Option to run QC/QA for all structures

[nmih]

Currently, QC/QA for structures stops when a representative structure is found. However the following case is possible:

• Multiple parts of the structure are homology modeled
• Another structure has a ligand or something that we are interested in

In these cases we want to have the alignment/residue mapping available for these structures but we might not have them. "set_representative_structure" doesn't sound like the right function to get that info. Also another issue is that the alignment info is stored as the "repchain_index" in the representative sequence itself. There should be a better place to store that info since we would want to map more than one structure to the sequence in these cases.

[nmih]

v0.9.5 should have addressed most of these ideas. QC/QA can't yet be run other for all proteins other than just doing the sequence alignments but that is the most important thing for now.