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A python library to work with molecules. Built on top of RDKit.

Project description

Molecular Manipulation Made Easy


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Datamol is a python library to work with molecules. It's a layer built on top of RDKit and aims to be as light as possible.

  • 🐍 Simple pythonic API
  • ⚗️ RDKit first: all you manipulate are rdkit.Chem.Mol objects.
  • ✅ Manipulating molecules often rely on many options; Datamol provides good defaults by design.
  • 🧠 Performance matters: built-in efficient parallelization when possible with optional progress bar.
  • 🕹️ Modern IO: out-of-the-box support for remote paths using fsspec to read and write multiple formats (sdf, xlsx, csv, etc).

Try Online

Visit Binder and try Datamol online.

Documentation

Visit https://doc.datamol.io.

Installation

Use conda:

mamba install -c conda-forge datamol

Quick API Tour

import datamol as dm

# Common functions
mol = dm.to_mol("O=C(C)Oc1ccccc1C(=O)O", sanitize=True)
fp = dm.to_fp(mol)
selfies = dm.to_selfies(mol)
inchi = dm.to_inchi(mol)

# Standardize and sanitize
mol = dm.to_mol("O=C(C)Oc1ccccc1C(=O)O")
mol = dm.fix_mol(mol)
mol = dm.sanitize_mol(mol)
mol = dm.standardize_mol(mol)

# Dataframe manipulation
df = dm.data.freesolv()
mols = dm.from_df(df)

# 2D viz
legends = [dm.to_smiles(mol) for mol in mols[:10]]
dm.viz.to_image(mols[:10], legends=legends)

# Generate conformers
smiles = "O=C(C)Oc1ccccc1C(=O)O"
mol = dm.to_mol(smiles)
mol_with_conformers = dm.conformers.generate(mol)

# 3D viz (using nglview)
dm.viz.conformers(mol, n_confs=10)

# Compute SASA from conformers
sasa = dm.conformers.sasa(mol_with_conformers)

# Easy IO
mols = dm.read_sdf("s3://my-awesome-data-lake/smiles.sdf", as_df=False)
dm.to_sdf(mols, "gs://data-bucket/smiles.sdf")

How to cite

Please cite Datamol if you use it in your research: DOI.

Compatibilities

Version compatibilities are an essential topic for production-software stacks. We are cautious about documenting compatibility between datamol, python and rdkit.

See below the associated versions of Python and RDKit, for which a minor version of Datamol has been tested during its whole lifecycle.

datamol python rdkit
0.4 [3.8, 3.9] [2020.09, 2021.03]
0.3 [3.8, 3.9] [2020.09, 2021.03]

CI Status

The CI run tests and perform code quality checks for the following combinations:

  • The three major platforms: Windows, OSX and Linux.
  • The two latest Python versions.
  • The two latest RDKit versions.
master
Lib build & Testing GitHub Workflow Status
Code Sanity (linting and type analysis) GitHub Workflow Status
Documentation Build GitHub Workflow Status

Changelogs

See the latest changelogs at CHANGELOG.rst.

License

Under the Apache-2.0 license. See LICENSE.

Authors

See AUTHORS.rst.

Download files

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