datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults
by k-dense-aiFree
Description
datamol is an agent skill for cheminformatics with datamol, a Pythonic wrapper around RDKit that offers a simpler interface and sensible defaults. It is preferred for standard drug discovery tasks, including SMILES parsing, standardisation and molecular operations. Its molecular objects are native RDKit molecule objects, so they work with the wider RDKit ecosystem. The skill also gives efficient parallelisation and modern input and output. The verified target is datamol 0.13.0, released on 9 September 2026, checked on Python 3.13 with RDKit 2026.03.6. Python 3.11 or newer and RDKit 2024.09 or newer are required. The 0.13 distribution includes runtime dependencies for SELFIES, visualisation, cloud, Excel and Parquet. The skill advises pinning the environment, because RDKit upgrades can change canonical representations and retained conformers. For that reason it suggests comparing chemical invariants rather than a fixed conformer count or an exact canonical string. Current API examples and verification limits are recorded in a review file. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars.…
Highlights
- Simpler interface over RDKit
- SMILES parsing and standardisation
- Native RDKit molecule objects
- Parallel processing and modern I/O
- Verified against datamol 0.13.0
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datamol FAQ
What is datamol?
A Pythonic wrapper around RDKit that simplifies molecular operations with sensible defaults.
Is it compatible with RDKit?
Yes. Its molecular objects are native RDKit molecule objects.
What does it require?
Python 3.11 or newer and RDKit 2024.09 or newer. The skill was verified with datamol 0.13.0 on Python 3.13 and RDKit 2026.03.6.
Why pin the environment?
The skill says RDKit upgrades can change canonical representations and retained conformers, so it recommends comparing chemical invariants instead.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill datamol.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub and Socket, and a warning from Snyk.
What are the best datamol alternatives?
Popular alternatives to datamol include medchem, rdkit and deepchem. See all datamol alternatives