This should clarify what the binding site.

Enables the full scoring experience with CAD score

- Tell the user that biounit indices are 0-based
- More info in output on what chains are actually processed

Corrupt residues may have some properties missing => Select("peptide=true")
may give an empty view.

Avoids issues in query language when funky characters appear in chain names

The previous error was a selection statement with no obvious connection to
that problem. Default minimum lengths are 10 for peptide chains and 4 for
nucleotide chains

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.