Add options to cath-ssap for specifying regions to be aligned

[tonyelewis]

It'd be useful it cath-ssap allowed users to specify sub-regions to aligned within the structures.

It'd also be useful if the hacky script cath-superpose-multi-temp-script provided a simple way to specify regions.

This follows on from #1, which covered equivalent functionality in cath-superpose.

[tonyelewis]

Implementation notes:

• Look at all mentions of restrict_to_regions() and restrict_to_regions_copy()
• restrict_to_regions() needs implementing
• That should be used as a general, fall-back approach but for some cases (in particular protein_from_pdb, it'd be better to use something more specific.
• To do that, implement it in the protein_source_file_set hierarchy with a non-pure virtual function that concrete protein_source_file_sets can override and then have read_files() call that rather than restrict_to_regions_copy().

[tonyelewis]

This has now been implemented, primarily in ee78d6109bda8ac7318159a16fb6a2b6df6b2191.