naming water and ion residues during solvate

[amburan]

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[codecov]

Codecov Report

❌ Patch coverage is 83.33333% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.61%. Comparing base (95149b0) to head (c1f260f).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
openpharmmdflow/pipeline/sm/pipeline.py	83.33%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #90      +/-   ##
==========================================
+ Coverage   72.32%   72.61%   +0.28%     
==========================================
  Files          22       22              
  Lines         683      701      +18     
==========================================
+ Hits          494      509      +15     
- Misses        189      192       +3     

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[mikemhenry]

Sweet! We don't have great unit tests setup yet, but the integration tests will catch any major issues. Have you had a chance to test to see if adding this metadata helps with the visualization?

[mikemhenry]

One other idea to explore is to check it metadata is preserved when solvating and then we can define the names of the atoms/mols before we solvate, which saves us from looping over all the molecules

Another idea is to just loop over the molecules in the system once, call to_smiles on each of them, and then if there is a match to Na, CL, or H20 we add the metadata, this will speed things up ~3x