initialize guess_atoms function PR

[cadeduckworth]

• add helper function to correctly guess atom/element types from topology
• helper function guess_atoms used in rdkit_conversion function
• temporary changes pending MDAnalysis guessers class bug fixes

[codecov[bot]]

Codecov Report

Merging #264 (3f90ad2) into develop (10922e8) will increase coverage by 0.17%. The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #264      +/-   ##
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+ Coverage    81.12%   81.29%   +0.17%     
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  Files           15       15              
  Lines         1960     1978      +18     
  Branches       296      297       +1     
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+ Hits          1590     1608      +18     
  Misses         278      278              
  Partials        92       92              

Files Changed	Coverage Δ
mdpow/workflows/base.py	83.07% <100.00%> (+5.52%)	:arrow_up:
mdpow/workflows/dihedrals.py	95.97% <100.00%> (+0.04%)	:arrow_up:

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[cadeduckworth]

@orbeckst please review

I did not try it out on any cases outside of the notebook during development, however, I did incorporate usage into the dihedrals module and also added the test for the base module. Everything passed locally, so hopefully there are no issues with the CI tests.

If you see any issues please let me know. If everything looks good I will update my SAMPL9 environment, do a test run, and add documentation once we are sure everything is working as intended.

If you would like more detail on the new loop added for creating the boolean array used for identifying problem cases I can upload the updated notebook here.. just let me know!

[orbeckst]

This needs some debugging. Ideally you can put whatever kills it at the moment in a test case.

[orbeckst]

@cadeduckworth see the bug https://github.com/MDAnalysis/mdanalysis/issues/4167 for LigParGen atom types and the fix PR https://github.com/MDAnalysis/mdanalysis/pull/4168 which is now in the latest released version of MDA. Do we still need our own fix?