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datamol

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.

by K-Dense-AI 40k MIT Updated Aug 31, 2026
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datamol skill by K-Dense-AI
datamol — Data skill by K-Dense-AI

Overview

datamol is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, par…”. The project has 40k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/datamol`.

What datamol does

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.

What’s inside

The SKILL.md for datamol is organised into these sections:

  • Overview
  • Installation and Setup
  • Core Workflows
  • Parallelization
  • Reference Documentation
  • Best Practices
  • Error Handling
  • Integration with Machine Learning
  • Troubleshooting
  • Additional Resources

Installation

Add datamol to your agent with:

git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/datamol

Review a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.

Supported agents

Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.

License

datamol is published under the MIT license.

Strengths

  • Clear MIT license — safe to read and adapt within its terms
  • Ships in K-Dense-AI/scientific-agent-skills, an established project with 40,410 GitHub stars
  • Actively maintained — repository updated in the last 30 days
  • Its repository gained 6,589 GitHub stars over the last 13 days

Author

K-Dense-AI 42 skills in the catalog · GitHub profile ↗
View skills

Topics

agent-skillsai-scientistbioinformaticschemoinformaticsclaudeclaude-skillsclaudecodeclinical-researchcomputational-biologydata-analysisdrug-discoverygenomicsmaterials-sciencemetabolomicsproteomicsscientific-computingscientific-visualization
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Frequently asked questions

What does datamol do?
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.
How do I install datamol?
Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/datamol in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
Is datamol free to use?
Yes. datamol is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
Where does datamol come from?
datamol ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 40,410 GitHub stars apply to that whole collection, not to this skill on its own.

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