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.

Based on a CAMEO target (8TRK) with KFM ligand (82944 symmetries) which
takes about 15 minutes per ligand pair. Limiting to 10000 (1E4) should
limit to more reasonable 2 minutes / ligand pair..

LogDebug never shown in optimized builds

If it's not an SDF file then the error was meaningless. Make it
clearer that we may not have an SDF file at all

This commits makes the SDFReader aware of IOProfiles. It allows bad
bond types in fault_tolerant mode (ie dative bonds from RDKit with
non-standard type 9).

Whether we used bb_pos or full_bb_pos for superposition. Avoids
returning the RMSD of a single atom.

No one uses it (fingers crossed) and it clutters documentation with
unnecessary stuff

SCHWED-6400

Potentially triggers an error though

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.