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Datamol Cheminformatics Skill

Guides Claude in using Datamol, the Pythonic RDKit wrapper, for SMILES parsing, standardization, fingerprints, clustering, and 3D conformers.

Dev & CodingIntermediate★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

  • Supplies idiomatic Datamol 0.12.x patterns: dm.to_mol, standardize_mol, to_fp, cluster_mols, pick_diverse, and more.
  • Covers ten workflow areas: format conversion (SMILES/SELFIES/InChI), standardization, descriptors, fingerprints & similarity, clustering and diversity picking, Bemis-Murcko scaffolds, BRICS/RECAP fragmentation, 3D conformers with RMSD clustering, visualization, and reaction SMARTS.
  • Handles SDF/CSV/Excel I/O plus remote S3/GCS/HTTP paths via fsspec, with n_jobs parallelization and progress bars.
  • Includes best practices (always standardize, check for None), scale limits (Butina clustering ~1,000 molecules), and a troubleshooting section.

Recommended for

  • Drug discovery and computational chemistry researchers.
  • Data scientists building cheminformatics pipelines who want less RDKit boilerplate.
  • ML engineers generating molecular features from fingerprints or descriptors.

Example uses

  1. "Standardize the 100k SMILES in this CSV, compute descriptors in parallel, and filter by Lipinski rules."
  2. "Read this SDF, compute ECFP4, pick 500 diverse compounds, and build a scaffold-disjoint train/test split."
  3. "Align a 20-molecule SAR series on a common core and render a publication-ready SVG grid."

· · · 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/datamol/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/datamol folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/datamol/.
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/datamol ~/.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 the skill: cp -r scientific-agent-skills/skills/datamol ~/.claude/skills/
  4. Verify the bundled references/ markdown files came along: ls ~/.claude/skills/datamol
  5. Install the library in your Python environment: uv pip install datamol (RDKit installs automatically). Add uv pip install s3fs or gcsfs only if you need cloud I/O.
  6. Restart Claude Code and try a prompt like "use datamol to standardize these SMILES" to trigger the skill.
View source on GitHub ↗License: MIT