That's the minimum length for a peptide chain to be considered in chain
mapping

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.

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

Move long description to separate properties

Yolo, this code is totally untested. Xavier, please give it a try ;)

Following fixes in cd701347, setting seqres=True is no longer required
for these things to work.

A null character is added by OST in case of empty insertion code. This is not part of the actual insertion code, and could make it harder for third party software to handle our output.

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).

A global chain mapping can now be enabled with --global-chain-mapping as
a complement to the existing local chain mapping. This can be evaluated
for the scoring paper.