remove warning for element changes

src/openfe/protocols/openmm_rfe/hybridtop_protocols.py

@@ -272,8 +272,6 @@ def _validate_mapping(
         ValueError
           * If there are more than one mapping or mapping is None
           * If the mapping components are not in the alchemical components.
-        UserWarning
-          * Mappings which involve element changes in core atoms
         """
         # if a single mapping is provided, convert to list
         if isinstance(mapping, ComponentMapping):
@@ -294,26 +292,6 @@ def _validate_mapping(
                         f"in alchemical components of state{state}"
                     )
 
-        # TODO: remove - this is now the default behaviour?
-        # Check for element changes in mappings
-        for m in mapping:
-            molA = m.componentA.to_rdkit()
-            molB = m.componentB.to_rdkit()
-            for i, j in m.componentA_to_componentB.items():
-                atomA = molA.GetAtomWithIdx(i)
-                atomB = molB.GetAtomWithIdx(j)
-                if atomA.GetAtomicNum() != atomB.GetAtomicNum():
-                    wmsg = (
-                        f"Element change in mapping between atoms "
-                        f"Ligand A: {i} (element {atomA.GetAtomicNum()}) and "
-                        f"Ligand B: {j} (element {atomB.GetAtomicNum()})\n"
-                        "No mass scaling is attempted in the hybrid topology, "
-                        "the average mass of the two atoms will be used in the "
-                        "simulation"
-                    )
-                    logger.warning(wmsg)
-                    warnings.warn(wmsg)
-
     @staticmethod
     def _validate_smcs(
         stateA: ChemicalSystem,

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

@@ -1,6 +1,7 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import logging
+import warnings
 
 import pytest
 from openff.units import unit as offunit
@@ -357,7 +358,8 @@ def test_too_many_prot_comps_error(
 
 
 def test_element_change_warning(atom_mapping_basic_test_files):
-    # check a mapping with element change gets rejected early
+    # in openfe <v1.11, this would raise a warning, but now is acceptable.
+    # TODO: can remove this test in v1.13 if we want
     l1 = atom_mapping_basic_test_files["2-methylnaphthalene"]
     l2 = atom_mapping_basic_test_files["2-naftanol"]
 
@@ -371,11 +373,11 @@ def test_element_change_warning(atom_mapping_basic_test_files):
 
     alchem_comps = {"stateA": [l1], "stateB": [l2]}
 
-    with pytest.warns(UserWarning, match="Element change"):
-        openmm_rfe.RelativeHybridTopologyProtocol._validate_mapping(
-            [mapping],
-            alchem_comps,
-        )
+    with warnings.catch_warnings(record=True) as record:
+        warnings.simplefilter("always")
+        openmm_rfe.RelativeHybridTopologyProtocol._validate_mapping([mapping], alchem_comps)
+        # there may be other warnings bubbling up, but we make sure mass scaling warning isn't here.
+        assert not any(["mass scaling" in str(r.message) for r in record])
 
 
 def test_charge_difference_no_corr(benzene_to_benzoic_mapping):