Merge pull request #1219 from rmcgibbo/fastcopy

Reinstate fast copy methods

wrappers/python/src/swig_doxygen/OpenMM.i

@@ -61,49 +61,3 @@ using namespace OpenMM;
   # namespace
   __all__ = [k for k in locals().keys() if not (k.endswith('_swigregister') or k.startswith('_'))]
 %}
-
-/*
-%extend OpenMM::XmlSerializer {
-    %template(XmlSerializer_serialize_AndersenThermostat) XmlSerializer::serialize<AndersenThermostat>;
-    %template(XmlSerializer_serialize_RBTorsionForce) XmlSerializer::serialize<RBTorsionForce>;
-    %template(XmlSerializer_serialize_CMAPTorsionForce) XmlSerializer::serialize<CMAPTorsionForce>;
-    %template(XmlSerializer_serialize_CMMotionRemover) XmlSerializer::serialize<CMMotionRemover>;
-    %template(XmlSerializer_serialize_CustomAngleForce) XmlSerializer::serialize<CustomAngleForce>;
-    %template(XmlSerializer_serialize_CustomBondForce) XmlSerializer::serialize<CustomBondForce>;
-    %template(XmlSerializer_serialize_CustomExternalForce) XmlSerializer::serialize<CustomExternalForce>;
-    %template(XmlSerializer_serialize_CustomGBForce) XmlSerializer::serialize<CustomGBForce>;
-    %template(XmlSerializer_serialize_CustomHbondForce) XmlSerializer::serialize<CustomHbondForce>;
-    %template(XmlSerializer_serialize_CustomNonbondedForce) XmlSerializer::serialize<CustomNonbondedForce>;
-    %template(XmlSerializer_serialize_CustomTorsionForce) XmlSerializer::serialize<CustomTorsionForce>;
-    %template(XmlSerializer_serialize_GBSAOBCForce) XmlSerializer::serialize<GBSAOBCForce>;
-    %template(XmlSerializer_serialize_GBVIForce) XmlSerializer::serialize<GBVIForce>;
-    %template(XmlSerializer_serialize_HarmonicAngleForce) XmlSerializer::serialize<HarmonicAngleForce>;
-    %template(XmlSerializer_serialize_HarmonicBondForce) XmlSerializer::serialize<HarmonicBondForce>;
-    %template(XmlSerializer_serialize_MonteCarloBarostat) XmlSerializer::serialize<MonteCarloBarostat>;
-    %template(XmlSerializer_serialize_MonteCarloAnisotropicBarostat) XmlSerializer::serialize<MonteCarloAnisotropicBarostat>;
-    %template(XmlSerializer_serialize_NonbondedForce) XmlSerializer::serialize<NonbondedForce>;
-    %template(XmlSerializer_serialize_RBTorsionForce) XmlSerializer::serialize<RBTorsionForce>;
-    %template(XmlSerializer_serialize_System) XmlSerializer::serialize<System>;
-
-    %template(XmlSerializer_deserialize_AndersenThermostat) XmlSerializer::deserialize<AndersenThermostat>;
-    %template(XmlSerializer_deserialize_RBTorsionForce) XmlSerializer::deserialize<RBTorsionForce>;
-    %template(XmlSerializer_deserialize_CMAPTorsionForce) XmlSerializer::deserialize<CMAPTorsionForce>;
-    %template(XmlSerializer_deserialize_CMMotionRemover) XmlSerializer::deserialize<CMMotionRemover>;
-    %template(XmlSerializer_deserialize_CustomAngleForce) XmlSerializer::deserialize<CustomAngleForce>;
-    %template(XmlSerializer_deserialize_CustomBondForce) XmlSerializer::deserialize<CustomBondForce>;
-    %template(XmlSerializer_deserialize_CustomExternalForce) XmlSerializer::deserialize<CustomExternalForce>;
-    %template(XmlSerializer_deserialize_CustomGBForce) XmlSerializer::deserialize<CustomGBForce>;
-    %template(XmlSerializer_deserialize_CustomHbondForce) XmlSerializer::deserialize<CustomHbondForce>;
-    %template(XmlSerializer_deserialize_CustomNonbondedForce) XmlSerializer::deserialize<CustomNonbondedForce>;
-    %template(XmlSerializer_deserialize_CustomTorsionForce) XmlSerializer::deserialize<CustomTorsionForce>;
-    %template(XmlSerializer_deserialize_GBSAOBCForce) XmlSerializer::deserialize<GBSAOBCForce>;
-    %template(XmlSerializer_deserialize_GBVIForce) XmlSerializer::deserialize<GBVIForce>;
-    %template(XmlSerializer_deserialize_HarmonicAngleForce) XmlSerializer::deserialize<HarmonicAngleForce>;
-    %template(XmlSerializer_deserialize_HarmonicBondForce) XmlSerializer::deserialize<HarmonicBondForce>;
-    %template(XmlSerializer_deserialize_MonteCarloBarostat) XmlSerializer::deserialize<MonteCarloBarostat>;
-    %template(XmlSerializer_deserialize_MonteCarloAnisotropicBarostat) XmlSerializer::deserialize<MonteCarloAnisotropicBarostat>;
-    %template(XmlSerializer_deserialize_NonbondedForce) XmlSerializer::deserialize<NonbondedForce>;
-    %template(XmlSerializer_deserialize_RBTorsionForce) XmlSerializer::deserialize<RBTorsionForce>;
-    %template(XmlSerializer_deserialize_System) XmlSerializer::deserialize<System>;
-};
-*/

