Implemented cloning of objects by serialization

serialization/include/openmm/serialization/XmlSerializer.h

@@ -74,6 +74,18 @@ public:
     static T* deserialize(std::istream& stream) {
         return reinterpret_cast<T*>(deserializeStream(stream));
     }
+    /**
+     * Clone an object by first serializing it, then deserializing it again.  This method constructs the
+     * new object directly from the SerializationNodes without first converting them to XML.  This means
+     * it is faster and uses less memory than making separate calls to serialize() and deserialize().
+     */
+    template <class T>
+    static T* clone(const T& object) {
+        const SerializationProxy& proxy = SerializationProxy::getProxy(typeid(object));
+        SerializationNode node;
+        proxy.serialize(&object, node);
+        return reinterpret_cast<T*>(proxy.deserialize(node));
+    }
 private:
     class StreamReader;
     static void serialize(const SerializationNode& node, std::ostream& stream);

serialization/tests/TestSerializeSystem.cpp

@@ -40,32 +40,7 @@
 using namespace OpenMM;
 using namespace std;
 
-void testSerialization() {
-    // Create a System.
-
-    System system;
-    for (int i = 0; i < 5; i++)
-        system.addParticle(0.1*i+1);
-    for (int i = 0; i < 4; i++)
-        system.addParticle(0.0);
-    system.addConstraint(0, 1, 3.0);
-    system.addConstraint(1, 2, 2.5);
-    system.addConstraint(4, 1, 1.001);
-    system.setDefaultPeriodicBoxVectors(Vec3(5, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 1.5));
-    system.setVirtualSite(5, new TwoParticleAverageSite(0, 1, 0.3, 0.7));
-    system.setVirtualSite(6, new ThreeParticleAverageSite(2, 4, 3, 0.5, 0.2, 0.3));
-    system.setVirtualSite(7, new OutOfPlaneSite(0, 3, 1, 0.1, 0.2, 0.5));
-    system.addForce(new HarmonicBondForce());
-
-    // Serialize and then deserialize it.
-
-    stringstream buffer;
-    XmlSerializer::serialize<System>(&system, "System", buffer);
-    System* copy = XmlSerializer::deserialize<System>(buffer);
-
-    // Compare the two systems to see if they are identical.
-
-    System& system2 = *copy;
+void compareSystems(System& system, System& system2) {
     ASSERT_EQUAL(system.getNumParticles(), system2.getNumParticles());
     for (int i = 0; i < system.getNumParticles(); i++)
         ASSERT_EQUAL(system.getParticleMass(i), system2.getParticleMass(i));
@@ -112,6 +87,38 @@ void testSerialization() {
         ASSERT(typeid(system.getForce(i)) == typeid(system2.getForce(i)))
 }
 
+void testSerialization() {
+    // Create a System.
+
+    System system;
+    for (int i = 0; i < 5; i++)
+        system.addParticle(0.1*i+1);
+    for (int i = 0; i < 4; i++)
+        system.addParticle(0.0);
+    system.addConstraint(0, 1, 3.0);
+    system.addConstraint(1, 2, 2.5);
+    system.addConstraint(4, 1, 1.001);
+    system.setDefaultPeriodicBoxVectors(Vec3(5, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 1.5));
+    system.setVirtualSite(5, new TwoParticleAverageSite(0, 1, 0.3, 0.7));
+    system.setVirtualSite(6, new ThreeParticleAverageSite(2, 4, 3, 0.5, 0.2, 0.3));
+    system.setVirtualSite(7, new OutOfPlaneSite(0, 3, 1, 0.1, 0.2, 0.5));
+    system.addForce(new HarmonicBondForce());
+
+    // Serialize and then deserialize it, then make sure the systems are identical.
+
+    stringstream buffer;
+    XmlSerializer::serialize<System>(&system, "System", buffer);
+    System* copy = XmlSerializer::deserialize<System>(buffer);
+    compareSystems(system, *copy);
+    delete copy;
+
+    // Now do the same thing but by calling clone().
+
+    copy = XmlSerializer::clone(system);
+    compareSystems(system, *copy);
+    delete copy;
+}
+
 int main() {
     try {
         testSerialization();

wrappers/python/src/swig_doxygen/swig_lib/python/extend.i

@@ -272,10 +272,15 @@ Parameters:
     def __setstate__(self, serializationString):
         system = XmlSerializer.deserializeSystem(serializationString)
         self.this = system.this
+    def __deepcopy__(self, memo):
+        return self.__copy__()
     def getForces(self):
         """Get the list of Forces in this System"""
         return [self.getForce(i) for i in range(self.getNumForces())]
   %}
+  OpenMM::System* __copy__() {
+      return OpenMM::XmlSerializer::clone<OpenMM::System>(*self);
+  }
 }
 
 %extend OpenMM::XmlSerializer {
@@ -444,14 +449,12 @@ Parameters:
 
 %extend OpenMM::Force {
   %pythoncode %{
-    def __copy__(self):
-        copy = self.__class__.__new__(self.__class__)
-        copy.__init__(self)
-        return copy
-
     def __deepcopy__(self, memo):
         return self.__copy__()
   %}
+  OpenMM::Force* __copy__() {
+      return OpenMM::XmlSerializer::clone<OpenMM::Force>(*self);
+  }
 }
 
 %extend OpenMM::Integrator {
@@ -463,5 +466,11 @@ Parameters:
     def __setstate__(self, serializationString):
         system = XmlSerializer.deserialize(serializationString)
         self.this = system.this
+
+    def __deepcopy__(self, memo):
+        return self.__copy__()
   %}
+  OpenMM::Integrator* __copy__() {
+      return OpenMM::XmlSerializer::clone<OpenMM::Integrator>(*self);
+  }
 }