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Turn off the infer_residues in compound.py #1135

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daico007
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@daico007 daico007 commented Jul 8, 2023

PR Summary:

This is a follow up PR to #1134. Turn out, my initial instinct was correct, in that the slow down was cause by the infer_residues in parmed conversion. The reason the last PR doesn't show any improvement is because I forgot to also the infer_residues in the to_parmed existing in compound.py (I only turned off in conversion.py).

PR Checklist


  • Includes appropriate unit test(s)
  • Appropriate docstring(s) are added/updated
  • Code is (approximately) PEP8 compliant
  • Issue(s) raised/addressed?

@daico007
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daico007 commented Jul 8, 2023

Screenshot 2023-07-08 at 00 37 59

This is the new speed up provided by turning off said option (when writing out to gsd).

I will probably force merge this once all test pass and make a patch release.

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codecov bot commented Jul 8, 2023

Codecov Report

Patch and project coverage have no change.

Comparison is base (54a6241) 87.11% compared to head (bc1e4c4) 87.11%.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1135   +/-   ##
=======================================
  Coverage   87.11%   87.11%           
=======================================
  Files          62       62           
  Lines        6451     6451           
=======================================
  Hits         5620     5620           
  Misses        831      831           
Impacted Files Coverage Δ
mbuild/compound.py 97.12% <ø> (ø)

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@daico007 daico007 merged commit cea141e into mosdef-hub:main Jul 8, 2023
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