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RDKit Cheminformatics Toolkit

A guide for doing molecular work with RDKit — parsing SMILES/SDF, descriptors, fingerprints, substructure search, reactions, and 2D/3D coordinates.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Guides molecular I/O (SMILES, MOL blocks, InChI, SDF suppliers/writers) and manual or partial sanitization control.
  • Covers descriptors (MW, LogP, TPSA, rotatable bonds), fingerprints via rdFingerprintGenerator (Morgan/ECFP, MACCS, atom pair, Avalon), Tanimoto similarity, and Butina clustering.
  • Adds SMARTS substructure searching, reaction SMARTS, ETKDG 3D embedding with force-field optimization, RMSD, scaffold/canonical hashes, and drawing with highlights.
  • Bundles runnable scripts: molecular_properties.py, similarity_search.py, substructure_filter.py.
  • Flags common pitfalls: unchecked None after parsing, missing explicit hydrogens, 2D vs 3D coordinates, and thread-unsafe MolSuppliers.

Who it's for

  • Drug discovery, computational chemistry, and cheminformatics researchers
  • Data scientists filtering or screening compound libraries
  • Users who need finer control than the datamol wrapper provides

Examples

  1. "Compute MW, LogP, TPSA and rotatable bonds for every molecule in this SDF and export a CSV."
  2. "Screen this library for Tanimoto similarity ≥ 0.7 against my reference compound, then cluster hits with Butina."
  3. "Filter molecules containing an amide group via SMARTS and render a grid image with the match highlighted."

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/rdkit/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/rdkit folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/rdkit/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/rdkit ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills directory: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/rdkit ~/.claude/skills/
  4. Confirm the references/ and scripts/ folders came along — they hold the API docs and worked examples the skill points to.
  5. Install RDKit: uv pip install rdkit for an existing Python environment, or conda create -c conda-forge -n my-rdkit-env rdkit && conda activate my-rdkit-env for a reproducible setup.
  6. Do not mix the conda rdkit build with the PyPI rdkit/rdkit-pypi packages in the same environment.
  7. Restart Claude Code and try a prompt like "Use RDKit to compute descriptors for this SMILES string."
View source on GitHub ↗License: MIT