rdkit
Cheminformatics 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.
npx skills add K-Dense-AI/scientific-agent-skills --skill rdkit --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.
# RDKit Cheminformatics Toolkit ## Overview RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for reading/writing molecular structures, calculating descriptors, fingerprinting, substructure searching, chemical reactions, 2D/3D coordinate generation, and molecular visualization. Use this skill for drug discovery, computational chemistry, and cheminformatics research tasks. **Current baseline (checked 2026-06-07):** RDKit **2026.03.3** is the latest GitHub/PyPI release (`rdkit` 2026.3.3 on PyPI). Official installation docs continue to recommend conda-forge for most users, while cross-platform PyPI wheels are published under the `rdkit` package name. `rdkit-pypi` is the old PyPI package name and should only appear when maintaining legacy environments. ## Installation and Setup Use `uv` when installing into an existing Python environment: ```bash uv pip install rdkit ``` For reproducible chemistry environments, especially when mixing compiled scientific packages, conda-forge remains the upstream recommendation: ```bash conda create -c conda-forge -n my-rdkit-env rdkit conda activate my-rdkit-env
- Overview
- Installation and Setup
- Core Capabilities
- Common Pitfalls
- Resources
- references/
- scripts/
uv pip install rdkit conda create -c conda-forge -n my-rdkit-env rdkit conda activate my-rdkit-env
What does the rdkit skill do?
Cheminformatics 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.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill rdkit --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 K-Dense-AI/scientific-agent-skills, a repository with 32,619 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.