Address review comments

src/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py

@@ -166,7 +166,7 @@ def _get_ion_parameters(
             continue
         charge, _, _ = nbf.getParticleParameters(atom.index)
         charge_val = charge.value_in_unit(omm_unit.elementary_charge)
-        if (abs(abs(charge_val) - 1.0) < 0.01 and np.sign(charge_val) == desired_sign):
+        if np.isclose(abs(charge_val), 1.0, atol=0.01) and np.sign(charge_val) == desired_sign:
             ion_counts[residue.name] += 1
             if residue.name not in ion_atom_indices:
                 ion_atom_indices[residue.name] = atom.index

src/openfe/protocols/openmm_rfe/hybridtop_protocols.py

@@ -437,22 +437,11 @@ class RelativeHybridTopologyProtocol(gufe.Protocol):
             )
             raise ValueError(errmsg)
 
-        # resolve ion names from SolventComponent or topology
-        if isinstance(solvent_component, SolventComponent):
-            positive_ion = solvent_component.positive_ion.strip("-+").upper()
-            negative_ion = solvent_component.negative_ion.strip("-+").upper()
-            ion = {-1: positive_ion, 1: negative_ion}[difference]
-            wmsg = (
-                f"A charge difference of {difference} is observed "
-                "between the end states. This will be addressed by "
-                f"transforming a water into a {ion} ion"
-            )
-        elif isinstance(solvent_component, SolvatedPDBComponent):
-            wmsg = (
-                f"A charge difference of {difference} is observed "
-                "between the end states. This will be addressed by "
-                "transforming a water into an ion."
-            )
+        wmsg = (
+            f"A charge difference of {difference} is observed "
+            "between the end states. This will be addressed by "
+            "transforming a water into an ion of opposite charge."
+        )
         logger.info(wmsg)
 
     @staticmethod

src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_validation.py

@@ -441,11 +441,10 @@ def test_get_charge_difference(mapping_name, result, request, caplog):
     mapping = request.getfixturevalue(mapping_name)
     caplog.set_level(logging.INFO)
 
-    ion = r"NA" if result == -1 else r"CL"
     msg = (
         f"A charge difference of {result} is observed "
         "between the end states. This will be addressed by "
-        f"transforming a water into a {ion} ion"
+        f"transforming a water into an ion of opposite charge"
     )
 
     openmm_rfe.RelativeHybridTopologyProtocol._validate_charge_difference(