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: http://oddt.readthedocs.org/en/latest
- Mailing list: oddt@googlegroups.com http://groups.google.com/d/forum/oddt
- Issues: https://github.com/oddt/oddt/issues
- 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+)
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
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
Automatic documentation for ODDT is available on Readthedocs.org. Additionally it can be build localy:
cd docs
make html
make latexpdf
ODDT is released under permissive 3-clause BSD license
If you found Open Drug Discovery Toolkit useful for your research, please cite us!
- 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