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# Open Drug Discovery Toolkit |
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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 |
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[](http://oddt.readthedocs.org/en/latest/) |
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[](https://travis-ci.org/oddt/oddt) |
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[](https://coveralls.io/github/oddt/oddt?branch=master) |
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[](https://landscape.io/github/oddt/oddt/master) |
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[](https://anaconda.org/oddt/oddt) |
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[](https://pypi.python.org/pypi/oddt/) |
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## Documentation, Discussion and Contribution: |
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* Documentation: http://oddt.readthedocs.org/en/latest |
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* Mailing list: oddt@googlegroups.com http://groups.google.com/d/forum/oddt |
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* Issues: https://github.com/oddt/oddt/issues |
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## Requirements |
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* Python 3.6+ |
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* OpenBabel (3.0+) or/and RDKit (2018.03+) |
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* Numpy (1.12+) |
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* Scipy (0.19+) |
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* Sklearn (0.18+) |
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* joblib (0.10+) |
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* pandas (0.19.2+) |
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* Skimage (0.12.3+) (optional, only for surface generation) |
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## Install |
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### Using PyPi (pip) |
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When all requirements are met, then installation process is simple |
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> python setup.py install |
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You can also use pip. All requirements besides toolkits (OpenBabel, RDKit) are installed if necessary. |
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Installing inside virtualenv is encouraged, but not necessary. |
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> pip install oddt |
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To upgrade oddt using pip (without upgrading dependencies): |
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> pip install -U --no-deps oddt |
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### Using conda |
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Install a clean [Miniconda environment](https://conda.io/miniconda.html), if you already don't have one. |
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Install ODDT: |
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> conda install -c oddt oddt |
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You can add a toolkit of your choice or install them along with oddt: |
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> conda install -c conda-forge oddt rdkit openbabel |
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(Optionally) Install OpenBabel (using [official channel](https://anaconda.org/openbabel/openbabel)): |
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> conda install -c conda-forge openbabel |
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(Optionally) Install RDKit (using [official channel](https://anaconda.org/rdkit/rdkit)): |
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> conda install -c conda-forge rdkit |
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Upgrading procedure using conda is straightforward: |
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> conda update -c oddt oddt |
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### Documentation |
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Automatic documentation for ODDT is available on [Readthedocs.org](https://oddt.readthedocs.org/). Additionally, it can be build locally: |
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> cd docs |
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> make html |
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> make latexpdf |
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### License |
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ODDT is released under permissive [3-clause BSD license](./LICENSE) |
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### Reference |
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If you found Open Drug Discovery Toolkit useful for your research, please cite us! |
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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) |
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[](https://github.com/igrigorik/ga-beacon) |