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Add smiles string conversion using pybel backend #1056

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merged 4 commits into from
Oct 25, 2022

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daico007
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PR Summary:

A quick path to go from mbuild compound to smiles string through openbabel. I am using openbabel to guess the bond orders of the resulted molecule and output a smile string. This can be a temp solution before we can have our own smiles string writer. Pending unit tests.

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 Sep 20, 2022

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.66%. Comparing base (fd3fe39) to head (efd129f).
Report is 146 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1056      +/-   ##
==========================================
- Coverage   90.53%   88.66%   -1.88%     
==========================================
  Files          60       60              
  Lines        8421     8423       +2     
==========================================
- Hits         7624     7468     -156     
- Misses        797      955     +158     

☔ View full report in Codecov by Sentry.
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Fix bleeding test, otherwise this LGTM

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LGTM after fixing bleeding test

@daico007
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So the issue with the bleeding test has to do with the python version specified. When updating the env with specs from foyer/gmso env.yml, the python version got updated to python 3.10. The fixes would need to be applied on gmso/foyer sides, by adding an upper constraint for python version

@daico007 daico007 merged commit ba6fead into mosdef-hub:main Oct 25, 2022
thangckt added a commit to thangckt/mbuild that referenced this pull request Oct 31, 2022
Add smiles string conversion using pybel backend (mosdef-hub#1056)
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2 participants