Boresch selection max_distance filter not applied to all relevant distance

[hannahbaumann]

I noticed that this max_distance filter is not being applied to all relevant protein - ligand atom distances. https://github.com/MobleyLab/SeparatedTopologies/blob/e7f712379472ea320cc049a78b19405014d8bbce/boresch_restraints.py#L390

The intent of this filter is to select protein atoms that are less than half the box size away from 1. the selected ligand atom(s) and 2. the other protein atoms. Currently, it e.g. doesn't check the distance between P1-L1 (in the case where no protein atoms had been provided by the user) which could potentially lead to pbc wrapping issues.