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.

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.

and some cleanup...

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

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.