Let the force field resolve the partial charge assignment by jthorton · Pull Request #2152 · OpenFreeEnergy/openfe

jthorton · 2026-08-12T10:33:52Z

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github-actions · 2026-08-12T10:34:25Z

No API break detected ✅

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Griffe output

$ griffe check "openfe" -s src --no-inspection --no-color --verbose -a origin/main

$ griffe check "openfecli" -s src --no-inspection --no-color --verbose -a origin/main

codecov · 2026-08-12T11:04:25Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.59%. Comparing base (110503a) to head (3eb3600).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2152      +/-   ##
==========================================
- Coverage   95.20%   90.59%   -4.61%     
==========================================
  Files         213      213              
  Lines       21138    21169      +31     
==========================================
- Hits        20124    19178     -946     
- Misses       1014     1991     +977

Flag	Coverage Δ
fast-tests	`90.59% <100.00%> (?)`
slow-tests	`?`

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IAlibay

quick first look

IAlibay · 2026-08-13T14:59:38Z

    RDKitToolkitWrapper,
 )
 from openff.units import unit
+from sympy.codegen.ast import continue_


Is this import necessary?

good catch not sure why pycharm pulled that in!

IAlibay · 2026-08-13T15:00:25Z

I liked your idea yesterday of having a "forcefield" entry to make it clear that this is the method that was being applied.

jthorton · 2026-08-19T16:56:22Z

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# Conflicts: # src/openfe/tests/protocols/test_openmmutils.py

IAlibay

Couple of things - mainly it doesn't look like the CLI would work right now (maybe it just needs a test to check it).

IAlibay · 2026-08-20T14:01:30Z

            off_toolkit_backend: ambertools
            number_of_conformers: None
            nagl_model: None
+            forcefields: None


Are there other changes necessary to enable this on the CLI? If so and you want them in a different PR, I'd move these changes to a separate CLI-focused PR.

Finished up the CLI support and added tests, I did intend to do it all in this PR.

IAlibay · 2026-08-20T14:15:15Z

    offmol: OFFMol,
    overwrite: bool,
-    method: Literal["am1bcc", "am1bccelf10", "nagl", "espaloma"],
+    method: Literal["am1bcc", "am1bccelf10", "nagl", "espaloma", "forcefield"],


We'll need to update the OpenFFPartialChargeSettings to match this.

IAlibay · 2026-08-20T14:17:47Z

+            forcefields = [forcefields]
+
+        # this expects the full file name of the force field offxml file, e.g. "openff-2.0.0.offxml"
+        # which is different to how settings work which can leave off the .offxml extension


I think now we can use .offxml directly right? Should we change the defaults?

Also what happens if this encounters a non .offxml str? Should we try to add it?

Updated to accept both and added a test, and yes maybe the default should now have the extension as well.

IAlibay · 2026-08-20T14:23:16Z

+    Charges are applied based on the following source preferences:
+     - Charges already present on the ligand are retained if overwrite is ``False``
+     - Charges are applied using the input method and settings
+     - the forcefield option will apply the default charges as intended by the force field.


I think this is no longer true, is that correct?

Updated to represent the correct ordering.

IAlibay · 2026-08-20T14:26:27Z

+        # which is different to how settings work which can leave off the .offxml extension
+        ff = ForceField(*forcefields)
+        # let the force field resolve the partial charge assignment
+        charges = ff.get_partial_charges(offmol)


I believe this needs to get wrapped around toolkit_registry_manager, otherwise we'll go back to encountering the annoying rdkit & openeye toolkit aren't compatible problem.

Probably but which registry would we use as it could influence the charge method used? I think the default is openeye and am1bccelf10 and then fall back to AmberToolsam1bcc?

IAlibay · 2026-08-20T14:38:55Z

+        )
+
+        assert uncharged_mol.partial_charges is not None
+        assert np.any(uncharged_mol.partial_charges)


Do you want to check against charging with ashgc directly?

Yeah extended the test to cover this.

jthorton · 2026-08-21T10:54:19Z

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try to get charges from the force field

cd183a8

jthorton commented Aug 12, 2026

View reviewed changes

Comment thread src/openfe/protocols/openmm_utils/charge_generation.py Outdated

IAlibay requested changes Aug 17, 2026

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Merge branch 'main' into charge_from_ff

d1ecb40

jthorton mentioned this pull request Aug 19, 2026

OpenFE silently ignores SMIRNOFF LibraryCharges and applies AM1-BCC when molecule charges are absent #2062

Open

jthorton added 2 commits August 19, 2026 17:53

add forcefield option for charge assignment

46c5bbf

remove import

f372a16

pre-commit-ci Bot and others added 3 commits August 19, 2026 16:56

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fix rename, update error message

00692ec

Merge remote-tracking branch 'origin/charge_from_ff' into charge_from_ff

ebf4e78

# Conflicts: # src/openfe/tests/protocols/test_openmmutils.py

jthorton requested a review from IAlibay August 20, 2026 08:32

update cli option, add readme

3eb3600

IAlibay requested changes Aug 20, 2026

View reviewed changes

finish CLI support and test, file extension handling

d700702

pre-commit-ci Bot and others added 2 commits August 21, 2026 10:54

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fix whitespace

38ff7c6

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jthorton commented Aug 19, 2026

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jthorton commented Aug 21, 2026

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jthorton commented Aug 12, 2026 •

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