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.

See announcement from PDB:
https://www.wwpdb.org/news/news?year=2023#65562f0ad78e004e766a96c1

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

'model_representation' no longer made sense now that it also applies to
cases where the ligand is too far. It was renamed to 'model_binding_site'
to be more accurate. 'binding_site' was renamed to 'target_binding_site'
to match.

This was a problem in CASP16 models L4004LG020_1F where all the model
ligands were disconnected but that was not picked up properly