remove warning for element changes

news/remove_element_change_warning.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* A warning is no longer raised by Hybrid Topology Protocols for mappings with element changes in core atoms (`Issue #1961 <https://github.com/OpenFreeEnergy/openfe/issues/1961>`_)
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

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

@@ -6,7 +6,6 @@
 from openff.units import unit as offunit
 
 import openfe
-from openfe import setup
 from openfe.protocols import openmm_rfe
 
 
@@ -356,28 +355,6 @@ 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
-    l1 = atom_mapping_basic_test_files["2-methylnaphthalene"]
-    l2 = atom_mapping_basic_test_files["2-naftanol"]
-
-    # We use the 'old' lomap defaults because the
-    # basic test files inputs we use aren't fully aligned
-    mapper = setup.LomapAtomMapper(
-        time=20, threed=True, max3d=1000.0, element_change=True, seed="", shift=True
-    )
-
-    mapping = next(mapper.suggest_mappings(l1, l2))
-
-    alchem_comps = {"stateA": [l1], "stateB": [l2]}
-
-    with pytest.warns(UserWarning, match="Element change"):
-        openmm_rfe.RelativeHybridTopologyProtocol._validate_mapping(
-            [mapping],
-            alchem_comps,
-        )
-
-
 def test_charge_difference_no_corr(benzene_to_benzoic_mapping):
     wmsg = (
         "A charge difference of 1 is observed between the end states. "