This improves error messages when the counts line is invalid and the
calls to substr() return raw C++ errors.

comes at limited additional runtime costs

trust me, its a bit better that way...

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.