alterlab-datamol

# Datamol Cheminformatics Skill ## Overview 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 ## Installation and Setup Guide users to install datamol: ```bash uv pip install datamol ``` Examples here are verified against **datamol 0.12.x** (pulls in RDKit automatically). The descriptor key names below are stable in this line; pin if you depend on them: `uv pip install 'datamol>=0.12,<0.13'`. **Import convention**: ```python import datamol as dm ``` ## Core Workflows ### 1. Basic Molecule Handling **Creating molecules from SMILES**: ```python import datamol as dm # Single molecule mol = dm.to_mol("CCO") # Ethanol # From list of SMILES smiles_list = ["CCO", "c1ccccc1", "CC(=O)O"] mols = [dm.to_mol(smi) for smi in smiles_list] # Error handling mol = dm.to_mol...