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Molecule processing with Datamol (RDKit) v1.0.0
Use this resource to process molecules: reading, standardization, descriptors and fingerprints
New
- 401 downloads
- 108 likes
- 193 saves
Free
Install with the CLI
In a terminal, from the folder you want:
npx --yes palatekit@latest install molecule-processing-rdkitWith no option, the skill goes to ~/.agents/skills/; add --agent claude-code (or codex, cursor…) to target an agent.
First time: connect the CLI with
npx --yes palatekit@latest loginThe agent converts SMILES, standardizes structures and computes descriptors and fingerprints with Datamol's defaults. You get native RDKit objects and batch processing code.
Mostly picked by
Updated November 2, 2026
Previews
Details
- Install guides
- Generates with
- Your agent's model
- Licence
- Apache-2.0
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What you get
- SKILL.md: installation, workflow and best practices
- references/: API, conformers, descriptors, fragments, I/O and reactions
Good fit for
- You are preparing a molecule library before screening
- You want fingerprints for a machine learning model
Not for
Tags
- molecules
- RDKit
- cheminformatics
About
You say
“Standardize this SMILES file and compute Lipinski descriptors for each molecule.”
Skill published by k-dense-ai under the Apache-2.0 license, delivered in its original version.
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How to use it
- Install the skill in your agent's skills folder
- Ask your agent to process molecules: reading, standardization, descriptors and fingerprints
- Review and adjust the result
Content preview
Files
- LICENSE1.1 KB
- NOTICE-PALATEKIT.md0.5 KB
- references/conformers_module.md4.5 KB
- references/core_api.md4.8 KB
- references/core_workflows.md9 KB
- references/descriptors_viz.md4.8 KB
- references/fragments_scaffolds.md4.3 KB
- references/io_module.md4.5 KB
- references/reactions_data.md4.4 KB
- references/review.md3.3 KB
- references/workflow_patterns.md5.4 KB
- SKILL.md10.9 KB
Origin and licence
Listed unmodified
- Author
- k-dense-ai
- Source
- github.com/k-dense-ai/scientific-agent-skills/tree/5f2bc0341354fd5590aef76a533ada1e1e5b4e62/skills/datamol
- Licence
- Apache-2.0
Notice
« datamol » (k-dense-ai, Apache-2.0) livré dans sa version d'origine : fiche en français et en anglais par PalateKit.
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