The PyRosetta initialization file format for precise reconstruction of Pose objects: Appendix material

Code and runtime environment for the appendix materials in the preprint publication:

Klima JC. The PyRosetta initialization file format for precise reconstruction of Pose objects. Zenodo; 2026. doi:10.5281/zenodo.18113110

Repository contents:

• appendix_a.py: Python script used to generate data in Table 1.
• appendix_b.py: Python script used to generate data in Figure 2.
• appendix_module.py: Python module file containing helper functions imported by the Python scripts.
• requirements.txt: uv project specifying the Python runtime environment used to run the Python scripts.
• LICENSE: MIT license file associated with the code.
• .gitignore, README.md, CITATION.cff: GitHub repository configuration files.

The PyRosetta build signature used to execute the Python scripts is the following: PyRosetta4.Release.python312.ubuntu.cxx11thread.serialization[extras:cxx11thread+serialization]2025.49+release.552382f5ef84f3c058ac922b717ceee014073be6

The uv (Version 0.9.17) project specifying the Python runtime environment used to run the Python scripts was exported with the following command: uv export --no-hashes --no-annotate --no-header

Citation

If you use this code, please cite the Zenodo software archive:

@software{klima_2026_18157982,
  author       = {Klima, Jason C.},
  title        = {The PyRosetta initialization file format for
                   precise reconstruction of Pose objects: Appendix
                   material
                  },
  month        = jan,
  year         = 2026,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.18157982},
  url          = {https://doi.org/10.5281/zenodo.18157982},
}

If you reference the associated preprint manuscript, please cite the Zenodo preprint archive:

@misc{klima_2026_18113110,
  author       = {Klima, Jason C.},
  title        = {The PyRosetta initialization file format for
                   precise reconstruction of Pose objects
                  },
  month        = jan,
  year         = 2026,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.18113110},
  url          = {https://doi.org/10.5281/zenodo.18113110},
}