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name: data-cli-integration description: "Use for RDKit data-file discovery, pharmacophore feature-definition files, PandasTools molecule DataFrames, lightweight database helpers, and public CLI-style integration workflows." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

RDKit Data, CLI, and Integration

Use this sub-skill when a task asks an agent to connect RDKit chemistry code to package data files, tabular data, pandas workflows, feature-definition files, SQL/database helpers, or small command-line workflows around installed RDKit.

Route Here

• Locate package data with rdkit.RDConfig.RDDataDir, including BaseFeatures.fdef, FunctionalGroups.txt, Salts.txt, RDData.sqlt, RDTests.sqlt, and sample NCI/ files.
• Build pharmacophore feature factories with rdkit.Chem.ChemicalFeatures.BuildFeatureFactory or BuildFeatureFactoryFromString.
• Annotate molecules from SMILES with feature families, types, atom ids, and coordinates using the bundled scripts/feature_finder.py helper.
• Use rdkit.Chem.PandasTools for SDF-to-DataFrame, SMILES-to-molecule columns, substructure filtering, SDF/SMILES/XLSX export, and HTML molecule rendering.
• Use rdkit.Dbase helpers for SQLite-style RDKit data tables or for understanding legacy DB utility boundaries.
• Triage installed-package integration issues such as missing data files, optional pandas/XLSX dependencies, database backend availability, or local checkout shadowing.

Route Elsewhere

• Basic molecule parsing, SDF/SMILES suppliers, sanitization, and molecule validation: ../molecule-io-core/.
• Descriptor calculation, fingerprints, similarity, clustering, or ML feature engineering: ../descriptors-fingerprints/.
• 2D/3D coordinates, conformers, drawing APIs, and image generation outside pandas export: ../conformers-drawing/.
• Reactions, standardization, salt stripping chemistry policy, tautomer handling, or R-group workflows: ../reactions-standardization/.
• Optional contributed utilities and standalone contributed scorers: ../contrib-utilities/.

Start With These References

• references/data-files-and-features.md for RDConfig, installed data files, FDef feature factories, and feature-finder usage.
• references/pandas-and-database.md for PandasTools, SDF/SMILES table round-trips, HTML/XLSX export, and DB helper boundaries.
• references/troubleshooting.md for missing data, pandas optional behavior, DB backend problems, and checkout-shadowing diagnostics.
• scripts/feature_finder.py for a safe installed-package CLI that reports RDKit chemical features for SMILES strings.

Common Patterns

• Prefer os.path.join(RDConfig.RDDataDir, "BaseFeatures.fdef") for the default pharmacophore feature-definition file instead of hard-coding install paths.
• Check os.path.isdir(RDConfig.RDDataDir) and os.path.exists(...) before assuming sample data or .fdef files are present in minimal packages.
• Import PandasTools only when pandas-backed behavior is needed, and catch ImportError for environments without pandas.
• Keep database examples SQLite-oriented unless the task explicitly asks for legacy PostgreSQL/DbCLI behavior; RDKit PostgreSQL cartridge work is outside this sub-skill's runtime scope.
• Treat Projects/DbCLI as historical/reference-only guidance unless the installed RDKit distribution exposes the same modules and dependencies.

Quick Smoke

Run the bundled feature helper in any environment where RDKit is importable:

python scripts/feature_finder.py --smiles "CC(=O)O" "c1ccncc1" --summary

Use an explicit feature-definition file when testing custom pharmacophore rules:

python scripts/feature_finder.py --fdef custom.fdef --smiles "CCO"