alterlab-medchem

# Medchem ## Overview Medchem (`datamol-io/medchem`) is a Python library for molecular filtering and prioritization in drug-discovery workflows: medicinal-chemistry rules, structural alerts (ChEMBL/NIBR/PAINS), chemical-group detection, complexity metrics, and a query DSL. Rules and filters are context-specific guidelines, not hard truth — combine with domain expertise. **Verified against `medchem==2.0.5` (RDKit 2026.3.x, Python 3.12).** API names below are checked against this version; earlier docs/blog posts described a different surface. ## When to Use This Skill This skill should be used when: - Applying drug-likeness rules (Lipinski, Veber, etc.) to compound libraries - Filtering molecules by structural alerts or PAINS patterns - Prioritizing compounds for lead optimization - Assessing compound quality and medicinal chemistry properties - Detecting reactive or problematic functional groups - Calculating molecular complexity metrics ## Installation ```bash uv pip install medchem # PyPI; pulls rdkit + datamol ``` Two features need extra native deps that PyPI cannot provide: - **Lilly demerits** (`lilly_demerit_filter`) shells out to compiled binaries — install via conda: `mamba install -c conda-forge lilly-medchem-rules`. Without them, the call raises `ImportError`. - The ChemAxon rule (`rule_of_chemaxon_druglikeness`) needs a licensed ChemAxon install. Everything else (RuleFilters, CommonAlerts, NIBR, complexity, groups, query) works from the PyPI wheel alone....