Add library charge checks

src/pontibus/components/extended_solvent_component.py

@@ -16,7 +16,7 @@
     _from_dict,
     GufeTokenizable,
 )
-from pontibus.utils.systems import WATER
+from pontibus.utils.molecules import WATER
 
 
 class ExtendedSolventComponent(SolventComponent):

src/pontibus/tests/utils/test_interchange_packmol.py

@@ -20,6 +20,7 @@
     _get_offmol_resname,
 )
 from pontibus.utils.systems import WATER
+from numpy.testing import assert_almost_equal
 
 
 @pytest.fixture()
@@ -30,8 +31,8 @@ def smc_components_benzene(benzene_modifications):
 
 
 @pytest.fixture()
-def methane():
-    m = Molecule.from_smiles("C")
+def methanol():
+    m = Molecule.from_smiles("CO")
     m.generate_conformers()
     m.assign_partial_charges(partial_charge_method="gasteiger")
     return m
@@ -110,7 +111,7 @@ def test_solv_but_no_solv_offmol(
 
 def test_solv_mismatch(
     smc_components_benzene,
-    methane,
+    methanol,
 ):
     assert ExtendedSolventComponent().smiles == "[H][O][H]"
     with pytest.raises(ValueError, match="does not match"):
@@ -120,7 +121,7 @@ def test_solv_mismatch(
             smc_components=smc_components_benzene,
             protein_component=None,
             solvent_component=ExtendedSolventComponent(),
-            solvent_offmol=methane,
+            solvent_offmol=methanol,
         )
 
 
@@ -161,6 +162,42 @@ def test_vacuum(smc_components_benzene):
     assert len(bond) == 3
 
 
+def test_noncharge_librarycharges(smc_components_benzene):
+    solvent_offmol = Molecule.from_smiles('O')
+    interchange, comp_resids = interchange_packmol_creation(
+        ffsettings=InterchangeFFSettings(),
+        solvation_settings=PackmolSolvationSettings(),
+        smc_components=smc_components_benzene,
+        protein_component=None,
+        solvent_component=SolventComponent(
+            smiles='O', neutralize=False,
+            ion_concentration=0 * unit.molar,
+        ),
+        solvent_offmol=solvent_offmol,
+    )
+
+
+def test_noncharge_nolibrarycharges(smc_components_benzene):
+    solvent_offmol = Molecule.from_smiles('c1ccccc1')
+    #solvent_offmol.generate_conformers()
+    #solvent_offmol.assign_partial_charges(partial_charge_method="gasteiger")
+    interchange, comp_resids = interchange_packmol_creation(
+        ffsettings=InterchangeFFSettings(
+            forcefields=["openff-2.0.0.offxml",]
+        ),
+        solvation_settings=PackmolSolvationSettings(),
+        smc_components=smc_components_benzene,
+        protein_component=None,
+        solvent_component=SolventComponent(
+            smiles='c1ccccc1', neutralize=False,
+            ion_concentration=0 * unit.molar,
+        ),
+        solvent_offmol=solvent_offmol,
+    )
+
+    mol = list(interchange.topology.molecules)[-1]
+    assert assert_almost_equal(np.array(mol.partial_charges), [0 for i in range(12)])
+
 """
 4. Named solvent
 5. Unamed solvent

src/pontibus/utils/system_creation.py

@@ -91,6 +91,31 @@ def _get_offmol_resname(offmol: OFFMolecule) -> Optional[str]:
     return resname
 
 
+def _check_library_charges(
+    force_field: ForceField,
+    offmol: OFFMolecule,
+) -> None:
+    """
+    Check that library charges exists for an input molecule.
+
+    force_field : openff.toolkit.ForceField
+      Force Field object with library charges.
+    offmol : openff.toolkit.Molecule
+      Molecule to check for matching library charges.
+
+    Raises
+    ------
+    ValueError
+      If no library charges are found for the molecule.
+    """
+     handler = force_field.get_parameter_handler('LibraryCharges')
+     matches = handler.find_matches(offmol.to_topology())
+
+     if len(matches) == 0:
+         errmsg = f"No library charges found for {offmol}"
+         raise ValueError(errmsg)
+
+
 def interchange_packmol_creation(
     ffsettings: InterchangeFFSettings,
     solvation_settings: PackmolSolvationSettings,
@@ -163,7 +188,7 @@ def interchange_packmol_creation(
             raise ValueError(errmsg)
 
     # 2. Get the force field object
-    # force_fields is a list so we unpack it
+    # forcefields is a list so we unpack it
     force_field = ForceField(*ffsettings.forcefields)
 
     # We also set nonbonded cutoffs whilst we are here
@@ -177,7 +202,7 @@ def interchange_packmol_creation(
     # Note: comp_resnames is dict[str, tuple[Component, list]] where the final
     # list is to append residues later on
     # TODO: we should be able to rely on offmol equality in the same way that
-    # intecharge does
+    # intechange does
     comp_resnames: dict[str, tuple[Component, list[Any]]] = {}
 
     # If we have solvent, we set its residue name
@@ -225,6 +250,9 @@ def interchange_packmol_creation(
         # otherwise we rely on library charges
         if solvation_settings.assign_solvent_charges:
             charged_mols.append(solvent_offmol)
+        else:
+            # Make sure we have library charges for the molecule
+            _check_library_charges(force_field, solvent_offmol)
 
         # Pick up the user selected box shape
         box_shape = {