Openeye license check #1896
Comments
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Thanks for the writeup. This is helping me understand the landscape of OE licenses better, since in our license file we just have a single key for Omega (that is, we don't have separate keys for, for example, I'll double check this soon, but I expect the issue is something like "oechem is correctly licensed so the entire OpenEyeToolkitWrapper is active, but then a certain feature in Omega isn't licensed so this error comes up". In the longer run we could try to implement more fine-grained license checks, but at the core of the issue is that your OE license doesn't cover the core use of omega/quacpac needed in OpenFF system creation. This isn't a big deal - The OpenFF Toolkit can use RDKit+AmberTools instead (and I see those are installed in your environment). So, I think a straightforward workaround to get your use case working would be to replace: ligand_system = force_field.create_openmm_system(off_topology)with from openff.toolkit.utils import toolkit_registry_manager, AmberToolsToolkitWrapper, RDKitToolkitWrapper, ToolkitRegistry
with toolkit_registry_manager(ToolkitRegistry([AmberToolsToolkitWrapper(), RDKitToolkitWrapper()])):
ligand_system = force_field.create_openmm_system(off_topology)Could you let me know if that works? |
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Oh, and maybe I missed this - Did your original script run successfully and just output the license error to the console, or did it crash before completing? Most of the time, when the OpenFF Toolkit calls to outside tools, it will attempt to use OpenEye first (if it's installed and might be licensed), and if anything goes wrong there it will try using RDKit+AmberTools instead. So I'm realizing that your script might have been completing successfully all along (by falling back to the RDKit+AmberTools backend), but just printing out a concerning license error in the process. |
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I'm pretty sure the problem is that I haven't reproduced this, but this should be testable via mocking |
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Good point @mattwthompson, I thought that Quacpac ELF10 calls internally used omega (in a way that we couldn't intercept) but it looks like I was wrong. I don't love the pattern of having ToolkitWrappers call each other (it adds complexity and reduces reproducibility) but given the value-add of Quacpac in charge assignment, I could live with a try/except here. |
Yes, it works. But, it would be nicer if I can use OEquacpac instead because it is much faster.
If this works, it would be our second best solution. FYI, there is a function call for checking the validity of OEomega toolkit.(https://docs.eyesopen.com/toolkits/python/omegatk/OEConfGenFunctions/OEOmegaIsLicensed.html) |
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I dug into this a little more and found some holes in how we handle users with some (but neither all nor none) OpenEye licenses. This test "passes," but shouldn't (see comments): import pytest
from openff.toolkit import Molecule
def test_am1bccelf10_no_omega(monkeypatch):
from openff.toolkit.utils import OpenEyeToolkitWrapper
from openeye import oeomega
monkeypatch.setattr(oeomega, "OEOmegaIsLicensed", lambda: False)
assert oeomega.OEOmegaIsLicensed() == False
wrapper = OpenEyeToolkitWrapper()
wrapper._check_licenses()
molecule = Molecule.from_smiles(10 * "C")
# works, but should not since Omega isn't licensed
molecule.generate_conformers(
n_conformers=200,
toolkit_registry=wrapper,
)
monkeypatch.setattr(oeomega, "OEOmega", lambda: print("Don't use Omega"))
# now this doesn't work, but I had to mock OEOmega directly to trigger
with pytest.raises(
AttributeError,
match="'NoneType' object has no attribute 'SetMaxConfs'",
):
molecule.generate_conformers(
n_conformers=200,
toolkit_registry=wrapper,
) |
Describe the bug
We have omega (but not omega toolkit) and oequacpac license. In this condition, openeye license check is not done correctly.
To Reproduce
This does not raise any exception but causes license error:
ligand.sdfandligand.pdbcan be any small molecule in the two different format.Output
LICENSE: No valid license found for omega
LICENSE: File(s) used: /path/to/oe_license.txt
LICENSE: Closest license failed because:
LICENSE: features
Computing environment (please complete the following information):
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