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...

we differentiate between pair states, i.e. errors related to a specific
pair of model/target ligands, and single ligand states, i.e. errors
That affect one particular ligand. An error state in the latter basically
takes that ligand out of the race for assignment.

This is mainly for debug purposes