mattwthompson
commented
3 years ago Thanks for the report! I can reproduce this and I agree it's a bug. I can't offer a solution or quick workaround at the moment (barring an OpenEye license).
This root of this is that the molecule doesn't survive our round-trips with RDKit:
>>> from openff.toolkit.topology import Molecule, Topology
>>> mol = Molecule.from_smiles('CC1=C/N/C(C#N)=C(C#N)\\N=C/C(C)=C\\N/C(C#N)=C(C#N)/N=C\\1')
>>> mol.to_rdkit()
[11:52:10] Conflicting single bond directions around double bond at index 6.
[11:52:10] BondStereo set to STEREONONE and single bond directions set to NONE.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/mwt/miniconda3/envs/openff-system/lib/python3.9/site-packages/openff/toolkit/utils/base_wrapper.py", line 51, in wrapped_function
value = func(*args, **kwargs)
File "/Users/mwt/miniconda3/envs/openff-system/lib/python3.9/site-packages/openff/toolkit/topology/molecule.py", line 5157, in to_rdkit
return toolkit.to_rdkit(self, aromaticity_model=aromaticity_model)
File "/Users/mwt/miniconda3/envs/openff-system/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 1793, in to_rdkit
cls._assign_rdmol_bonds_stereo(molecule, rdmol)
File "/Users/mwt/miniconda3/envs/openff-system/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2405, in _assign_rdmol_bonds_stereo
assert stereo_rdbond.GetStereo() == desired_rdk_stereo_code
AssertionErrorAs a separate issue, there are probably other ways to do this "is the molecule already in my set of reference molecules?" check here. This will magically dissipate when the TopologyMolecule paradigm is deprecated. Changing that logic in the mean time would side-step this issue, except it could push failures to a different stage in a pipeline.
FWIW these behaviors are specific to the RDKit interface; none pop up using OpenEye toolkits. (Not suggesting this as a solution, only as information for diagnosing the issue.)
j-wags
peastman
Describe the bug I've run into a strange case where I can create a Molecule without problem, but I get an exception when I try to add it to a Topology.
To Reproduce
Output
Computing environment (please complete the following information):
Ubuntu 18.04
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