restores old behaviour but as far as I can see, this change has no
consequence at all.

Key differences:
 - LigandScorer does not automatically extract non-polymer ligands
   anymore, ligand extraction must happen externally
 - LigandScorer performs cleanup of receptor structure 1) removal of
   hydrogens 2) removal of residues for which there is no entry in
   the PDB component dictionary 3) removal of residues that are not
   peptide linking or nucleotide linking according to PDB component
   dictionary 4) removal of atoms that are not defined for the
   respective entry in the PDB component dictionary.
 - Cleanup is Logged and available as output
 - compare-ligand-structures action does not support automatic
   extraction of ligands from PDB structures anymore. This feature
   still works if structures are provided as mmCIF.
 - compare-ligand-structures action adds receptor structure cleanup
   logs and input parameter in json output to improve
   reproducibility of results.

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.

The rmsd_ prefix was more confusing than helpful to Mike

This will allow Andriy's to add target, model and group information
cleanly and directly to the CSV without the need for an extra script.

This makes the verbose output of the action more readable

This changes the CSV output file to list one model ligand per line,
instead of one reference ligand.

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

QS-score which is used as default target function for chain mappings.
However, thats protein specific. As soon as nucleotides are involved,
lDDT with an increased inclusion radius of 30A is now used
in ChainMapper.GetMapping.

It was a bit embarassing that lDDT mappings were about an order of
magnitude slower than QS-score mappings. A specialized backbone only
lDDT has therefore been introduced that uses matrix operations.
This is not a replacement of the lDDTScorer. But it doesnt need to
produce per-residue scores and doesn't need to deal with symmetries
etc.

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.