PyRosettaCluster: a Python framework for scalable and reproducible bio-macromolecular modeling and design: Supplementary materials

Python code, Jupyter notebooks, RosettaScripts scripts, PyMOL scripts, runtime environment configurations, and output data for "Example #1" and "Example #2" in the preprint publication: Jason C. Klima. PyRosettaCluster: a Python framework for scalable and reproducible bio-macromolecular modeling and design. ChemRxiv. 01 May 2026.DOI: https://doi.org/10.26434/chemrxiv.15002628/v1 Archive contents: envs/: Pixi environment configurations for Example #1 and Example #2. notebooks/: Jupyter notebooks used to run the original and reproduction simulations for Example #1 and Example #2. pymol/: PyMOL scripts used to programatically visualize the PDB files presented in Figures 2E, 2F, 3C and 3D of the preprint publication. results/: PDB and JSON file data for the original and reproduction simulations of Example #1 and Example #2. PDB files are made available under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license (see the "license" entry of the "instance" entry in the PyRosettaCluster full simulation record of each PDB file). JSON files are made available under the LICENSE file (MIT license). src/: Python module files and RosettaScripts scripts used by the Jupyter notebooks. README.md: Overview of the repository contents. LICENSE: MIT license file associated with the Python code, Jupyter notebooks, RosettaScripts scripts, PyMOL scripts, runtime environment configurations, and JSON files. .gitignore: GitHub repository configuration file. Pixi version 0.63.2 was used to create the environment for the original simulation and to recreate the environment for the reproduction simulation for both Example #1 and Example #2.