Simon found issues when reading and writing CONECT statements
in PDB io and provided code to fix it. yay

Reading: OpenStructure did not read CONECT statements at all. By default,
it still doesnt. Many PDB files out there don't provide these
statements and we really don't want to rely on them. We rather want
to assign connectivity based on the chemical component dictionary from
the PDB. However, a valid use case are novel compounds that are not
in the component dictionary. Reading connect statements can now be
enabled in the pdb reader through the IOProfile. This may give issues
in processing after reading. OpenStructure implements processors that
are responsible for connectivity. Now that we build some of the
connectivity already at the reading stage, this might cause trouble.
To remedy most of the nightmares that can come out of that, the
processors can now optionally skip connectivities between Hetatoms.

Writing: That was a plain bug when writing CONECT statements for
bond orders > 1.

PDB announced they're running out of three letter codes for compounds and
switch to longer names soon. This commit ensures that OpenStructure is ready
for that switch.

This may be necessary in case SDF ligands have the same chain/residue
number, which can happen with some input.

This should clarify what the binding site.

- 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.