A python library to work with molecules. Built on top of RDKit.
Project description
datamol - molecular processing made easy
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.Molobjects. - ✅ Manipulating molecules often relies on many options; Datamol provides good defaults by design.
- 🧠 Performance matters: built-in efficient parallelization when possible with an optional progress bar.
- 🕹️ Modern IO: out-of-the-box support for remote paths using
fsspecto read and write multiple formats (sdf, xlsx, csv, etc).
Try Online
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Documentation
Visit https://docs.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:
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. It does not mean other combinations does not work but that those are not tested.
datamol |
python |
rdkit |
|---|---|---|
0.9 |
[3.9, 3.10, 3.11] |
[2022.03, 2022.09] |
0.8 |
[3.8, 3.9, 3.10] |
[2021.09, 2022.03, 2022.09] |
0.7 |
[3.8, 3.9] |
[2021.09, 2022.03] |
0.6 |
[3.8, 3.9] |
[2021.09] |
0.5 |
[3.8, 3.9] |
[2021.03, 2021.09] |
0.4 |
[3.8, 3.9] |
[2020.09, 2021.03] |
0.3 |
[3.8, 3.9] |
[2020.09, 2021.03] |
CI Status
The CI runs tests and performs 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.
main |
|
|---|---|
| Lib build & Testing |  |
| Code Sanity (linting and type analysis) |  |
| Documentation Build |  |
Changelogs
See the latest changelogs at CHANGELOG.rst.
License
Under the Apache-2.0 license. See LICENSE.
Authors
See AUTHORS.rst.
Release history Release notifications | RSS feed
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