Addition of flag (-save-pae-json) resulting in output of seperate pae.json files linked to predicted structures

[MHvegholm]

The option to output separate pae.json files removes post-processing before custom visualization of pae plots when using tools like paeviewer.

This feature is already present in alphafold2 as _save_pae_json_file() which is defined and applied in run_alphafold.py

[jkosinski]

Hi @MHvegholm, thanks, we will think about it @DimaMolod just added a feature that saves PAE to the CIF files. We might want to choose that option instead by default. Adding an additional script that creates the jsons based on the saved pkl files is a good idea to increase compatibility with other packages. I created a feature request based on this discussion.