Individual skill
datamol
Wraps RDKit through the datamol Python library (import datamol as dm) for molecular cheminformatics, returning native rdkit.Chem.Mol objects. Covers SMILES/SELFIES/InChI conversion, sanitization and standardization, descriptors, fingerprints and similarity, Butina clustering and diverse subset picking, Bemis-Murcko scaffolds, BRICS/RECAP fragmentation, 3D conformers, reactions, SDF/CSV/Excel I/O including cloud paths, and parallel batch processing. Use when parsing or standardizing SMILES from external sources, computing descriptors or fingerprints for a compound library, clustering or selecting diverse molecules, making scaffold-based train/test splits, or generating conformers. Use when running a molecule-processing pipeline with n_jobs. For fine-grained control or custom parameters, use RDKit directly instead.
plugins/KalarisLabs/research-agent-skills/skills/datamol/SKILL.md
Source commit d780783eba4ecc7c8b9429f95c9362df95f07c61
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 4, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 1,533
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-coding Repository topic
- awesome Repository topic
- awesome-list Repository topic
- codex Repository topic
- codex-plugins Repository topic
- openai Repository topic
- codex-skill Repository topic
- codex-skills Repository topic
- marketplace Repository topic
- codex-marketplace Repository topic
- cheminformatics,-rdkit,-molecules,-smiles,-drug-discovery Declared skill tag
- testing Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
SKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesSKILL.mdcore · 9,081 bytesreferences/conformers_module.mddoc · 5,022 bytesreferences/core_api.mddoc · 4,721 bytesreferences/core_workflows.mddoc · 12,013 bytesreferences/descriptors_viz.mddoc · 7,366 bytesreferences/fragments_scaffolds.mddoc · 5,808 bytesreferences/io_module.mddoc · 4,812 bytesreferences/reactions_data.mddoc · 6,742 bytesreferences/workflow_patterns.mddoc · 2,798 bytes
Read excerpt
# Datamol Cheminformatics Skill
## Overview
Datamol is a Python library that provides a lightweight, Pythonic abstraction layer over RDKit for molecular cheminformatics. Simplify complex molecular operations with sensible defaults, efficient parallelization, and modern I/O capabilities. All molecular objects are native `rdkit.Chem.Mol` instances, ensuring full compatibility with the RDKit ecosystem.
**Version note:** Examples target **datamol 0.12.x** (PyPI stable: **0.12.5**, June 2024). Since 0.10.0, modules are lazy-loaded by default (set `DATAMOL_DISABLE_LAZY_LOADING=1` to disable). Since 0.12.2, RDKit is a direct PyPI dependency of datamol. Fingerprints use RDKit's `rdFingerprintGenerator` API (0.12.5+).
**Key capabilities**:
- Molecular format conversion (SMILES, SELFIES, InChI)
- Structure standardization and sanitization
- Molecular descriptors and fingerprints
- 3D conformer generation and analysis
- Clustering and diversity selection