Turn off the infer_residues in compound.py

daico007 commented 1 year ago

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 commented 1 year ago

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.

codecov[bot] commented 1 year ago

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

```diff @@ Coverage Diff @@ ## main #1135 +/- ## ======================================= Coverage 87.11% 87.11% ======================================= Files 62 62 Lines 6451 6451 ======================================= Hits 5620 5620 Misses 831 831 ``` | [Impacted Files](https://app.codecov.io/gh/mosdef-hub/mbuild/pull/1135?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub) | Coverage Δ | | |---|---|---| | [mbuild/compound.py](https://app.codecov.io/gh/mosdef-hub/mbuild/pull/1135?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=mosdef-hub#diff-bWJ1aWxkL2NvbXBvdW5kLnB5) | `97.12% <ø> (ø)` | |

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mosdef-hub / mbuild