Added missing serialization support for CustomNonbondedForce interaction groups.

serialization/src/CustomNonbondedForceProxy.cpp

@@ -76,6 +76,20 @@ void CustomNonbondedForceProxy::serialize(const void* object, SerializationNode&
     SerializationNode& functions = node.createChildNode("Functions");
     for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
         functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
+
+    SerializationNode& interactionGroups = node.createChildNode("InteractionGroups");
+    for (int i = 0; i < force.getNumInteractionGroups(); i++) {
+      SerializationNode& interactionGroup = interactionGroups.createChildNode("InteractionGroup");
+      std::set<int> set1;
+      std::set<int> set2;
+      force.getInteractionGroupParameters(i, set1, set2);
+      SerializationNode& set1node = interactionGroup.createChildNode("Set1");
+      for (std::set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
+	set1node.createChildNode("Particle").setIntProperty("index", *it);
+      SerializationNode& set2node = interactionGroup.createChildNode("Set2");
+      for (std::set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
+	set2node.createChildNode("Particle").setIntProperty("index", *it);
+    }
 }
 
 void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) const {
@@ -129,6 +143,21 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }
+        const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
+        for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
+            const SerializationNode& interactionGroup = interactionGroups.getChildren()[i];
+	    // Get set 1.
+	    const SerializationNode& set1node = interactionGroup.getChildNode("Set1");
+	    std::set<int> set1;
+	    for (int j = 0; j < (int) set1node.getChildren().size(); j++)
+	      set1.insert(set1node.getChildren()[j].getIntProperty("index"));
+	    // Get set 2.
+	    const SerializationNode& set2node = interactionGroup.getChildNode("Set2");
+	    std::set<int> set2;
+	    for (int j = 0; j < (int) set2node.getChildren().size(); j++)
+	      set2.insert(set2node.getChildren()[j].getIntProperty("index"));
+	    force->addInteractionGroup(set1, set2);
+	}
         return force;
     }
     catch (...) {