Feature request: Create a Function to Generate a PyMOL Script in Analogy to the Chimera Script

[berntpopp]

Description

The pipeline currently generates a Chimera script for visualizing protein structures with pathogenicity information. To broaden compatibility and provide similar functionality for PyMOL users, a new function should be created to generate an equivalent PyMOL script.

Proposed Solution

• Develop a generate_pymol_script function that mirrors the logic of the Chimera script generation.
• The PyMOL script should:
  • Load the PDB file.
  • Apply color coding to residues based on pathogenicity scores using PyMOL's color command.
  • Optionally, show ClinVar variants as spheres (related to the above issue).
  • Save the session or generate a PyMOL script that can be easily executed by users.

Acceptance Criteria

• The generate_pymol_script function successfully generates a PyMOL script with analogous functionality to the Chimera script.
• Residue coloring for pathogenicity is correctly applied.
• ClinVar variants can be optionally represented as spheres (if this feature is implemented in the Chimera script).
• The PyMOL script is fully functional when executed, without errors.

Additional Notes

• Consider creating a common utility module to share code between the Chimera and PyMOL script generators, ensuring consistency across both visualization platforms.
• Update relevant documentation to guide users on how to run the PyMOL script, along with any necessary dependencies or setup instructions.