datamol - Perform cheminformatics with datamol
Provides a Pythonic interface for molecular parsing, standardization, descriptors, fingerprints, clustering, conformers, fragmentation, visualization, and file I/O.
Tags
Updated: 2026-10-04Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Parse molecular formats
- Standardize molecular structures
- Compute molecular descriptors
- Generate molecular fingerprints
- Calculate molecular distances
- Cluster molecular structures
- Select diverse molecules
- Extract molecular scaffolds
- Fragment molecular structures
- Generate 3D conformers
- Apply chemical reactions
- Read and write molecular files
- Process molecular data in parallel
- Access remote molecular files
Inputs
- Molecular strings
- Molecule objects
- Molecular data files
- Cloud storage URIs
- Processing parameters
Outputs
- RDKit molecule objects
- Molecular strings
- Descriptor data
- Fingerprint data
- Distance matrices
- Molecule clusters
- Selected molecule subsets
- Scaffold structures
- Fragment sets
- 3D conformers
- Visualization files
- Processed molecular files
Requirements
- Python environment
- Installed datamol package
- RDKit support
- Required file or cloud access permissions