Fixed --write_full_pae and --write_full_pde options. Fixes #585

[tomgoddard]

Implemented --write_full_pae and --write_full_pde options. Previously these options were available but ignored by the code and the PAE and PDE files were always written for boltz2 predictions, despite the documentation saying the default was false. Since the files have been written since boltz2 was released I made the default to write these files (ie. True). To not write them use --no_write_full_pae and --no_write_full_pde.

[gcorso]

Thank you for pointing this out @tomgoddard ! Could you add a note about --no_write_full_pae/pde in the documentation table?

[tomgoddard]

Ok, I added --no_write_full_pae and --no_write_full_pde to the documentation options table. Even though the default is true I left --write_full_pae and --write_full_pde in the options table since people may have been using that before and would be puzzled if it was not listed.