alterlab-rdkit
From the author
Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization, specialized fingerprint or descriptor algorithms, reaction enumeration, or conformer generation demand direct API control; for a high-level pandas-friendly wrapper over RDKit prefer alterlab-datamol, and for turning molecules into ML feature vectors prefer alterlab-molfeat. Part of the AlterLab Academic Skills suite.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-rdkit -a claude-code
Installs to .claude/skills/alterlab-rdkit/ · Each command fetches the skill straight from GitHub with the open skills CLI.
Byte-identical to the scanned commit, with the repository’s licence and a SOURCE.txt.
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Why 77
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Similar skills
Closest to this one by what they do and when they are used.
- alterlab-datamolAlterLab-IEU/AlterLab-Academic-SkillsWraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold analysis, and parallel batch processing, returning native rdkit.Chem.Mol objects. Use when running standard cheminformatics pipelines on molecule tables with minimal boilerplate; for low-level control, custom sanitization, or specialized algorithms prefer alterlab-rdkit. Part of the AlterLab Academic Skills suite.Data★ 78
- alterlab-molfeatAlterLab-IEU/AlterLab-Academic-SkillsFeaturizes molecules for machine learning with molfeat — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, pharmacophore and shape descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, CheMeleon) exposed as scikit-learn transformers that convert SMILES into feature vectors. Use when turning molecules into ML-ready feature matrices for QSAR/QSPR or virtual screening, or benchmarking fingerprint against descriptor and embedding representations; for training models and MoleculeNet benchmarks on those features prefer alterlab-deepchem, and for low-level fingerprint or descriptor primitives prefer alterlab-rdkit. Part of the AlterLab Academic Skills suite.Other★ 78
- rdkitforyourhealth111-pixel/Vibe-SkillsCore cheminformatics toolkit for SMILES/SDF/InChI parsing, descriptors (MW, LogP, TPSA), fingerprints, ECFP/Morgan fingerprints, substructure search, 2D/3D generation, similarity, reactions, and datamol-style molecule standardization when no separate wrapper skill is routed.Science★ 3.8K
- rdkit-cheminformaticsjaechang-hits/SciAgent-SkillsCheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure filtering, Lipinski drug-likeness, reaction enumeration, 2D/3D coordinates. For simpler API use datamol; use RDKit for fine-grained sanitization, custom fingerprints, or SMARTS/reaction control.Science★ 383
- datamolK-Dense-AI/scientific-agent-skillsPythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.Design★ 54.5K
- molfeatK-Dense-AI/scientific-agent-skillsFeaturizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints, RDKit descriptors, pharmacophores, pretrained embeddings, configuration persistence, and molecule-to-label alignment.Science★ 54.5K
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