medchem
Filters and triages small-molecule libraries with the Python medchem library (datamol-io, v2.0.5) on top of RDKit and datamol. Covers drug-likeness rules (Lipinski, Veber, CNS, lead-like) via RuleFilters, structural alerts (ChEMBL-derived sets, NIBR, PAINS, Brenk), chemical group detection, ZINC-based complexity thresholds, scaffold constraints, and the medchem query language (QueryFilter). Use when screening a compound library for drug-likeness, removing PAINS or other structural-alert compounds, prioritizing hits for hit-to-lead or lead optimization, detecting functional groups, or combining criteria in one query. Not for computing general descriptors or fingerprints; use RDKit directly.
- Version
- 1.2
- License
- Apache-2.0 license
- Compatibility
- Requires Python 3.9+ and datamol (installed with medchem). Optional Lilly demerit filter requires separate `lilly-medchem-rules` conda package.
Pinned to revision df088027ff23, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
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Files
- skills/medchem/SKILL.md
- skills/medchem/references/api_guide.md
- skills/medchem/references/rules_catalog.md
- skills/medchem/scripts/filter_molecules.py
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