Arpeggio output handling

[stuartmac]

table_generator is has been yielding FileNotFound errors from the ARPEGGIOrunner (e.g., FileNotFoundError: [Errno 2] No such file or directory: './pdbx/1exa_new.amam'). Weirdly it will work the second time it is run if override=False.

I think this comes down to the fact that Arpeggio often does not produce many of its possible outputs for all structures, when "special" contacts are not found.

When I was first getting prointvar to work with my data I may have come upon this same but that I thought I'd fixed by setting parse_special=False but whilst this is part of a temporary fix, I wasn't cleaning the output between runs so I only came upon this when I wanted to rerun the analysis with bio units.

Complicated!