datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: 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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill datamol --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Datamol Cheminformatics Skill ## Overview Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify complex molecular operations with sensible defaults, efficient parallelization, and modern I/O capabilities. All molecular objects are native `rdkit.Chem.Mol` instances, ensuring full compatibility with the RDKit ecosystem. **Key capabilities**: - Molecular format conversion (SMILES, SELFIES, InChI) - Structure standardization and sanitization - Molecular descriptors and fingerprints - 3D conformer generation and analysis - Clustering and diversity selection - Scaffold and fragment analysis - Chemical reaction application - Visualization and alignment - Batch processing with parallelization - Cloud storage support via fsspec ## Installation and Setup Guide users to install datamol: ```bash uv pip install datamol ``` **Import convention**: ```python import datamol as dm ``` ## Core Workflows ### 1. Basic Molecule Handling **Creating molecules from SMILES**: ```python import datamol as dm # Single molecule mol = dm.to_mol("CCO") # Ethanol # From list of SMILES smiles_list = ["CCO", "c1ccccc1", "CC(=O)O"] mol
- Overview
- Installation and Setup
- Core Workflows
- 1. Basic Molecule Handling
- 2. Reading and Writing Molecular Files
- 3. Molecular Descriptors and Properties
- 4. Molecular Fingerprints and Similarity
- 5. Clustering and Diversity Selection
- 6. Scaffold Analysis
- 7. Molecular Fragmentation
- 8. 3D Conformer Generation
- 9. Visualization
- 10. Chemical Reactions
- Parallelization
uv pip install datamol
What does the datamol skill do?
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: 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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill datamol --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.