Datamol Cheminformatics Skill
Skill Verified ActivePythonic 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. Part of the AlterLab Academic Skills suite.
To simplify complex molecular operations for drug discovery and related research by offering a user-friendly interface with sensible defaults over the RDKit library.
Features
- SMILES parsing and standardization
- Molecular descriptor and fingerprint computation
- 3D conformer generation and analysis
- Clustering and diversity selection
- Scaffold and fragment analysis
- Support for various molecular file formats (SDF, SMILES, CSV, Excel)
- Remote file support via fsspec
- Parallel processing for batch operations
Use Cases
- Standardizing and cleaning molecular datasets
- Calculating molecular properties for filtering or QSAR
- Generating diverse sets of molecules for screening
- Analyzing scaffold diversity in compound libraries
- Visualizing molecular structures and conformers
Non-Goals
- Providing a full replacement for RDKit's advanced control
- Handling highly specialized or non-standard cheminformatics tasks
- Advanced quantum chemistry calculations
Workflow
- Load molecular data from files or strings
- Standardize and sanitize molecules
- Compute descriptors or fingerprints
- Perform clustering, diversity selection, or scaffold analysis
- Generate 3D conformers if needed
- Visualize results or export processed data
Practices
- Data standardization
- Molecular descriptor calculation
- Similarity analysis
- Structure-activity relationship analysis
- Machine learning feature generation
Prerequisites
- Python environment
- uv pip installed
Installation
npx skills add AlterLab-IEU/AlterLab-Academic-SkillsRuns the Vercel skills CLI (skills.sh) via npx — needs Node.js locally and at least one installed skills-compatible agent (Claude Code, Cursor, Codex, …). Assumes the repo follows the agentskills.io format.
Quality Score
VerifiedTrust Signals
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