CreateBU always returns a valid entity. We already check if it's empty
separately.

Minimum length for a chain in the target structure
to be considered in chain mapping. The chain mapping algorithm first
performs an all vs. all pairwise sequence alignment to identify
"equal" chains within the target structure. We go for simple sequence
identity there. Short sequences can be problematic as they may
produce high sequence identity alignments by pure chance.

BUT: if you're scoring peptides or short nucleotides, you
really want to be able to reduce the default thresholds
(pep: 10, nuc: 4)

There are two use cases for this parameter: 1) decide whether a chain
mapping problem is actually solvable by naive enumeration and crash out if not
2) As a decision whether one should use naive enumeration or a heuristic
approach for chain mapping.

For the latter, n_max_naive meant the number of chains in the underlying
structure. Now its number of possible mappings for both cases.

- Make original structures available as attribute in mol.alg.Scorer object.
  Thats the actual input structures without Molck etc.
- Ensure unique interface definitions by lexicographically sorting the respective
  chain name lists
- Optionally dump additional alignment information in the compare-structures action.
  Explicitely dump residue numbers etc. of the aligned residues.

requested by Andriy. Computes all IPS metrics on a per-interface basis

requested by Andriy. Computes all ICS metrics on a per-interface basis

enable contact scores and separate dockq and per-interface qs scores

CAD score computation requires residue numbers in model and reference
to match. This raises an error in the Scorer object otherwise.
Catch this early on and raise an error specific to compare-structures
action with instructions on how to get rid of it.

Mainly for reporting in the compare-structures action
residues are reported as strings in format:
<cname>.<rnum>.<ins_code>, atoms are reported as
<cname>.<rnum>.<ins_code>.<aname>. This changes behaviour of
compare-structures and ost.mol.alg.stereochemistry
(ToJSON functions of violation info objects for the latter).

- 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.

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