Metadata-Version: 2.1 Name: datamol Version: 0.12.5 Summary: A python library to work with molecules. Built on top of RDKit. Author-email: Hadrien Mary License: Apache Project-URL: Website, https://datamol.io Project-URL: Source Code, https://github.com/datamol-io/datamol Project-URL: Bug Tracker, https://github.com/datamol-io/datamol/issues Project-URL: Documentation, https://docs.datamol.io Classifier: Development Status :: 5 - Production/Stable Classifier: Intended Audience :: Developers Classifier: Intended Audience :: Healthcare Industry Classifier: Intended Audience :: Science/Research Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence Classifier: Topic :: Scientific/Engineering :: Bio-Informatics Classifier: Topic :: Scientific/Engineering :: Information Analysis Classifier: Topic :: Scientific/Engineering :: Medical Science Apps. Classifier: Natural Language :: English Classifier: Operating System :: OS Independent Classifier: Programming Language :: Python Classifier: Programming Language :: Python :: 3 Classifier: Programming Language :: Python :: 3.8 Classifier: Programming Language :: Python :: 3.9 Classifier: Programming Language :: Python :: 3.10 Classifier: Programming Language :: Python :: 3.11 Requires-Python: >=3.8 Description-Content-Type: text/markdown License-File: LICENSE Requires-Dist: tqdm Requires-Dist: loguru Requires-Dist: joblib Requires-Dist: fsspec >=2021.9 Requires-Dist: pandas Requires-Dist: numpy Requires-Dist: scipy Requires-Dist: matplotlib Requires-Dist: pillow Requires-Dist: selfies Requires-Dist: platformdirs Requires-Dist: scikit-learn Requires-Dist: packaging Requires-Dist: typing-extensions Requires-Dist: importlib-resources Requires-Dist: rdkit

datamol - molecular processing made easy

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--- [![DOI](https://zenodo.org/badge/341603042.svg)](https://zenodo.org/badge/latestdoi/341603042) [![Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/datamol-io/datamol/main?urlpath=lab/tree/docs/tutorials/The_Basics.ipynb) [![PyPI](https://img.shields.io/pypi/v/datamol)](https://pypi.org/project/datamol/) [![Conda](https://img.shields.io/conda/v/conda-forge/datamol?label=conda&color=success)](https://anaconda.org/conda-forge/datamol) [![PyPI - Downloads](https://img.shields.io/pypi/dm/datamol)](https://pypi.org/project/datamol/) [![Conda](https://img.shields.io/conda/dn/conda-forge/datamol)](https://anaconda.org/conda-forge/datamol) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/datamol)](https://pypi.org/project/datamol/) [![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/datamol-io/datamol/blob/main/LICENSE) [![GitHub Repo stars](https://img.shields.io/github/stars/datamol-io/datamol)](https://github.com/datamol-io/datamol/stargazers) [![GitHub Repo stars](https://img.shields.io/github/forks/datamol-io/datamol)](https://github.com/datamol-io/datamol/network/members) [![Codecov](https://codecov.io/gh/datamol-io/datamol/branch/main/graph/badge.svg?token=2ETG8SA7IG)](https://codecov.io/gh/datamol-io/datamol) Datamol is a python library to work with molecules. It's a layer built on top of [RDKit](https://www.rdkit.org/) and aims to be as light as possible. - 🐍 Simple pythonic API - ⚗ī¸ RDKit first: all you manipulate are `rdkit.Chem.Mol` objects. - ✅ 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. - 🕹ī¸ 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](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/datamol-io/datamol/main?urlpath=lab/tree/docs/tutorials/The_Basics.ipynb) and try Datamol online. ## Documentation Visit . ## Installation Use conda: ```bash mamba install -c conda-forge datamol ``` ## Quick API Tour ```python 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](https://zenodo.org/badge/341603042.svg)](https://zenodo.org/badge/latestdoi/341603042). ## 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` | | --------- | ------------------- | ----------------------------- | | `0.12.x` | `[3.10, 3.11]` | `[2023.03, 2023.09]` | | `0.11.x` | `[3.9, 3.10, 3.11]` | `[2022.09, 2023.03]` | | `0.10.x` | `[3.9, 3.10, 3.11]` | `[2022.03, 2022.09]` | | `0.9.x` | `[3.9, 3.10, 3.11]` | `[2022.03, 2022.09]` | | `0.8.x` | `[3.8, 3.9, 3.10]` | `[2021.09, 2022.03, 2022.09]` | | `0.7.x` | `[3.8, 3.9]` | `[2021.09, 2022.03]` | | `0.6.x` | `[3.8, 3.9]` | `[2021.09]` | | `0.5.x` | `[3.8, 3.9]` | `[2021.03, 2021.09]` | | `0.4.x` | `[3.8, 3.9]` | `[2020.09, 2021.03]` | | `0.3.x` | `[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 | [![test](https://github.com/datamol-io/datamol/actions/workflows/test.yml/badge.svg)](https://github.com/datamol-io/datamol/actions/workflows/test.yml) | | Code Sanity (linting and type analysis) | [![code-check](https://github.com/datamol-io/datamol/actions/workflows/code-check.yml/badge.svg)](https://github.com/datamol-io/datamol/actions/workflows/code-check.yml) | | Documentation Build | [![doc](https://github.com/datamol-io/datamol/actions/workflows/doc.yml/badge.svg)](https://github.com/datamol-io/datamol/actions/workflows/doc.yml) | ## License Under the Apache-2.0 license. See [LICENSE](LICENSE).