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RDKit Cheminformatics Toolkit

Gives Claude fine-grained RDKit guidance for SMILES/SDF parsing, descriptors, fingerprints, substructure search, reactions and 2D/3D generation.

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

What it does

Provides structured guidance for cheminformatics work with the RDKit Python API.

  • Molecular I/O: SMILES, MOL blocks, InChI, SDF suppliers, multithreaded reading and writers
  • Descriptors: MW, LogP, TPSA, H-bond donors/acceptors, rotatable bonds, drug-likeness filters
  • Fingerprints & similarity: Morgan/ECFP via rdFingerprintGenerator, MACCS, atom pair, Tanimoto, Butina clustering
  • Substructure search: SMARTS queries plus a library of common functional-group patterns
  • Reactions: reaction SMARTS application and reaction fingerprints
  • 2D/3D coordinates: depiction, template alignment, ETKDG embedding, force-field optimization, constrained embedding, RMSD
  • Visualization & standardization: grid images, highlighting, Murcko scaffolds, canonical hashes

It also documents common pitfalls (unchecked None molecules, sanitization failures, missing hydrogens, thread-unsafe suppliers) and ships reference docs plus example scripts.

Who it's for

  • Drug discovery and computational chemistry researchers or grad students
  • Data scientists screening or filtering compound libraries
  • ML engineers building molecular property datasets
  • Anyone who needs more control than the simpler datamol wrapper offers

Examples

  1. "Compute MW, LogP and TPSA for these SMILES and flag Lipinski rule-of-five violations."
  2. "Screen this SDF for molecules with Tanimoto similarity ≥ 0.7 to my reference and render a grid image."
  3. "Enumerate an amide-coupling virtual library with reaction SMARTS, then embed 3D conformers with ETKDG and minimize them."

· · · Install guide · · ·

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 /tmp/scientific-agent-skills && mkdir -p ~/.claude/skills && cp -r /tmp/scientific-agent-skills/skills/rdkit ~/.claude/skills/

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

  1. Open a terminal.
  2. Clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills folder: mkdir -p ~/.claude/skills
  4. Copy the skill: cp -r scientific-agent-skills/skills/rdkit ~/.claude/skills/
  5. Install RDKit: uv pip install rdkit (or with conda: conda create -c conda-forge -n my-rdkit-env rdkit then conda activate my-rdkit-env)
  6. Restart Claude Code and try a prompt like "Calculate the molecular weight and LogP for this SMILES."
  7. Note: avoid installing conda rdkit and PyPI rdkit/rdkit-pypi into the same environment.
View source on GitHub ↗License: MIT