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Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
Passed 19 of 23 test cases with the skill, and 12 of 23 without it.
and 4 more in the full report
7 fixed12 passed either way4 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 7 test cases the skill fixed. Same model, same prompt, with and without the skill.
In an RDKit pipeline that calculates fragment descriptors and tautomer/protomer hashes, what fix was introduced in the 2024.09 release regarding unbranched alkanes?
| Checked | Without skill | With skill |
|---|---|---|
| States that RDKit 2024.09 corrected SMARTS definitions for unbranched-alkane fragment descriptors. | Missed | Passed |
The instructions your model reads when the skill loads.
RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for reading/writing molecular structures, calculating descriptors, fingerprinting, substructure searching, chemical reactions, 2D/3D coordinate generation, and molecular visualization. Use this skill for drug discovery, computational chemistry, and cheminformatics research tasks.
Current baseline (checked 2026-06-07): RDKit 2026.03.3 is the latest GitHub/PyPI release (rdkit 2026.3.3 on PyPI). Official installation docs continue to recommend conda-forge for most users, while cross-platform PyPI wheels are published under the rdkit package name. rdkit-pypi is the old PyPI package name and should only appear when maintaining legacy environments.
Use uv when installing into an existing Python environment:
uv pip install rdkit
For reproducible chemistry environments, especially when mixing compiled scientific packages, conda-forge remains the upstream recommendation:
conda create -c conda-forge -n my-rdkit-env rdkit
conda activate my-rdkit-env
Avoid installing both conda rdkit and PyPI rdkit/rdkit-pypi into the same environment unless you are deliberately debugging packaging behavior. Mixed installs can make it unclear which binary extension is being imported.
Reading Molecules:
Read molecular structures from various formats:
from rdkit import Chem
# From SMILES strings
mol = Chem.MolFromSmiles('Cc1ccccc1') # Returns Mol object or None
# From MOL files
test cases passed, vs 12 / 23 without
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