Apply crude collision detection to avoid pairwise distance computations
between chains that are far apart.

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.

Performance wise this doesn't really make a difference but properly
setting the IsLigand property depends on it.

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.

This is False by default and forces a single assignment
for both RMSD and lDDT-PLI, based on RMSD.
This can then be assessed in the scoring paper.

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.