Molecule.enumerate_protomers() does not preserve SD tags for the OpenEye toolkit backend #1776
Comments
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I agree #1771 is likely the cause: In [1]: from openff.toolkit import Molecule
In [2]: offmol = Molecule.from_smiles('COOH')
In [3]: offmol.properties['annotation'] = 'acetic acid'
In [4]: offmol.enumerate_protomers()
> /Users/mattthompson/software/openff-toolkit/openff/toolkit/utils/openeye_wrapper.py(844)enumerate_protomers()
843 import ipdb; ipdb.set_trace()
--> 844 mol = self.from_openeye(
845 protomer, allow_undefined_stereo=True, _cls=molecule.__class__
ipdb> type(protomer)
<class 'openeye.oechem.OEMolBase'>let's see if we can that behavior and then re-visit this |
5 tasks
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This is resolved by #1778 (whichever release follows 0.14.5) In [1]: from openff.toolkit import __version__
In [2]: __version__
Out[2]: '0.14.5+4.g9b23790e.dirty'
In [3]: from openff.toolkit.topology import Molecule
In [4]: offmol = Molecule.from_smiles('COOH')
In [5]: offmol.properties['annotation'] = 'acetic acid'
...:
In [6]: offmol.properties
Out[6]: {'annotation': 'acetic acid'}
In [7]: [print(microstate.properties) for microstate in offmol.enumerate_proto
...: mers()]
{'annotation': 'acetic acid'}
Out[7]: [None] |
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Describe the bug
The
.enumerate_protomers()method ofMoleculedoes not preserve SD tags for the OpenEye toolkit backend.(I did not test the RDKit backend.)
To Reproduce
Output
See above.
Computing environment (please complete the following information):
Linux version 3.10.0-1160.45.1.el7.x86_64 ([email protected]) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) ) #1 SMP Wed Oct 13 17:20:51 UTC 2021conda listAdditional context
I believe this may be due to #1711.
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