openff-toolkit: OpenEye Toolkit 2023.1.0 fails to assign am1bccelf10 charges that work in 2022.1.1

Describe the bug The newer version of openeye-toolkits fails to assign partial charges where the previous version did so successfully. The core of the attached Python script is

from openff.toolkit.utils.toolkits import OpenEyeToolkitWrapper
oe = OpenEyeToolkitWrapper()
oe.assign_partial_charges(mol, partial_charge_method="am1bccelf10")

where mol is an openff.toolkit.Molecule.

To Reproduce Create two conda environments:

mamba create -n openeye-2022.1.1 -c openeye 'openeye-toolkits=2022.1.1' openff-qcsubmit
mamba create -n openeye-2023.1.0 -c openeye 'openeye-toolkits=2023.1.0' openff-qcsubmit

Run the included example.py script with both environments

mamba run -n openeye-2022.1.1 --no-capture-output python example.py
mamba run -n openeye-2023.1.0 --no-capture-output python example.py

Output The first one will print 52 succeeded, 0 failed, while the second will print 0 succeeded, 52 failed.

Additional context For an even smaller test set, the 2 SMILES below fail to charge in the new version but charge in the old version:

[H:11][c:1]1[c:2]([c:4]([n:9][c:5]([c:3]1[H:13])[N@:10]([C:7]([H:18])([H:19])[H:20])[C:8]([H:21])([H:22])[C:6]([H:15])([H:16])[H:17])[H:14])[H:12]
[H:16][c:1]1[c:3]([c:7]([c:11]([c:8]([c:4]1[H:19])[H:23])[C:14]([H:29])([H:30])[N@:15]([c:12]2[c:9]([c:5]([c:2]([c:6]([c:10]2[H:25])[H:21])[H:17])[H:20])[H:24])[C:13]([H:26])([H:27])[H:28])[H:22])[H:18]

And these two charge successfully in both cases:

[H:20][c:1]1[c:2]([c:8]([c:14]([c:9]([c:3]1[H:22])[H:28])[c:15]2[c:10]([c:4]([c:5]([c:11]([c:16]2[c:17]3[c:12]([c:6]([c:7]([c:13]([c:18]3[C:19]([H:33])([H:34])[H:35])[H:32])[H:26])[H:25])[H:31])[H:30])[H:24])[H:23])[H:29])[H:27])[H:21]
[H:17][c:1]1[c:2]([c:5]([c:9]([c:8]([c:4]1[H:20])[C:10]2=[C:6]([C:3](=[C:7]([C:11](=[O:15])[N:14]2[C:12]([H:24])([H:25])[H:26])[H:23])[H:19])[H:22])[O:16][C:13]([H:27])([H:28])[H:29])[H:21])[H:18]

repro.zip

About this issue

Original URL
State: closed
Created 9 months ago
Reactions: 1
Comments: 17 (17 by maintainers)

Most upvoted comments

I wonder if this is an OpenEye support issue; if the OpenEye toolkit previously could generate conformers for these but now it cannot, is that on their end?

davidlmobley on Oct 6, 2023

I think so; if we’re not likely to do anything about it and if it’s too esoteric to document here, there is no reason to keep this open

mattwthompson on Feb 8, 2024

I updated my last comment with some additional details and just sent an email to OpenEye support!

ntBre on Oct 10, 2023

This fails with 2023.1.0 and works with 2022.1.1:

from openeye import oechem, oeomega

smiles = "[H]C1(C2=C(N=C(N2C([H])([H])[H])N3C(C(C(C(C3([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[N@](C([N@]1C([H])([H])[H])([H])[H])C([H])([H])[H])[H]"

# steps taken from
# https://docs.eyesopen.com/toolkits/python/oechemtk/molctordtor.html#construction-from-smiles
mol = oechem.OEMol()
assert oechem.OESmilesToMol(mol, smiles)

omega = oeomega.OEOmega()
assert omega(mol)

ntBre on Oct 6, 2023