SKILL.md

datamol

Agent skill fromK-Dense-AI/scientific-agent-skills

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.

install datamol

# install the scientific-agent-skills pack with the skills CLI

npx skills add K-Dense-AI/scientific-agent-skills

# or add only this skill to Claude Code: copy the folder

skills/datamol/

# into

~/.claude/skills/datamol/ (all projects)

.claude/skills/datamol/ (one project)

skills/datamol/SKILL.md

MITFull file

1# Datamol Cheminformatics Skill
2 
3## Overview
4 
5Datamol 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.
6 
7**Verified target:** datamol **0.13.0**, released September 9, 2026. Local checks used
8Python 3.13 and RDKit 2026.03.6. Python 3.11+ and RDKit 2024.09+ are required.
9The 0.13 distribution includes SELFIES, visualization, cloud, Excel and Parquet
10runtime dependencies. Current API examples and verification limits are recorded in
11[references/review.md](references/review.md). Pin the environment: RDKit upgrades can
12change canonical representations and retained conformers. Compare chemical invariants,
13not a fixed conformer count or an exact version-dependent canonical string.
14 
15**Key capabilities**:
16- Molecular format conversion (SMILES, SELFIES, InChI)
17- Structure standardization and sanitization
18- Molecular descriptors and fingerprints
19- 3D conformer generation and analysis
20- Clustering and diversity selection
21- Scaffold and fragment analysis
22- Chemical reaction application
23- Visualization and alignment
24- Batch processing with parallelization
25- Cloud storage support via fsspec
26 
27## Installation and Setup
28 
29Guide users to install datamol:
30 
31```bash
32uv pip install "datamol==0.13.0"
33```
34…

Excerpt shown under the repository's MIT license.

How to install datamol

skills/datamol/SKILL.md

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