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: http://oddt.readthedocs.org/en/latest
• Mailing list: [email protected] http://groups.google.com/d/forum/oddt
• Issues: https://github.com/oddt/oddt/issues

• Python 3.12+
• OpenBabel (3.0+) or/and RDKit (2018.03+)
• Numpy (1.13+)
• Scipy (0.19+)
• Sklearn (0.18+)
• joblib (0.10+)
• pandas (0.19.2+)
• packaging (20+)
• Skimage (0.12.3+) (optional, only for surface generation)

CI tests Python 3.12 and 3.14 with both chemistry backends, using RDKit 2026.03.1+ and Open Babel 3.2.1+. Python 3.14 is the latest supported version; Python 3.13 is supported but is not in the current CI matrix.

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

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

Create the Python 3.12 environment with both chemistry backends:

conda env create -n oddt-dev -f environment.yml
conda activate oddt-dev
python -m pip install --no-build-isolation --no-deps -e .
ODDT_TOOLKIT=rdk python -m pytest tests
ODDT_TOOLKIT=ob python -m pytest tests

The same environment includes conda-forge Vina 1.2.7+ and uses its Python API for docking and scoring. RDKit 2026.03.1 and Vina 1.2.7 share Boost 1.86, so there is no separate tool environment or additional library search path.

Vina 1.1.2 remains supported through its command-line executable. If both the Python package and a legacy binary are available, pass the legacy binary's path as executable to select it explicitly. CI installs the selected Vina version in the ODDT environment: Python 3.12 and 3.14 test both interfaces. Native tests are skipped only when neither the Python package nor an executable is available.

Vina 1.2 affinity comes from the Python API. Its unweighted interaction terms are reconstructed with ODDT's internal scorer because the API does not expose them separately. Vina 1.1.2 retains the original native scoring path.

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

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!

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