Fix ABFE restraint written twice when there is no position restraint (#…

…50)

python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py

@@ -400,7 +400,6 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
                 match_waters=False,
                 property_map=self._property_map,
             )
-            self._apply_ABFE_restraint()
 
     def _apply_ABFE_restraint(self):
         # Write the restraint to the topology file

tests/Sandpit/Exscientia/Process/test_gromacs.py

@@ -226,7 +226,27 @@ def test_regular_protocol(self, setup, tmp_path_factory):
         # Run the process and check that it finishes without error.
         run_process(system, protocol, restraint=restraint, work_dir=str(tmp_path))
         with open(tmp_path / "test.top", "r") as f:
-            assert "intermolecular_interactions" in f.read()
+            text = f.read()
+            assert text.count("intermolecular_interactions") == 1
+
+    def test_position_restraint_protocol(self, setup, tmp_path_factory):
+        """Test if the restraint has been written in a way that could be processed
+        correctly.
+        """
+        tmp_path = tmp_path_factory.mktemp("out")
+        system, restraint = setup
+        # Create a short production protocol.
+        protocol = BSS.Protocol.FreeEnergy(
+            runtime=BSS.Types.Time(0.0001, "nanoseconds"),
+            perturbation_type="full",
+            restraint="heavy",
+        )
+
+        # Run the process and check that it finishes without error.
+        run_process(system, protocol, restraint=restraint, work_dir=str(tmp_path))
+        with open(tmp_path / "test.top", "r") as f:
+            text = f.read()
+            assert text.count("intermolecular_interactions") == 1
 
     def test_restraint_lambda(self, setup, tmp_path_factory):
         """Test if the restraint has been written correctly when restraint lambda is evoked."""