updating open babel energy minimization to no longer use temp file

[chrisiacovella]

PR Summary:

This is related to issue #1077. Rather that relying on a temporary .mol2 file to perform open babel energy minimization, this PR will directly set the relevant parameters in the open babel OBMol class, and extract energy minimized coordinates from this class for updating of the positions in the Compound.

My initial plan was to simply store Compound.name information, overwrite it with Compound.element before generating the .mol2 file, and then revert Compound.name parameters to the original entries. However, using the API directly to set the info seems like it would be better with less overhead.

PR Checklist

---

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

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.54%. Comparing base (042f814) to head (40f4297).
Report is 129 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1078   +/-   ##
=======================================
  Coverage   90.54%   90.54%           
=======================================
  Files          61       61           
  Lines        6186     6190    +4     
=======================================
+ Hits         5601     5605    +4     
  Misses        585      585           

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[chrisiacovella]

linux tests are failing...appears related to try to access atomic number. I think I need to check to make sure element is properly set.

The bit of code in the energy_minimize function that tries to infer atom type from name, never actually set the element field with the atom info that was inferred. Not sure how the tests were every passing before.

[chrisiacovella]

All tests are now passing after a quick change of the test_energy_minimize_non_element function to reflect the changes in the code itself.

Interestingly, the incorrectly written test passed on macOS (both my local machine running pytest and CI), but appropriately failed on linux. The incorrectly written test did not raise an MBuildError like it should, but pytest didn't consider that a failure for some reason.

I'm not seeing anything wrong in the syntax...maybe just a weird bug and I guess good that linux caught it.

 with pytest.raises(MBuildError):
            octane.energy_minimize() 

[chrisiacovella]

I found a minor bug in the to_gmso function in the compound class. kwargs are not passed to the function conversion.to_gmso. This is detailed in #1081

[chrisiacovella]

Tests were failing when I had to_gmso() properly pass kwargs, because tests were set up to handle the yet to be implemented infer_hierarchy (without passing kwargs infer_hierarchy would be ignored). I added in a TODO note to change the function call of the tests back when this is implemented.

[daico007]

I think a good chunk of conversion stuff already existed in the to_pybel method, which I think should be used as the base here (fix/add new features as needed). The conversion back looks good.

[CalCraven]

I think this is looking pretty much done.

[daico007]

LGTM!

[chrisiacovella]

Read the docs is failing, but that can be addressed separately.