rdkit
Cheminformatics toolkit for fine-grained molecular control. Parse and write SMILES, SDF, MOL and InChI; compute descriptors (MW, LogP, TPSA, QED, Bertz); build fingerprints (Morgan/ECFP, RDKit, MACCS, atom pair, torsion) and score Tanimoto, Dice or cosine similarity; run SMARTS substructure search and reaction SMARTS; generate 2D depictions and ETKDG 3D conformers; extract Murcko scaffolds and canonical hashes; control sanitization and stereochemistry directly. Also trigger on rdkit, Chem.MolFromSmiles, rdFingerprintGenerator, SDMolSupplier, SMARTS query, ETKDG, or FilterCatalog. For standard workflows with a simpler interface use the datamol skill, which wraps RDKit; use rdkit for advanced control, custom sanitization, and specialized algorithms.
- Version
- 1.4
- License
- MIT
- Compatibility
- Examples target RDKit 2026.03.x. Use conda-forge for the broadest binary support or PyPI package `rdkit` for supported platform wheels; `rdkit-pypi` is the legacy PyPI name.
Pinned to revision f67572246d9b, 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.
- Read
- Write
- Edit
- Bash
Files
- skills/rdkit/SKILL.md
- skills/rdkit/references/api_reference.md
- skills/rdkit/references/core_capabilities.md
- skills/rdkit/references/descriptors_reference.md
- skills/rdkit/references/smarts_patterns.md
- skills/rdkit/references/workflows_and_best_practices.md
- skills/rdkit/scripts/molecular_properties.py
- skills/rdkit/scripts/similarity_search.py
- skills/rdkit/scripts/substructure_filter.py
Every link opens the file at its source, pinned to the revision this page describes.