Unhandled conformer generation failures

[mattwthompson]

Describe the bug

To Reproduce

>>> from openff.toolkit.utils.toolkits import OpenEyeToolkitWrapper, RDKitToolkitWrapper, AmberToolsToolkitWrapper, ToolkitRegistry
>>> from openff.toolkit.topology import Molecule
>>> molecule = Molecule.from_smiles(100*"CC")

Directly generating conformers with RDKitToolkitWrapper is just missed, leading to a confusing traceback:

>>> molecule.generate_conformers(n_conformers=1, toolkit_registry=RDKitToolkitWrapper())
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mwt/software/openforcefield/openff/toolkit/topology/molecule.py", line 3230, in generate_conformers
    return toolkit.generate_conformers(
  File "/Users/mwt/software/openforcefield/openff/toolkit/utils/rdkit_wrapper.py", line 898, in generate_conformers
    for conformer in molecule2._conformers:
TypeError: 'NoneType' object is not iterable

It's caught with OpenEye:

>>> molecule.generate_conformers(n_conformers=1, toolkit_registry=OpenEyeToolkitWrapper())
Warning: : Failed to build structure from CT
Warning: : Failed to build structure from CT
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mwt/software/openforcefield/openff/toolkit/topology/molecule.py", line 3230, in generate_conformers
    return toolkit.generate_conformers(
  File "/Users/mwt/software/openforcefield/openff/toolkit/utils/openeye_wrapper.py", line 1692, in generate_conformers
    raise Exception("OpenEye Omega conformer generation failed")
Exception: OpenEye Omega conformer generation failed

This is descriptive, but it's also the most general Exception and would be tricky to capture as a downstream user.

This can affect charge assignment:

>>> molecule.assign_partial_charges(partial_charge_method='am1bcc')
Warning: : Failed to build structure from CT
Warning: : Failed to build structure from CT
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mwt/software/openforcefield/openff/toolkit/topology/molecule.py", line 3439, in assign_partial_charges
    toolkit_registry.call(
  File "/Users/mwt/software/openforcefield/openff/toolkit/utils/toolkit_registry.py", line 380, in call
    raise ValueError(msg)
ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name '' and SMILES '[H]C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]', 'partial_charge_method': 'am1bcc', 'use_conformers': None, 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
Available toolkits are: [ToolkitWrapper around OpenEye Toolkit version 2021.1.1, ToolkitWrapper around The RDKit version 2021.03.4, ToolkitWrapper around AmberTools version 21.0, ToolkitWrapper around Built-in Toolkit version None]
 ToolkitWrapper around OpenEye Toolkit version 2021.1.1 <class 'Exception'> : OpenEye Omega conformer generation failed
 ToolkitWrapper around The RDKit version 2021.03.4 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1bcc' is not available from RDKitToolkitWrapper. Available charge methods are ['mmff94']
 ToolkitWrapper around AmberTools version 21.0 <class 'TypeError'> : 'NoneType' object is not iterable
 ToolkitWrapper around Built-in Toolkit version None <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : Partial charge method "am1bcc"" is not supported by the Built-in toolkit. Available charge methods are ['zeros', 'formal_charge']
>>> molecule.assign_partial_charges(partial_charge_method='am1bcc', toolkit_registry=ToolkitRegistry([AmberToolsToolkitWrapper, RDKitToolkitWrapper]))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mwt/software/openforcefield/openff/toolkit/topology/molecule.py", line 3439, in assign_partial_charges
    toolkit_registry.call(
  File "/Users/mwt/software/openforcefield/openff/toolkit/utils/toolkit_registry.py", line 380, in call
    raise ValueError(msg)
ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name '' and SMILES '[H]C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]', 'partial_charge_method': 'am1bcc', 'use_conformers': None, 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
Available toolkits are: [ToolkitWrapper around AmberTools version 21.0, ToolkitWrapper around The RDKit version 2021.03.4]
 ToolkitWrapper around AmberTools version 21.0 <class 'TypeError'> : 'NoneType' object is not iterable
 ToolkitWrapper around The RDKit version 2021.03.4 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1bcc' is not available from RDKitToolkitWrapper. Available charge methods are ['mmff94']

This might be hard to handle, since it's difficult to distinguish between a wrapper not being able to do something and it trying and failing, but "No registered toolkits can provide the capability" is maybe not the right way to communicate this, since they have the general capability but fail on bad cases like this obtusely large molecule.

