Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, par…
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name: datamol
description: Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
license: Apache-2.0 license
allowed-tools: Read Write Edit Bash
compatibility: Requires Python 3.8+ and datamol (uv pip install). RDKit is installed automatically as a datamol dependency (since 0.12.2). Optional s3fs/gcsfs for cloud I/O via fsspec.
metadata: {"version": "1.0", "skill-author": "K-Dense Inc."}
---
# 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
- Scaffold and fragment analysis
- Chemical reaction application… load the full skill through Skill Me