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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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Fix and speedup box bonding #110

Closed speleo3 closed 3 years ago

speleo3 commented 3 years ago

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

codecov[bot] commented 3 years ago

Codecov Report

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

Impacted file tree graph

@@            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%) :arrow_down:

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speleo3 commented 3 years ago

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