Molecules With Undefined Sterochemistry Can't Be Parametrized

[SimonBoothroyd]

Describe the bug
Attempting to parameterize a molecule which has been created with the option allow_undefined_stereo=True will yield an exception when used with the OpenEye backend (I don't think this is true for the RDKit backend).

This is caused by the strict stereochemistry option being set when running Omega. It would be good if the allow_undefined_stereo option was honored by all methods operating on molecules created using it, otherwise the option seems a bit redundant.

To Reproduce

from openforcefield.topology import Molecule, Topology
from openforcefield.typing.engines.smirnoff import ForceField

molecule = Molecule.from_smiles('CC1CCC(=O)O1', allow_undefined_stereo=True)
topology = Topology.from_molecules([molecule])

force_field = ForceField('smirnoff99Frosst.offxml')
force_field.create_openmm_system(topology)

Output

Warning: : Failed due to unspecified stereochemistry
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/XXX/lib/python3.7/site-packages/openforcefield/typing/engines/smirnoff/forcefield.py", line 1139, in create_openmm_system
    parameter_handler.create_force(system, topology, **kwargs)
  File "/XXX/lib/python3.7/site-packages/openforcefield/typing/engines/smirnoff/parameters.py", line 2463, in create_force
    temp_mol.generate_conformers(n_conformers=10, toolkit_registry=toolkit_registry)
  File "/XXX/lib/python3.7/site-packages/openforcefield/topology/molecule.py", line 1980, in generate_conformers
    clear_existing=clear_existing)
  File "/XXX/lib/python3.7/site-packages/openforcefield/utils/toolkits.py", line 3006, in call
    return method(*args, **kwargs)
  File "/XXX/lib/python3.7/site-packages/openforcefield/utils/toolkits.py", line 1116, in generate_conformers
    raise Exception("OpenEye Omega conformer generation failed")
Exception: OpenEye Omega conformer generation failed

Computing environment (please complete the following information):

• Operating system: MacOS
• Toolkit Version: 0.4.1
• OpenEye Version: 2019.4.2

[davidlmobley]

@SimonBoothroyd presumably this would work if you were starting with coordinates for the molecule?

Just thinking out loud, you can't go ahead and do a simulation of a molecule unless you have starting coordinates for it. Assigning parameters is perhaps still useful though, because we may want to inspect the parameters. So, I agree this should work and it's a bug that it doesn't. That said... we may want to also warn people abundantly in such cases.