Datamol

A Pythonic wrapper around RDKit that handles the most common drug discovery cheminformatics tasks without forcing you to dig through RDKit's sprawling API. Use it for SMILES parsing, molecular standardization, computing descriptors and fingerprints, clustering compounds, and generating 3D conformers. It returns native rdkit.Chem.Mol objects so you can drop back to RDKit anytime you need fine-grained control. The batch processing with parallelization is solid for datasets up to a few thousand molecules, and it supports reading from S3 or GCS out of the box. If you're doing standard molecular informatics work and want sensible defaults instead of configuration archaeology, this is the right abstraction layer.

skills.sh installs: 207
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill datamol --agent claude-code

Installs into .claude/skills of the current project.

Files

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.

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
Visualization and alignment
Batch processing with parallelization
Cloud storage support via fsspec

Installation and Setup

Guide users to install datamol:

uv pip install datamol

Import convention:

import datamol as dm

Core Workflows

1. Basic Molecule Handling

Creating molecules from SMILES:

import datamol as dm

# Single molecule
mol = dm.to_mol("CCO")  # Ethanol

SKILL.md on GitHub

Details

Repository: github.com/davila7/claude-code-templates
Categories: Data Science & ML, Automation & Workflows, Sales & Marketing
First seen: Jun 3, 2026