The reason for removing MATCH and IDENTITY is to only have matrices
which are also available in the parasail library. This simplifies the
usage of parasail as a drop-in replacement. To be honest: I doubt that
anyone used these matrices.

The trace directionality for the internal coordinate system was
established in a recursive fashion. This likely caused filling up
stack memory for very large polymers with large recursive depth.
The fix implements the same functionality in a non-recursive
fashion.

They have the exact same quaternary structure in the end... This definition
has been generalized to: if there are no contacts observed, QS-score is 1.0
if the scored structures have the same stoichiometry, 0.0 otherwise.
This becomes a bit more abstract for higher order complexes but in principle
they still have the exact same quaternary structure if they match in
stoichiometry but have no single contact.

The score is simply not valid and returning 0.0 as done before is incorrect.
Delegates further treatment of the problem to the caller which might want to
say: if both structures are monomer, I still give it a value of 1. Or, to
extend that definition, if I reproduced the correct stoichiometry, I still
give it a value of 1.

Parasail: https://github.com/jeffdaily/parasail

It's faster than the pairwise sequence algorithms we have in
OpenStructure. However, the main reason to check out another solution
is the fact that OpenStructure may return suboptimal alignment
results. This is a result of how the dynamic programming table is built.
If for a certain cell in the dynamic programming table a match state and
insertion state score equally, match is preferred. There is a chance
that we would get a better score later on if we would stick with the
insertion state (gap open penalties vs. gap extension penalties).
Not sure if this will be fixed in the near future.

This is in order to be consistent with the behavior of the Scorer

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

Scoring classes can now be imported directly from ost.mol.alg.

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

and some cleanup...