Fix and speedup box bonding

[speleo3]

First commit fixes #97.
Second commit makes box bonding 5 times faster.

[codecov]

Codecov Report

Merging #110 (c78345c) into master (45aa08a) will decrease coverage by 0.22%.
The diff coverage is 96.42%.

@@            Coverage Diff             @@
##           master     #110      +/-   ##
==========================================
- Coverage   73.31%   73.09%   -0.23%     
==========================================
  Files          24       24              
  Lines        3987     3958      -29     
==========================================
- Hits         2923     2893      -30     
- Misses       1064     1065       +1     

Impacted Files	Coverage Δ
propka/bonds.py	55.40% <96.42%> (-5.56%)	⬇️

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[sobolevnrm]

Looks great! FWIW, I've been using https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.KDTree.html for most of my distance lookups lately at it works great. It's not the right solution for this (overkill and don't want to introduce additional dependencies) but thought I'd share the finding, regardless.

[speleo3]

I fully agree, scipy.spatial.KDTree is fantastic, but scipy is a pretty hefty dependency.