Running inputs with stereo centers using the openff harness errors because of missing chirality information:
QCEngine Execution Error:
Traceback (most recent call last):
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/qcengine/util.py", line 114, in compute_wrapper
yield metadata
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/qcengine/compute.py", line 91, in compute
output_data = executor.compute(input_data, config)
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/qcengine/programs/openmm.py", line 269, in compute
off_mol = offtop.Molecule(rdkit_mol)
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/topology/molecule.py", line 5836, in __init__
super(Molecule, self).__init__(*args, **kwargs)
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/topology/molecule.py", line 2089, in __init__
result = toolkit_registry.call(
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/utils/toolkit_registry.py", line 366, in call
raise e
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/utils/toolkit_registry.py", line 362, in call
return method(*args, **kwargs)
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 163, in from_object
return _cls.from_rdkit(obj, allow_undefined_stereo=allow_undefined_stereo)
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/utils/base_wrapper.py", line 51, in wrapped_function
value = func(*args, **kwargs)
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/topology/molecule.py", line 5000, in from_rdkit
molecule = toolkit.from_rdkit(
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 1472, in from_rdkit
self._detect_undefined_stereo(
File "/home/baedorf/mambaforge/envs/openff/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2336, in _detect_undefined_stereo
raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from RDMol: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom C (index 173)
To Reproduce
@benbaed Do you have an input for reproducing this which is smaller than the ~400 atom system you send me?
Expected behavior
Detect chirality from provided three-dimensional structure and bond orders.
Describe the bug
Running inputs with stereo centers using the
openff
harness errors because of missing chirality information:To Reproduce
@benbaed Do you have an input for reproducing this which is smaller than the ~400 atom system you send me?
Expected behavior
Detect chirality from provided three-dimensional structure and bond orders.
Additional context
cc @mattwthompson, @j-wags, @dotsdl