AFDB v4 files are invalid as there is a mismatch between _citation.id
("primary") and _citation_author.citation_id ("1"). This can now be read
by setting fault_tolerant=True. In this case, a warning is logged and
no authors are set.

In principle we have three types of structures in the scorer (terrible I know).
1) the actual strucures that are only molcked 2) the structures as they are used
in the chain mapper (complete backbone) 3) same as 1) but stereochecked.
The alignments required at this position are of category 3 but they were 2.

This code is considered deprecated as of release 2.4.0. The new lDDT
implementation has already been integrated into
qsscoring.py/compare-structures. I prefer to leave this completely legacy.

same behaviour as old compare-structures

Before the program wrote the traceback into the output json but
exited silently. Now we re-raise upon writing the output.

commited for further review, currently co-exists with compare-structures

Only the fast residue number alignment has the requirement of no insertion
codes and strictly increasing residue numbers.

That was 1) strictly increasing (no idea why it was there in a first place)
2) no ins codes (The residue mapper is a dict which now has actual residue
numbers as key - can handle insertion codes)