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name: rdkit description: "Use for RDKit cheminformatics tasks: molecule parsing and validation, descriptors and fingerprints, conformers and drawing, reactions and standardization, data integrations, optional Contrib utilities, or RDKit repository development." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

RDKit Skill

Use this repo skill when a task involves RDKit, the open-source C++/Python cheminformatics toolkit. RDKit is commonly used for molecule I/O, structure validation, descriptors, fingerprints, similarity, conformers, drawing, reactions, standardization, R-group decomposition, feature definitions, tabular cheminformatics, optional Contrib utilities, and maintaining the RDKit source tree.

Install and Import Check

For normal Python use, prefer the documented binary install route:

conda install -c conda-forge rdkit
python - <<'PY'
from rdkit import Chem
mol = Chem.MolFromSmiles('c1ccccc1O')
assert mol is not None
print(Chem.MolToSmiles(mol))
PY

Use scripts/check_rdkit_env.py when an agent needs a quick installed-package smoke check, module availability report, or diagnosis for a local source checkout that shadows an installed RDKit package.

Route by Task

• sub-skills/molecule-io-core/ handles molecule creation, SMILES/SMARTS/MolBlock/SDF I/O, sanitization, hydrogens, atom/bond/ring queries, substructure matching, and editable molecules.
• sub-skills/descriptors-fingerprints/ handles scalar descriptors, QED/Lipinski/Crippen/TPSA properties, Morgan/RDKit/atom-pair/topological-torsion fingerprints, DataStructs similarity, feature tables, and Butina clustering.
• sub-skills/conformers-drawing/ handles ETKDG conformer generation, UFF/MMFF optimization, 3D alignment/RMSD, 2D coordinates, and SVG/PNG/grid rendering.
• sub-skills/reactions-standardization/ handles reaction SMARTS/RXN workflows, product sanitization, MolStandardize cleanup/normalization/fragment/tautomer workflows, R-group decomposition, and stereochemistry/CIP handling.
• sub-skills/data-cli-integration/ handles RDConfig data files, feature-definition files, chemical feature factories, PandasTools, lightweight DB helpers, and installed-package CLI-style helpers.
• sub-skills/contrib-utilities/ handles optional community Contrib utilities such as SA Score, NP Score, NIBR filters, Fraggle, MMPA, FreeWilson, and MolVS-derived recipes.
• sub-skills/repo-development/ handles editing, building, testing, formatting, wrapper boundaries, generated stubs/docstrings, and source-checkout diagnostics for RDKit itself.

Shared References

• references/capability-map.md maps common user requests to sub-skills, bundled scripts, and verification evidence.
• references/troubleshooting.md covers cross-cutting install/import, source-checkout shadowing, optional dependency, data-file, and compiled-extension failures.
• references/repo-provenance.md records the source snapshot, selected evidence paths, dirty state, and inspection-package facts for future refresh decisions.

Quick Decision Rules

• If a task starts with invalid SMILES, suppliers, None molecules, properties on atoms/bonds, or substructure matching, start with molecule-io-core before any downstream chemistry.
• If a task asks for feature vectors, similarity search, clustering, or descriptor columns, start with descriptors-fingerprints and cross-link back to molecule validation when inputs are untrusted.
• If a task mentions 3D coordinates, RMSD, force fields, or images, start with conformers-drawing; do not treat 2D depiction coordinates as 3D conformers.
• If a task transforms molecules chemically, standardizes salts/tautomers, runs reactions, or decomposes analog series into R groups, start with reactions-standardization.
• If a task asks where RDKit data lives, how to use BaseFeatures.fdef, how to attach molecules to a DataFrame, or how to make a tiny CLI around installed RDKit, start with data-cli-integration.
• If a task mentions Contrib, SA/NP score, Fraggle, MMPA, FreeWilson, or optional community scripts, start with contrib-utilities and check availability before assuming modules/data are installed.
• If a task is about changing this repository or an import fails from an unbuilt checkout with rdBase missing, start with repo-development.

Working Safely

• Prefer installed RDKit package APIs for user workflows; only use source-tree instructions for repository-development tasks.
• Validate molecule creation before passing objects to descriptors, fingerprints, reactions, conformer embedding, or drawing.
• Treat optional wrappers and integrations such as PostgreSQL cartridge, Java/C# wrappers, FreeSASA, InChI, Avalon, CoordGen, Contrib tools, and database helpers as availability-dependent.
• Keep long-running native tests, benchmarks, fuzzers, full CMake builds, and database workflows out of routine user tasks unless the user explicitly asks for maintainer validation.
• Do not depend on original RDKit repository examples or scripts at runtime; use the bundled references and scripts in this skill tree.