datamol

Topics in the source

• Datamol Cheminformatics Skill
• Overview
• Installation and Setup
• Core Workflows
• 1. Basic Molecule Handling
• 2. Reading and Writing Molecular Files
• 3. Molecular Descriptors and Properties
• 4. Molecular Fingerprints and Similarity

Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify complex molecular operations with sensible defaults, efficient parallelization, and modern I/O capabilities. All molecular objects are native rdkit.Chem.Mol instances, ensuring full compatibility with the RDKit ecosystem. Key capabilities: Molecular format conversion (SMILES, SELFIES, InChI) Structure standardization and sanitization Molecular descriptors and fingerprints 3D conformer generation and analysis Clustering and diversity selection Scaffold and fragment analysis Chemical reaction application Visualization and alignment Batch processing with parallelization Cloud storage support via fsspec Guide users to install datamol: Import convention: Creating molecules from SMILES: Converting molecules to SMILES: Standardization and sanitization (always recommend for user-provided molecules): Refer to references/iomodule.md for comprehensive I/O documentation. Reading files: Writing files: Remote file support (S3, GCS, HTTP): Refer to references/descriptorsviz.md for detailed descriptor documentation. Computing descriptors for a single molecule: Batc

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