OST writes invalid atom serial numbers if they exceed the PDB format limits.
That's a feature not a bug. The new behaviour is that invalid serial numbers
don't get parsed. Any processing function working with these serial numbers
need to manually check for that. The only current effect is when reading
CONECT statements. Atoms with invalid serial numbers are not connected.

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.

Make assigning Mol IDs more permissive in PDB reader. I.e. allow COMPND
keywords for chains that are not in the finally loaded entity if no_hetatms
is True in the IO profile. They're missing if solely composed of hetatms.

silences a compiler warning in gcc 8.3 and is a good idea anyway

Hetatms are potentially skipped but if they come with an ANISOU record,
ost expects them to be there. As a solution we simply increase the
permissiveness as we already do it when having the calpha_only option
active.

wrong branch, big sorry

This reverts commit e77d08a6.

The gnu c++ size() implementation for stl containers has O(n) complexity
while empty() has O(1) complexity

Unit tests are working, except the ones relying on the
HeuristicProcessor, which is currently only a stub.

silencing warnings during testing; swapping std::cout for LOG_WARNING when there is a chain with no MOL_ID assigned

Changed behaviour on > 99999 atoms: now ***** is always used. Fixed PDB writer, reader, added unit test.

Signed-off-by: Stefan Bienert <stefan.bienert@unibas.ch>

This greatly speeds up the opening of pdb files that have more
than 100k atoms.

in quack mode, atoms of residues that have identical numbers but different
names are no longer ignored to ensure all atoms are loaded

(ANISOU entries in microheterogeneity captured)

It's intentional to only check for duplicate atoms during PDB import an not directly in InsertAtom, since it is completely valid for a few fileformats to have more than one atom with the same name.

This is based on exhaustive testing on the complete files of the PDB.
There are still a few unresolved issues. However it is not clear to me,
whether the problems are due to errors in the PDB files or our
misunderstanding.

The residue names listed in the SEQRES record get automatically translated to
one-letter-codes. Requires the presence of the rule-based builder to work
properly. Turned off by default