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Add smiles string conversion using pybel backend
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?
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%) |
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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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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