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -243,22 +243,37 @@ class SwigInputBuilder:
                         forceSubclassList.append(shortClassName)
                     elif baseName == 'OpenMM::Integrator':
                         integratorSubclassList.append(shortClassName)
+
         self.fOut.write("%factory(OpenMM::Force& OpenMM::System::getForce")
         for name in sorted(forceSubclassList):
             self.fOut.write(",\n         OpenMM::%s" % name)
         self.fOut.write(");\n\n")
+
+        self.fOut.write("%factory(OpenMM::Force* OpenMM::Force::__copy__")
+        for name in sorted(forceSubclassList):
+            self.fOut.write(",\n         OpenMM::%s" % name)
+        self.fOut.write(");\n\n")
+
         self.fOut.write("%factory(OpenMM::Force* OpenMM_XmlSerializer__deserializeForce")
         for name in sorted(forceSubclassList):
             self.fOut.write(",\n         OpenMM::%s" % name)
         self.fOut.write(");\n\n")
+
+        self.fOut.write("%factory(OpenMM::Integrator* OpenMM::Integrator::__copy__")
+        for name in sorted(integratorSubclassList):
+            self.fOut.write(",\n         OpenMM::%s" % name)
+        self.fOut.write(");\n\n")
+
         self.fOut.write("%factory(OpenMM::Integrator* OpenMM_XmlSerializer__deserializeIntegrator")
         for name in sorted(integratorSubclassList):
             self.fOut.write(",\n         OpenMM::%s" % name)
         self.fOut.write(");\n\n")
+
         self.fOut.write("%factory(OpenMM::Integrator& OpenMM::Context::getIntegrator")
         for name in sorted(integratorSubclassList):
             self.fOut.write(",\n         OpenMM::%s" % name)
         self.fOut.write(");\n\n")
+
         self.fOut.write("%factory(OpenMM::VirtualSite& OpenMM::System::getVirtualSite, OpenMM::TwoParticleAverageSite, OpenMM::ThreeParticleAverageSite, OpenMM::OutOfPlaneSite);\n\n")
         self.fOut.write("\n")
 

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

@@ -467,14 +467,13 @@ Parameters:
         system = XmlSerializer.deserialize(serializationString)
         self.this = system.this
 
-    def __copy__(self):
-        copy = self.__class__.__new__(self.__class__)
-        copy.__init__(self)
-        return copy
-
     def __deepcopy__(self, memo):
         return self.__copy__()
   %}
+  %newobject __copy__;
+  OpenMM::Force* __copy__() {
+      return OpenMM::XmlSerializer::clone<OpenMM::Force>(*self);
+  }
 }
 
 %extend OpenMM::Integrator {
@@ -487,12 +486,11 @@ Parameters:
         system = XmlSerializer.deserialize(serializationString)
         self.this = system.this
 
-    def __copy__(self):
-        copy = self.__class__.__new__(self.__class__)
-        copy.__init__(self)
-        return copy
-
     def __deepcopy__(self, memo):
         return self.__copy__()
   %}
+  %newobject __copy__;
+  OpenMM::Integrator* __copy__() {
+      return OpenMM::XmlSerializer::clone<OpenMM::Integrator>(*self);
+  }
 }