Output

[mattwthompson]

>>> from openff.toolkit.topology import Molecule
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
>>> from openff.toolkit.utils.toolkits import *
>>> mol = Molecule.from_smiles("F[U](F)(F)(F)(F)(F)")
>>> mol.generate_conformers(n_conformers=1)
Warning: OEMMFFParams::PrepMol() : unable to type atom 1 U
Warning: : Force field setup failed due to missing parameters
Warning: OEMMFFParams::PrepMol() : unable to type atom 1 U
Warning: : Force field setup failed due to missing parameters
[17:13:59] UFFTYPER: Unrecognized atom type: U_ (1)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mwt/software/openforcefield/openff/toolkit/topology/molecule.py", line 3221, in generate_conformers
    return toolkit_registry.call(
  File "/Users/mwt/software/openforcefield/openff/toolkit/utils/toolkit_registry.py", line 380, in call
    raise ValueError(msg)
ValueError: No registered toolkits can provide the capability "generate_conformers" for args "(Molecule with name '' and SMILES 'F[U](F)(F)(F)(F)F',)" and kwargs "{'n_conformers': 1, 'rms_cutoff': None, 'clear_existing': True}"
Available toolkits are: [ToolkitWrapper around OpenEye Toolkit version 2021.1.1, ToolkitWrapper around The RDKit version 2021.03.5, ToolkitWrapper around AmberTools version 21.0, ToolkitWrapper around Built-in Toolkit version None]
 ToolkitWrapper around OpenEye Toolkit version 2021.1.1 <class 'openff.toolkit.utils.exceptions.ConformerGenerationError'> : OpenEye Omega conformer generation failed
 ToolkitWrapper around The RDKit version 2021.03.5 <class 'openff.toolkit.utils.exceptions.ConformerGenerationError'> : RDKit conformer generation failed.

>>> mol.generate_conformers(n_conformers=1, toolkit_registry=OpenEyeToolkitWrapper())
Warning: OEMMFFParams::PrepMol() : unable to type atom 1 U
Warning: : Force field setup failed due to missing parameters
Warning: OEMMFFParams::PrepMol() : unable to type atom 1 U
Warning: : Force field setup failed due to missing parameters
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mwt/software/openforcefield/openff/toolkit/topology/molecule.py", line 3231, in generate_conformers
    return toolkit.generate_conformers(
  File "/Users/mwt/software/openforcefield/openff/toolkit/utils/openeye_wrapper.py", line 1693, in generate_conformers
    raise ConformerGenerationError(
openff.toolkit.utils.exceptions.ConformerGenerationError: OpenEye Omega conformer generation failed
>>> mol.generate_conformers(n_conformers=1, toolkit_registry=RDKitToolkitWrapper())
[17:14:13] UFFTYPER: Unrecognized atom type: U_ (1)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mwt/software/openforcefield/openff/toolkit/topology/molecule.py", line 3231, in generate_conformers
    return toolkit.generate_conformers(
  File "/Users/mwt/software/openforcefield/openff/toolkit/utils/rdkit_wrapper.py", line 894, in generate_conformers
    raise ConformerGenerationError("RDKit conformer generation failed.")
openff.toolkit.utils.exceptions.ConformerGenerationError: RDKit conformer generation failed.
>>> mol.generate_conformers(n_conformers=1, toolkit_registry=AmberToolsToolkitWrapper())
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mwt/software/openforcefield/openff/toolkit/topology/molecule.py", line 3231, in generate_conformers
    return toolkit.generate_conformers(
AttributeError: 'AmberToolsToolkitWrapper' object has no attribute 'generate_conformers'

Over the course of #1050, I implemented everything I was originally confused about not having, so I'm going to close this.