Openeye license check
insukjoung opened this issue · 6 comments
insukjoung commented
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
from openmm.app import PDBFile
from openff.toolkit.topology import Molecule, Topology
from openff.toolkit.typing.engines.smirnoff import ForceField as off_ForceField
ligand_sdf = 'ligand.sdf'
ligand_pdb = 'ligand.pdb'
force_field = off_ForceField("openff_unconstrained-2.0.0.offxml")
ligand = Molecule.from_file(ligand_sdf, allow_undefined_stereo=True)
ligand_pdb = PDBFile(ligand_pdb)
off_topology = Topology.from_openmm(openmm_topology=ligand_pdb.topology, unique_molecules=[ligand])
ligand_system = force_field.create_openmm_system(off_topology)This does not raise any exception but causes license error:
ligand.sdf and ligand.pdb can 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):
- Operating system: Ubuntu 22.04.3 LTS
- Output of running
conda list
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
_py-xgboost-mutex 2.0 gpu_0 conda-forge
agate 1.9.1 py39hf3d152e_0 conda-forge
agate-dbf 0.2.2 pyhd8ed1ab_0 conda-forge
agate-excel 0.2.3 py_0 conda-forge
agate-sql 0.5.8 pyhd8ed1ab_0 conda-forge
aioeasywebdav 2.4.0 py39hf3d152e_1001 conda-forge
aiohttp 3.9.3 py39hd1e30aa_1 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
alabaster 0.7.16 pyhd8ed1ab_0 conda-forge
ambertools 23.3 py39h7fa913e_6 conda-forge
amberutils 21.0 pypi_0 pypi
amply 0.1.6 pyhd8ed1ab_0 conda-forge
annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge
anyio 3.7.1 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h27087fc_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39hb9d737c_3 conda-forge
argtable2 2.13 h14c3975_1001 conda-forge
arpack 3.8.0 nompi_h0baa96a_101 conda-forge
ase 3.22.1 pyhd8ed1ab_1 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge
atk-1.0 2.38.0 hd4edc92_1 conda-forge
attmap 0.13.2 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
automl 0.0.1 pypi_0 pypi
aws-c-auth 0.7.0 hf8751d9_2 conda-forge
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aws-c-compression 0.2.17 h862ab75_1 conda-forge
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aws-c-http 0.7.11 hbe98c3e_0 conda-forge
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aws-c-s3 0.3.13 heb0bb06_2 conda-forge
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babel 2.14.0 pyhd8ed1ab_0 conda-forge
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bcrypt 4.1.2 py39h9fdd4d6_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
binutils_linux-64 2.40 hbdbef99_2 conda-forge
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black 23.3.0 py39hf3d152e_1 conda-forge
blas 2.116 openblas conda-forge
blas-devel 3.9.0 16_linux64_openblas conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
blinker 1.7.0 pyhd8ed1ab_0 conda-forge
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cfitsio 4.2.0 hd9d235c_0 conda-forge
cftime 1.6.2 py39h2ae25f5_1 conda-forge
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charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge
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click 8.1.7 unix_pyh707e725_0 conda-forge
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coin-or-utils 2.11.9 hee58242_0 conda-forge
coincbc 2.10.10 0_metapackage conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
colorlog 6.8.2 py39hf3d152e_0 conda-forge
comm 0.1.3 pyhd8ed1ab_0 conda-forge
configargparse 1.7 pyhd8ed1ab_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
contourpy 1.0.7 py39h4b4f3f3_0 conda-forge
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cuda-cudart 11.8.89 0 nvidia
cuda-cupti 11.8.87 0 nvidia
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dav1d 1.2.1 hd590300_0 conda-forge
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lzo 2.10 h516909a_1000 conda-forge
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melloddy-tuner 3.0.3a0 dev_0
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mmgbsa-tool 0.1.0 dev_0
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molgrid 0.5.2 cuda118py39h7277d68_3 conda-forge
mordred 1.2.0 py_1 conda-forge
motor 2.5.1 pyhd8ed1ab_1 conda-forge
mpc 1.3.1 hfe3b2da_0 conda-forge
mpfr 4.2.1 h9458935_0 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.1.5 py39h6cbbaa3_0 conda-forge
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mpiplus v0.0.2 pyhd8ed1ab_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
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munkres 1.1.4 pyh9f0ad1d_0 conda-forge
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j-wags commented
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, omega-toolkit vs omega-c++) , but it looks like the single license key covers multiple sub-features, since it contains the line #FEATURES: gas-phase;toolkit;python;java;clr.
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?
j-wags commented
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.
mattwthompson commented
I'm pretty sure the problem is that OpenEyeToolkitWrapper only uses itself to generate conformers, implying that it can't fall back to RDKit for conformer generation as you'd expect Molecule.generate_conformers to try. I think Quacpac charges with RDKit conformers is a valid use case (and probably one users would expect if they have a Quacpac license).
I haven't reproduced this, but this should be testable via mocking oeomega.OEOmegaIsLicensed
j-wags commented
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.
insukjoung commented
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?
Yes, it works. But, it would be nicer if I can use OEquacpac instead because it is much faster.
I think Quacpac charges with RDKit conformers is a valid use case (and probably one users would expect if they have a Quacpac license).
If this works, it would be our second best solution.
The best solution for us would be using openeye's oeomega/flipper (binary) + OEquacpac.
That is, the ideal fallback path would be OEomega toolkit --> OEomega binary (not currently implemented) --> RDkit.
FYI, there is a function call for checking the validity of OEomega toolkit.(https://docs.eyesopen.com/toolkits/python/omegatk/OEConfGenFunctions/OEOmegaIsLicensed.html)
mattwthompson commented
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. OpenEyeToolkitWrapper check at initialization if any licenses are found but doesn't check later. So in a case like we have here, the crash isn't observed until omega.OEOmega() is called. This makes it hard to programmatically work with each of the methods that might take different licenses or combinations of 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,
)