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Add smiles string conversion using pybel backend

Open daico007 opened this issue 2 years ago • 1 comments

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?

daico007 avatar Sep 20 '22 22:09 daico007

Codecov Report

Base: 90.53% // Head: 88.66% // Decreases project coverage by -1.87% :warning:

Coverage data is based on head (efd129f) compared to base (fd3fe39). Patch coverage: 100.00% of modified lines in pull request are covered.

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     
Impacted Files Coverage Δ
mbuild/compound.py 97.58% <100.00%> (+<0.01%) :arrow_up:
mbuild/formats/hoomd_forcefield.py 0.00% <0.00%> (-78.46%) :arrow_down:
mbuild/formats/hoomd_snapshot.py 73.77% <0.00%> (-5.25%) :arrow_down:

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codecov[bot] avatar Sep 20 '22 23:09 codecov[bot]

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 avatar Oct 25 '22 19:10 daico007