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

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.

This avoids clashes between lDDTScorer classes in ost.mol.alg
and ost.mol.alg.lddt.

affects fnat/fnonnat/irmsd/dockq scores by
1) lowering distance threshold for two residues considered to be in contact
(5A -> 4A)
2) definition of interface residues. A residue is defined as interface
residue if any of its atoms is within 10A of another chain. CAPRI suggests
to lower the default to 8A in combination with only considering CB atoms
for protein peptide interactions.

This is similar to ilddt which is used as target metric in the new
AlphaFold3 paper

The Scorer object provides two mappings. The default mapping which is
QS-score based and the rigid_mapping which is RMSD based.
The rigid_mapping is now the basis for global superposition based
scores such as RMSD and GDT. And here's the thing, OpenStructure got
a brand new GDT implementation! Scanning of best possible superpositions
is a bit simpler than in LGA but the results are similar.
Benchmarking against CASP15 TS models returns GDT_TS score where 99.2%
are within 3 GDT points with the LGA results and the maximum observed
difference is 7.39. There is a tendency for slightly lower scores in
OpenStructure meaning LGA sometimes found better superpositions.

BUT: Oligo/RNA support comes for free in the Scorer object!

Special characters in chain names, such as '.' will break things otherwise

That's the minimum length for a peptide chain to be considered in chain
mapping

Minimum length for a chain in the target structure
to be considered in chain mapping. The chain mapping algorithm first
performs an all vs. all pairwise sequence alignment to identify
"equal" chains within the target structure. We go for simple sequence
identity there. Short sequences can be problematic as they may
produce high sequence identity alignments by pure chance.

BUT: if you're scoring peptides or short nucleotides, you
really want to be able to reduce the default thresholds
(pep: 10, nuc: 4)

The assignment dropped all changes that were made by molck

Note: entities with chains named ' and " will still fail

There are two use cases for this parameter: 1) decide whether a chain
mapping problem is actually solvable by naive enumeration and crash out if not
2) As a decision whether one should use naive enumeration or a heuristic
approach for chain mapping.

For the latter, n_max_naive meant the number of chains in the underlying
structure. Now its number of possible mappings for both cases.

- Make original structures available as attribute in mol.alg.Scorer object.
  Thats the actual input structures without Molck etc.
- Ensure unique interface definitions by lexicographically sorting the respective
  chain name lists
- Optionally dump additional alignment information in the compare-structures action.
  Explicitely dump residue numbers etc. of the aligned residues.

requested by Andriy. Computes all IPS metrics on a per-interface basis

requested by Andriy. Computes all ICS metrics on a per-interface basis

enable contact scores and separate dockq and per-interface qs scores

Calls the currently preferred chain mapping method that should
deal with most chain mapping cases in a reasonable runtime.

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