Spheronizator

Spheronizator is a Python research utility designed to voxelize protein structural data from existing PDB files for use in machine learning training sets. The utility is intended to be a part of your data processing pipeline, with an interface that is convenient to use with IPython, Jupyter, or similar. Please see the detailed documentation for more information, usage, and examples.

Documentation

Detailed documentation for the project can be found here: https://spheronizator.readthedocs.io/

Documentation for the project is written in Markdown, rendered to a static site with mdBook, and hosted by Read the Docs.

Installation

The precompiled package is hosted on PyPI and can be easily installed with pip:

pip install spheronizator

Using a Conda Environment

If you prefer to install the package into a Conda environment, you can use configuration from the repository.

First download the configuration:

curl -L -o spheronizator_env.yml https://raw.githubusercontent.com/mattlrich/spheronizator/refs/heads/main/spheronizator_env.yml

Now create a Conda environment using the configuration:

conda env create -f spheronizator_env.yml

conda activate spheronizator

You can now install the package into the environment with pip:

pip install spheronizator

Development

Packaging and building of the project is handled by Poetry.

To install the development version, first install Poetry:

pipx install poetry

then clone the repository:

git clone git@github.com:mattlrich/spheronizator.git

then install the package in development mode to a virtual environment:

poetry install

You can build the source and wheels archives with:

poetry build

Bugs and Issues

If you encounter any issues with the package, please report them through the GitHub Issue Tracker.

Contributing

The project is happy to accept contibutions and enhancements. All contributions are to be made through GitHub pull requests. See CONTRIBUTING for more information.

Contact

• Matthew Richardson — richardson.m@ufl.edu
• Jose Cleydson — jferreiradasilva@ufl.edu
• José Cediel-Becerra — jcedielbecerra@ufl.edu
• Raquel Dias — raquel.dias@ufl.edu

License

Spheronizator is licensed under the BSD 3-Clause License. Please see LICENSE for more information.