Rotate perturbable and non-perturbable molecules independently.

[closes #354]

Author: lohedges

python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py

@@ -1238,8 +1238,9 @@ def rotateBoxVectors(
 
         from sire.system import System
 
-        # Create a cursor.
-        cursor = System(self._sire_object).cursor()
+        # Create a cursor for the non-perturbable molecules.
+        system = System(self._sire_object)
+        cursor = system["not property is_perturbable"].cursor()
 
         # Rotate all vector properties.
 
@@ -1267,8 +1268,15 @@ def rotateBoxVectors(
         except:
             pass
 
+        # Update the molecules in the system.
+        system.update(cursor.commit())
+        self._sire_object = system._system
+
         # Now deal with any perturbable molecules.
         if self.nPerturbableMolecules() > 0:
+            # Create a cursor for the perturbable molecules.
+            cursor = system["property is_perturbable"].cursor()
+
             # Coordinates.
             try:
                 prop_name = property_map.get("coordinates", "coordinates") + "0"
@@ -1307,8 +1315,9 @@ def rotateBoxVectors(
             except:
                 pass
 
-        # Commit the changes.
-        self._sire_object = cursor.commit()._system
+            # Update the perturbable molecules in the system.
+            system.update(cursor.commit())
+            self._sire_object = system._system
 
     def reduceBoxVectors(self, bias=0, property_map={}):
         """

python/BioSimSpace/_SireWrappers/_system.py

@@ -1186,8 +1186,9 @@ def rotateBoxVectors(
 
         from sire.system import System
 
-        # Create a cursor.
-        cursor = System(self._sire_object).cursor()
+        # Create a cursor for the non-perturbable molecules.
+        system = System(self._sire_object)
+        cursor = system["not property is_perturbable"].cursor()
 
         # Rotate all vector properties.
 
@@ -1215,8 +1216,15 @@ def rotateBoxVectors(
         except:
             pass
 
+        # Update the molecules in the system.
+        system.update(cursor.commit())
+        self._sire_object = system._system
+
         # Now deal with any perturbable molecules.
         if self.nPerturbableMolecules() > 0:
+            # Create a cursor for the perturbable molecules.
+            cursor = system["property is_perturbable"].cursor()
+
             # Coordinates.
             try:
                 prop_name = property_map.get("coordinates", "coordinates") + "0"
@@ -1255,8 +1263,9 @@ def rotateBoxVectors(
             except:
                 pass
 
-        # Commit the changes.
-        self._sire_object = cursor.commit()._system
+            # Update the perturbable molecules in the system.
+            system.update(cursor.commit())
+            self._sire_object = system._system
 
     def reduceBoxVectors(self, bias=0, property_map={}):
         """