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: oddt@googlegroups.com 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, 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):
conda install -c conda-forge openbabel
(Optionally) Install RDKit (using official channel):
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. Additionally, it can be build locally:
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!
- 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