Based on a CAMEO target (8TRK) with KFM ligand (82944 symmetries) which
takes about 15 minutes per ligand pair. Limiting to 10000 (1E4) should
limit to more reasonable 2 minutes / ligand pair..

LogDebug never shown in optimized builds

Whether we used bb_pos or full_bb_pos for superposition. Avoids
returning the RMSD of a single atom.

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

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.

'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.

Use full backbone atoms (N, CA, C for peptide residues, O5', C5', C4', C3',
O3 for nucleotide residues) if number of mapped residues is below 3.
This has a direct impact on RMSD. The behaviour before was a random value
as the fallback transformation in these cases was an identity matrix.
While RMSD is still computed on CA/C3' only, we now apply the transformation
derived from all backbone atoms.

Optimization has been improved by sampling several window sizes. The results
come really close to LGA (avg diff of 0.16 GDT points when evaluation all
CASP15 TS models).

In the previous implementation, an error was thrown when number of positions
was lower than the window size parameter. Now, the window size is just set
to the number of positions in that case and the algorithm runs through.
Special cases of only one or two positions are handled separately to produce
sensible output.

Silences a Sphinx warning.

Avoid confusion, as the editors don't come with context managers.

Added script-level info on progress; warnings upon crazy chain mappings;
silenced Verbose logging about selections; generally increased verbosity.