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

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

Requrements

• Python 2.7+ or 3.4+
• OpenBabel (2.3.2+) or/and RDKit (2014.03)
• Numpy (1.8+)
• Scipy (0.13+)
• Sklearn (0.18+)
• joblib (0.8+)
• pandas (0.17+)

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

Add conda channel which contains OpenBabel and ODDT [link]

conda config --add channels mwojcikowski

Optionally you can add RDKit's channel

conda config --add channels rdkit

Install ODDT:

conda install oddt

Optionally install RDKit:

conda install rdkit

Upgrading procedure using conda is straightforward:

conda update oddt

Documentation

Automatic documentation for ODDT is available on Readthedocs.org. Additionally it can be build localy:

cd docs

make html

make latexpdf

License

ODDT is released under permissive 3-clause BSD 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