Add --pdb-infile option to cath-ssap and use it in --do-the-ssaps

[tonyelewis]

ATM, when cath-superpose calls cath-ssap under the --do-the-ssaps option, it only specifies IDs but it'd be much better if it specified the actual files it's used.

Even better: use the parsed PDB structures it's already loaded. What's involved in that?