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https://github.com/datamol-io/datamol
Molecular Processing Made Easy.
https://github.com/datamol-io/datamol
cheminformatics drug-design drug-discovery medicinal-chemistry molecule molecules python rdkit
Last synced: 2 days ago
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Molecular Processing Made Easy.
- Host: GitHub
- URL: https://github.com/datamol-io/datamol
- Owner: datamol-io
- License: apache-2.0
- Created: 2021-02-23T15:39:33.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-06-10T19:22:38.000Z (8 months ago)
- Last Synced: 2024-10-29T17:37:32.249Z (3 months ago)
- Topics: cheminformatics, drug-design, drug-discovery, medicinal-chemistry, molecule, molecules, python, rdkit
- Language: Python
- Homepage: https://docs.datamol.io
- Size: 114 MB
- Stars: 463
- Watchers: 16
- Forks: 48
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Codeowners: .github/CODEOWNERS
- Security: .github/SECURITY.md
Awesome Lists containing this project
- awesome-materials-informatics - datamol - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit (**Python**). [](https://github.com/datamol-org/datamol) (Software and products)
README
datamol - molecular processing made easy
---
[](https://zenodo.org/badge/latestdoi/341603042)
[](https://mybinder.org/v2/gh/datamol-io/datamol/main?urlpath=lab/tree/docs/tutorials/The_Basics.ipynb)
[](https://pypi.org/project/datamol/)
[](https://anaconda.org/conda-forge/datamol)
[](https://pypi.org/project/datamol/)
[](https://anaconda.org/conda-forge/datamol)
[](https://pypi.org/project/datamol/)
[](https://github.com/datamol-io/datamol/blob/main/LICENSE)
[](https://github.com/datamol-io/datamol/stargazers)
[](https://github.com/datamol-io/datamol/network/members)
[](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.
- đ Simple pythonic API
- âī¸ RDKit first: all you manipulate are `rdkit.Chem.Mol` objects.
- â
Manipulating molecules often relies on many options; Datamol provides good defaults by design.
- đ§ Performance matters: built-in efficient parallelization when possible with an optional progress bar.
- đšī¸ 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 [](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: [](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 | [](https://github.com/datamol-io/datamol/actions/workflows/test.yml) |
| Code Sanity (linting and type analysis) | [](https://github.com/datamol-io/datamol/actions/workflows/code-check.yml) |
| Documentation Build | [](https://github.com/datamol-io/datamol/actions/workflows/doc.yml) |
## License
Under the Apache-2.0 license. See [LICENSE](LICENSE).