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https://github.com/oddt/oddt
Open Drug Discovery Toolkit
https://github.com/oddt/oddt
cheminformatics docking openbabel python rdkit scoring screening
Last synced: about 1 month ago
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Open Drug Discovery Toolkit
- Host: GitHub
- URL: https://github.com/oddt/oddt
- Owner: oddt
- License: bsd-3-clause
- Created: 2014-08-20T14:01:11.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2022-12-13T21:05:19.000Z (over 1 year ago)
- Last Synced: 2024-03-23T10:41:39.090Z (3 months ago)
- Topics: cheminformatics, docking, openbabel, python, rdkit, scoring, screening
- Language: Python
- Size: 45.8 MB
- Stars: 392
- Watchers: 22
- Forks: 115
- Open Issues: 30
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Lists
- awesome-python-chemistry - oddt - Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. (Simulations)
- awesome-python-chemistry - oddt - Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. (Simulations)
README
# Open Drug Discovery Toolkit
Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and make extensive use of Numpy/Scipy
[](http://oddt.readthedocs.org/en/latest/)
[](https://travis-ci.org/oddt/oddt)
[](https://coveralls.io/github/oddt/oddt?branch=master)
[](https://landscape.io/github/oddt/oddt/master)
[](https://anaconda.org/oddt/oddt)
[](https://pypi.python.org/pypi/oddt/)
## Documentation, Discussion and Contribution:
* Documentation: http://oddt.readthedocs.org/en/latest
* Mailing list: [email protected] http://groups.google.com/d/forum/oddt
* Issues: https://github.com/oddt/oddt/issues
## Requirements
* Python 3.6+
* OpenBabel (3.0+) or/and RDKit (2018.03+)
* Numpy (1.12+)
* Scipy (0.19+)
* Sklearn (0.18+)
* joblib (0.10+)
* pandas (0.19.2+)
* Skimage (0.12.3+) (optional, only for surface generation)
## Install
### Using PyPi (pip)
When all requirements are met, then installation process is simple
> python setup.py install
You can also use pip. All requirements besides toolkits (OpenBabel, RDKit) are installed if necessary.
Installing inside virtualenv is encouraged, but not necessary.
> pip install oddt
To upgrade oddt using pip (without upgrading dependencies):
> pip install -U --no-deps oddt
### Using conda
Install a clean [Miniconda environment](https://conda.io/miniconda.html), if you already don't have one.
Install ODDT:
> conda install -c oddt oddt
You can add a toolkit of your choice or install them along with oddt:
> conda install -c conda-forge oddt rdkit openbabel
(Optionally) Install OpenBabel (using [official channel](https://anaconda.org/openbabel/openbabel)):
> conda install -c conda-forge openbabel
(Optionally) Install RDKit (using [official channel](https://anaconda.org/rdkit/rdkit)):
> conda install -c conda-forge rdkit
Upgrading procedure using conda is straightforward:
> conda update -c oddt oddt
### Documentation
Automatic documentation for ODDT is available on [Readthedocs.org](https://oddt.readthedocs.org/). Additionally, it can be build locally:
> cd docs
> make html
> make latexpdf
### License
ODDT is released under permissive [3-clause BSD license](./LICENSE)
### Reference
If you found Open Drug Discovery Toolkit useful for your research, please cite us!
1. Wójcikowski, M., Zielenkiewicz, P., & Siedlecki, P. (2015). Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field. Journal of Cheminformatics, 7(1), 26. [doi:10.1186/s13321-015-0078-2](https://dx.doi.org/10.1186/s13321-015-0078-2)
[](https://github.com/igrigorik/ga-beacon)