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 ## When to Use This Skill Use this skill when the user wants to: - Load, standardize, and de-duplicate molecule tables (CSV/SDF/Excel/Parquet, local or cloud) with little boilerplate - Compute datamol's descriptor set, fingerprints, and Tanimoto distance matrices for a compound set - Cluster, pick diverse subsets, extract Murcko scaffolds, or fragment (BRICS/RECAP) a library - Generate and cluster 3D conformers, or render aligned molecule grids for SAR review ### Does NOT Trigger | Scenario | Use Instead | |----------|-------------| | Low-level control: custom sanitization flags, atom-mapped reaction details, specialised fingerprint/descriptor algorithms | `alterlab-rdkit`...