mosdef-hub / mbuild

A hierarchical, component based molecule builder
https://mbuild.mosdef.org
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Add smiles string conversion using pybel backend #1056

Closed daico007 closed 1 year ago

daico007 commented 1 year ago

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


codecov[bot] commented 1 year ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files ```diff @@ 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 ```

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daico007 commented 1 year ago

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