Merge branch 'main' into maint/pydantic_3.13

Author: atravitz

news/empty_mapping_validation.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* The RelativeHybridTopologyProtocol will now raise a ValueError during validation if the atom mapping is empty preventing execution of the simulation.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/openfe/protocols/openmm_rfe/hybridtop_protocols.py

@@ -274,6 +274,7 @@ 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.
+          * If the atom mapping is empty.
         """
         # if a single mapping is provided, convert to list
         if isinstance(mapping, ComponentMapping):
@@ -294,6 +295,10 @@ def _validate_mapping(
                         f"in alchemical components of state{state}"
                     )
 
+            # make sure the mapping is not empty
+            if not m.componentA_to_componentB:
+                raise ValueError("No atoms are mapped between the two alchemical components.")
+
     @staticmethod
     def _validate_smcs(
         stateA: ChemicalSystem,

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

@@ -2541,3 +2541,27 @@ def fake_gather(*args, ligand_selection="resname UNK"):
         )
 
     assert captured["ligand_selection"] == "resname LIG"
+
+
+def test_empty_atom_mapping(tmp_path, benzene_vacuum_system, toluene_vacuum_system, vac_settings):
+    """Make sure an informative error is raised if the user supplies an empty atom mapping which is not supported."""
+
+    protocol = openmm_rfe.RelativeHybridTopologyProtocol(
+        settings=vac_settings,
+    )
+
+    blank_mapping = gufe.LigandAtomMapping(
+        componentA=benzene_vacuum_system["ligand"],
+        componentB=toluene_vacuum_system["ligand"],
+        componentA_to_componentB={},
+    )
+
+    with pytest.raises(
+        ValueError, match="No atoms are mapped between the two alchemical components."
+    ):
+        # create the DAG and run validation
+        _ = protocol.create(
+            stateA=benzene_vacuum_system,
+            stateB=toluene_vacuum_system,
+            mapping=blank_mapping,
+        )