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Datamol Cheminformatics Toolkit

Lets the agent parse, standardize, describe and compare molecules using the datamol RDKit wrapper.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
10 files

What it does

Once installed, the agent knows how to work with chemical structures written as text (such as SMILES strings) using the datamol Python library. It can convert and clean molecules, read and write chemistry files (SDF, CSV, Excel), compute descriptors and fingerprints, cluster or pick diverse compounds, analyse scaffolds, generate 3D conformers, draw structures, and apply reaction rules. It writes Python code for these tasks and points to reference guides for detailed API use.

Great for

  • Medicinal chemists or cheminformatics students who want quick, sensible-default scripts for molecule datasets
  • Data scientists preparing compound libraries for machine learning or virtual screening
  • Developers building pipelines on top of RDKit who want a simpler interface

Skip it if

  • Organometallic or formulation work where automatic metal disconnection, salt stripping or neutralization would change the assayed entity; the skill itself warns against applying these automatically
  • Advanced RDKit users who need custom parameters, since the skill says to use RDKit directly for that
  • Anyone expecting validated safety or regulatory conclusions from the output; it only performs computational chemistry operations

Try asking

  • “Standardize this list of SMILES strings, log any invalid rows, and compute Morgan fingerprints”
  • “Cluster my compound library by Tanimoto similarity and pick a diverse subset of 50 molecules”
  • “Generate 3D conformers for these ligands and report RMSD-based representative conformers”
  • “Read this SDF file from S3, compute standard descriptors in parallel, and export to Excel”
Step-by-step guide: how to use Datamol Cheminformatics ToolkitInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 10 original files, the MIT licence and an attribution note.

    datamol.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip datamol.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip datamol.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Pin datamol to 0.13.0 and record your RDKit version, since upgrades can change canonical SMILES and conformers; compare chemical invariants rather than exact strings
  • Keep original structures and IDs alongside standardized ones, and set n_jobs and a positive batch_size (e.g. 128) for parallel descriptor work
  • Ask the agent to review the generated scripts before running them on remote data, and supply only the credentials needed for the specific bucket

What's inside

  • references/conformers_module.md
  • references/core_api.md
  • references/core_workflows.md
  • references/descriptors_viz.md
  • references/fragments_scaffolds.md
  • references/io_module.md
  • references/reactions_data.md
  • references/review.md
  • references/workflow_patterns.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.