Datamol Cheminformatics Skill
技能 已验证 活跃Pythonic 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.
功能
- 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
使用场景
- 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
非目标
- Providing a full replacement for RDKit's advanced control
- Handling highly specialized or non-standard cheminformatics tasks
- Advanced quantum chemistry calculations
工作流
- 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
实践
- Data standardization
- Molecular descriptor calculation
- Similarity analysis
- Structure-activity relationship analysis
- Machine learning feature generation
先决条件
- Python environment
- uv pip installed
安装
npx skills add AlterLab-IEU/AlterLab-Academic-Skills通过 npx 运行 Vercel skills CLI(skills.sh)— 需要本地安装 Node.js,以及至少一个兼容 skills 的智能体(Claude Code、Cursor、Codex 等)。前提是仓库遵循 agentskills.io 格式。
质量评分
已验证类似扩展
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