STCRpy

Author: Nele Quast

Pre-release alpha version (v0.1.24)

We anticipate changes to this repository. Please feel free to reach out with any comments or feedback. Manuscript in preparation, please cite:

Nele, Deane, C., & Raybould, M. (2025). STCRpy: a software suite for TCR:pMHC structure parsing, interaction profiling, and machine learning dataset preparation (0.1.24). Zenodo. https://doi.org/10.5281/zenodo.14962269

Installation

The core stcrpy package can be installed from PyPi. After installing stcrpy, the anarci HMM models must be built to enable annotation.

pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple stcrpy
ANARCI --build_models

Certain extensions and functionality have additional dependencies:

PyTorch dataset generation

pip install torch --index-url https://download.pytorch.org/whl/cpu
pip install torch_geometric

PyMOL visualisations

conda install -c conda-forge -c schrodinger pymol-bundle numpy -y

Building and deploying

In case build and twine arent installed:

pip install --upgrade build
pip install --upgrade twine

To build the package run: (this will build the wheel and compress the source code to stcrpy/dist)

python -m build

To deploy the package to the test-pypi server:

python3 -m twine upload --repository testpypi dist/*

!! Note that to re-deploy the code the version number in setup.py must be updated so that pypi can stage the package.

Debugging

To install a development version of stcrpy and enable local debugging:

pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple anarci-mhc
ANARCI --build_models
pip install -e .