Datamol Cheminformatics

About

Datamol provides a streamlined interface for complex molecular operations, offering sensible defaults and built-in parallelization for high-performance chemical data processing. It facilitates essential drug discovery tasks such as SMILES/SELFIES parsing, structure standardization, 3D conformer generation, and molecular fingerprinting while maintaining full compatibility with the RDKit ecosystem. This skill is ideal for researchers and developers building automated pipelines for chemical property prediction, virtual screening, and molecular data analysis.

Key Features

• Advanced 3D conformer generation with energy minimization
• High-performance batch computation of molecular descriptors and fingerprints
• Universal molecular file I/O with native S3, GCS, and HTTP support
• Efficient SMILES/SELFIES parsing and structure standardization
• 3,718 GitHub stars
• Scaffold and fragment analysis for chemical library diversity selection

Use Cases

• Clustering large compound libraries based on structural similarity
• Generating diverse 3D conformer ensembles for spatial molecular analysis
• Standardizing and cleaning chemical datasets for machine learning training