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Turn off infer_residues for visualize step #1129

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merged 5 commits into from
Jun 29, 2023

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PR Summary:

I bump into the case when visualize big compound becomes extremely slow. I was able to determine the bottle neck, which is the pull_residues step when converting from mbuild to parmed (to save out to a mol2 file) when the infer_residue is True. This PR will turn that option off, and we probably need to look into optimize the pull_residues method in the near future.

PR Checklist


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

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codecov bot commented Jun 27, 2023

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (474b65f) 87.11% compared to head (3491b5e) 87.11%.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1129   +/-   ##
=======================================
  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)
mbuild/utils/io.py 83.62% <100.00%> (ø)

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@daico007 daico007 merged commit 0f7c070 into mosdef-hub:main Jun 29, 2023
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2 participants