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...

This is no final product but just a first working version as a
starting point. Plenty of testing/cleanup/speedup required.

Document default values for minimum peptide/nucleotide lengths

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

Until now, the actions were failing with somewhat cryptic messages
raised from arbitrary locations. This one should be more user-friendly.

CreateBU always returns a valid entity. We already check if it's empty
separately.

This is made possible now that we have a CreateBU function.

It turns out for some reason we were reading them from chains, based on
the ChainType of the chain. This prevented extracting anything from
legacy PDB files and didn't match the documented behavior in the action.

Now extraction is based on the IsLigand flag only, and documentation is
consistent throughout. Behavior on PDB files is tested.

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)

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

Move long description to separate properties