirements
- Python environment
- RDKit library