A Python interface to the OECD QSAR Toolbox. It only works on Windows since it is the only operating system for which QSAR Toolbox is released.
Install it with pip:
pip install git+https://github.com/USEtox/PyQSARToolbox.git
For developers, you can clone the repository, and run
pip install -e .
The main dependency is the requests package. Other dependencies (now and in the future) are the usual scientific Python packages, e.g. numpy, pandas, etc.
The QSAR Toolbox can be downloaded for free. I recommend installing VEGA and OPERA add-ons, which can be downloaded via the toolbox. They will need a working Java installation. I have Java on my system and everything worked out of the box. If you encounter any problems, contact me.
The class QSARToolbox provides an interface to the web API of the QSAR Toolbox. It can be used locally by running the QSAR Toolbox WebSuite program that is installed with the QSAR Toolbox. After running it, the user can connect to a local host at http://127.0.0.1:[port] where the port can be a different value given by the program in the following message:
WebAPI running on port [port]
where [port] is a 4 or 5 digit integer (may be different on your system).
Using the API is quite straightforward with some practical issues that I have discovered and try to clarify in this notebook.
Start the QSAR Toolbox WebSuite and wait for the port number to appear. Then load the class QSARTooolbox and create a QSARToolbox object:
from pyqsartoolbox import QSARTooolbox
qs = QSARToolbox(port=51946)
api_version = qs.webapi_version()
toolbox_version = qs.toolbox_version()
print(f"API version: {api_version}")
print(f"Toolbox version: {toolbox_version}")API documents are here. You can also look at the notebooks folder to find notebooks with extensive examples of the usage of this package for real world problems.
Releases are automated from Git tags and published to PyPI by GitHub Actions.
Prerequisite (one-time): configure the PyPI project for Trusted Publishing with this GitHub repository.
To release version 0.2.0:
git checkout main
git pull
uv sync
uv build
uvx twine check dist/*
git tag -a v0.2.0 -m "Release v0.2.0"
git push origin v0.2.0
Or use the helper script to create and push the tag:
uv run python scripts/release_tag.py 0.2.0
Optional flags:
uv run python scripts/release_tag.py 0.2.0 --dry-run
uv run python scripts/release_tag.py 0.2.0 --remote origin
Pushing a v* tag triggers .github/workflows/publish.yml, which builds the package and publishes to PyPI.
Please cite it as
Eftekhari, Ali A., PyQSARToolbox: a Python interface to the OECD QSAR Toolbox, https://usetox.github.io/PyQSARToolbox/, 2025
You can obtain experimental data and estimations for many physicochemical properties, environmental health, fate, and transport, and ecotoxicological information, as depicted in the following graph:
