No one uses it (fingers crossed) and it clutters documentation with
unnecessary stuff

SCHWED-6400

Potentially triggers an error though

also fixes inconsistencies in scoring.Scorer doc strings

That means: apply chain mapping and then remove all model residues
for which there is no target counterpart. We therefore remove
model contacts for which we simply have no experimental evidence.

See announcement from PDB:
https://www.wwpdb.org/news/news?year=2023#65562f0ad78e004e766a96c1

The rmsd_ prefix was more confusing than helpful to Mike

This will allow Andriy's to add target, model and group information
cleanly and directly to the CSV without the need for an extra script.

This makes the verbose output of the action more readable

'model_representation' no longer made sense now that it also applies to
cases where the ligand is too far. It was renamed to 'model_binding_site'
to be more accurate. 'binding_site' was renamed to 'target_binding_site'
to match.

This was a problem in CASP16 models L4004LG020_1F where all the model
ligands were disconnected but that was not picked up properly

In principle one can have the following alignment:

XXXXXXXXXXA--------
----------AYYYYYYYY

It has a 100% sequence identity! The previously implemented logic of gap
thresholds was also not very helpfil to filter out these cases as it
operated on fraction of gaps between first and last aligned column in
the alignment. That's 0.0 and thus perfect.

This commit simplifies this logic and simply checks for a sequence identity
threshold and a minimum number of aligned columns when grouping sequences
together. This should make grouping these cases together very unlikely.

If residue number alignments are enabled, one can assume that two
consecutive residues in terms of residue numbers are connected.
The conop Processor does not necessarily connect them if the bond
is considered unfeasible. This gives inaccurate results in
subsequent stereochemistry checks.
This change forces these connections if and only if resnum_alignments
are enabled

lrmsd defines the longer chain as receptor and uses it for superposition.
If both chains have the same length, the selection becomes random.
This commit implements the same random selection as DockQ v2.2.1.
This is no conceptual change of the score itself! It just makes the
two implementations more similar.

The latter is only relevant if mmcif_conform is True and triggered a segfault
before.