This may be necessary in case SDF ligands have the same chain/residue
number, which can happen with some input.

This should clarify what the binding site.

- Tell the user that biounit indices are 0-based
- More info in output on what chains are actually processed

This code is considered deprecated as of release 2.4.0. The new lDDT
implementation has already been integrated into
qsscoring.py/compare-structures. I prefer to leave this completely legacy.

same behaviour as old compare-structures

Before the program wrote the traceback into the output json but
exited silently. Now we re-raise upon writing the output.

commited for further review, currently co-exists with compare-structures

before: Scoring was only affected by mapped chains. Penalties for additional
chains in reference/model could be added by enabling "penalize_extra_chains"
flag.
now: Non-mapped chains from the reference penalize the lDDT score. Penalties
for additional chains in model can be added by enabling "penalize_extra_chains"
flag.

If fault_tolerant is enabled, it might happily read a cif file as PDB file.
As a consequence, there are no residues in the returned entity.

Executed command: 2to3-2.7 -n -w actions/ost-compare-structures