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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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CLI parameters for the -g and -w options did not output to .pka out file #124

Closed danny305 closed 2 years ago

danny305 commented 3 years ago

I was trying to get more granular free energy and protein charge output in the .pka file. However, passing in different parameters to the -g and -w CLI parameters did not modify the out .pka file.

I made changes in the source code to address this and solved some floating point rounding issues along the way (used the decimal library).

All tests passed.

codecov[bot] commented 3 years ago

Codecov Report

Merging #124 (c37f54b) into master (68007f0) will increase coverage by 0.04%. The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #124      +/-   ##
==========================================
+ Coverage   73.05%   73.09%   +0.04%     
==========================================
  Files          24       25       +1     
  Lines        3963     3970       +7     
==========================================
+ Hits         2895     2902       +7     
  Misses       1068     1068
Impacted Files Coverage Δ
propka/output.py 57.31% <100.00%> (+0.52%) :arrow_up:
propka/__init__.py 100.00% <0.00%> (ø)

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danny305 commented 2 years ago

what is needed for this to be merged???

intendo commented 2 years ago

I think @orbeckst still needs to review this before we can merge this PR.