Alterlab Rdkit
Skill Verified ActiveCheminformatics 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. Part of the AlterLab Academic Skills suite.
To equip researchers and developers with a powerful and flexible toolkit for detailed molecular analysis and manipulation, enabling advanced cheminformatics tasks in research and discovery.
Features
- Molecular I/O and creation from various formats (SMILES, SDF, MOL, etc.)
- Comprehensive molecular descriptors and property calculations (MW, LogP, TPSA)
- Generation and comparison of diverse molecular fingerprints (Morgan, MACCS, etc.)
- Precise substructure searching and SMARTS pattern matching
- 2D and 3D coordinate generation and optimization
- Chemical reaction definition and application
Use Cases
- Analyzing drug-likeness and lead-likeness of molecules
- Screening large compound libraries for similarity to a query
- Identifying molecules containing specific functional groups or structural motifs
- Generating and visualizing 3D molecular conformers for docking studies
- Working with chemical reactions for synthesis planning
Non-Goals
- Providing a simplified interface for common workflows (use datamol for that)
- Performing basic file format conversions without cheminformatics context
- Acting as a general-purpose chemistry simulation engine beyond RDKit's scope
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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