Fixed lots of compilation errors on Windows

plugins/amoeba/serialization/include/openmm/serialization/AmoebaGeneralizedKirkwoodForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaGeneralizedKirkwoodForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaGeneralizedKirkwoodForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaGeneralizedKirkwoodForceProxy : public SerializationProxy {
 public:
     AmoebaGeneralizedKirkwoodForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/AmoebaInPlaneAngleForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaInPlaneAngleForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaInPlaneAngleForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaInPlaneAngleForceProxy : public SerializationProxy {
 public:
     AmoebaInPlaneAngleForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/AmoebaMultipoleForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaMultipoleForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaMultipoleForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaMultipoleForceProxy : public SerializationProxy {
 public:
     AmoebaMultipoleForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/AmoebaOutOfPlaneBendForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaOutOfPlaneBendForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaOutOfPlaneBendForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaOutOfPlaneBendForceProxy : public SerializationProxy {
 public:
     AmoebaOutOfPlaneBendForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/AmoebaPiTorsionForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaPiTorsionForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaPiTorsionForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaPiTorsionForceProxy : public SerializationProxy {
 public:
     AmoebaPiTorsionForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/AmoebaStretchBendForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaStretchBendForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaStretchBendForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaStretchBendForceProxy : public SerializationProxy {
 public:
     AmoebaStretchBendForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/AmoebaTorsionTorsionForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaTorsionTorsionForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaTorsionTorsionForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaTorsionTorsionForceProxy : public SerializationProxy {
 public:
     AmoebaTorsionTorsionForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/AmoebaVdwForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaVdwForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaVdwForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaVdwForceProxy : public SerializationProxy {
 public:
     AmoebaVdwForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/AmoebaWcaDispersionForceProxy.h

@@ -32,7 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
+#include "openmm/internal/windowsExportAmoeba.h"
 #include "openmm/serialization/SerializationProxy.h"
 
 namespace OpenMM {
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing AmoebaWcaDispersionForce objects.
  */
 
-class OPENMM_EXPORT_AMOEBA_SERIALIZATION AmoebaWcaDispersionForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_AMOEBA AmoebaWcaDispersionForceProxy : public SerializationProxy {
 public:
     AmoebaWcaDispersionForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/amoeba/serialization/include/openmm/serialization/internal/windowsExportAmoebaSerialization.h

-#ifndef OPENMM_WINDOWSEXPORTAMOEBASERIALIZATION_H_
-#define OPENMM_WINDOWSEXPORTAMOEBASERIALIZATION_H_
-
-/*
- * Shared libraries are messy in Visual Studio. We have to distinguish three
- * cases:
- *   (1) this header is being used to build the OpenMM shared library
- *       (dllexport)
- *   (2) this header is being used by a *client* of the OpenMM shared
- *       library (dllimport)
- *   (3) we are building the OpenMM static library, or the client is
- *       being compiled with the expectation of linking with the
- *       OpenMM static library (nothing special needed)
- * In the CMake script for building this library, we define one of the symbols
- *     OPENMM_AMOEBA_SERIALIZATION_BUILDING_{SHARED|STATIC}_LIBRARY
- * Client code normally has no special symbol defined, in which case we'll
- * assume it wants to use the shared library. However, if the client defines
- * the symbol OPENMM_USE_STATIC_LIBRARIES we'll suppress the dllimport so
- * that the client code can be linked with static libraries. Note that
- * the client symbol is not library dependent, while the library symbols
- * affect only the OpenMM library, meaning that other libraries can
- * be clients of this one. However, we are assuming all-static or all-shared.
- */
-
-#ifdef _MSC_VER
-    // We don't want to hear about how sprintf is "unsafe".
-    #pragma warning(disable:4996)
-    // Keep MS VC++ quiet about lack of dll export of private members.
-    #pragma warning(disable:4251)
-    #if defined(OPENMM_AMOEBA_SERIALIZATION_BUILDING_SHARED_LIBRARY)
-        #define OPENMM_EXPORT_AMOEBA_SERIALIZATION __declspec(dllexport)
-    #elif defined(OPENMM_AMOEBA_SERIALIZATION_BUILDING_STATIC_LIBRARY) || defined(OPENMM_AMOEBA_SERIALIZATION_USE_STATIC_LIBRARIES)
-        #define OPENMM_EXPORT_AMOEBA_SERIALIZATION
-    #else
-        #define OPENMM_EXPORT_AMOEBA_SERIALIZATION __declspec(dllimport)   // i.e., a client of a shared library
-    #endif
-#else
-    #define OPENMM_EXPORT_AMOEBA_SERIALIZATION // Linux, Mac
-#endif
-
-#endif // OPENMM_WINDOWSEXPORTAMOEBASERIALIZATION_H_

plugins/amoeba/serialization/src/AmoebaSerializationProxyRegistration.cpp

@@ -65,11 +65,10 @@
 #include "openmm/serialization/AmoebaTorsionTorsionForceProxy.h"
 #include "openmm/serialization/AmoebaVdwForceProxy.h"
 #include "openmm/serialization/AmoebaWcaDispersionForceProxy.h"
-#include "openmm/serialization/internal/windowsExportAmoebaSerialization.h"
 
 #if defined(WIN32)
     #include <windows.h>
-    extern "C" OPENMM_EXPORT_AMOEBA_SERIALIZATION void registerAmoebaSerializationProxies();
+    extern "C" OPENMM_EXPORT_AMOEBA void registerAmoebaSerializationProxies();
     BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
         if (ul_reason_for_call == DLL_PROCESS_ATTACH)
             registerAmoebaSerializationProxies();
@@ -81,7 +80,7 @@
 
 using namespace OpenMM;
 
-extern "C" OPENMM_EXPORT_AMOEBA_SERIALIZATION void registerAmoebaSerializationProxies() {
+extern "C" OPENMM_EXPORT_AMOEBA void registerAmoebaSerializationProxies() {
     SerializationProxy::registerProxy(typeid(AmoebaGeneralizedKirkwoodForce),         new AmoebaGeneralizedKirkwoodForceProxy());
     SerializationProxy::registerProxy(typeid(AmoebaBondForce),                new AmoebaBondForceProxy());
     SerializationProxy::registerProxy(typeid(AmoebaAngleForce),               new AmoebaAngleForceProxy());

plugins/amoeba/wrappers/generateAmoebaWrappers.py

+from __future__ import print_function
 import sys, os
 import time
 import getopt
@@ -305,16 +306,16 @@ class CHeaderGenerator(WrapperGenerator):
         return type
 
     def writeOutput(self):
-        print >>self.out, """
+        print("""
 #ifndef AMOEBA_OPENMM_CWRAPPER_H_
 #define AMOEBA_OPENMM_CWRAPPER_H_
 
 #ifndef OPENMM_EXPORT_AMOEBA
 #define OPENMM_EXPORT_AMOEBA
-#endif"""
+#endif""", file=self.out)
         self.writeGlobalConstants()
         self.writeTypeDeclarations()
-        print >>self.out, """
+        print("""
 typedef struct OpenMM_2D_IntArray_struct OpenMM_2D_IntArray;
 typedef struct OpenMM_3D_DoubleArray_struct OpenMM_3D_DoubleArray;
 
@@ -325,16 +326,16 @@ extern "C" {
 /* OpenMM_3D_DoubleArray */
 OPENMM_EXPORT_AMOEBA OpenMM_3D_DoubleArray* OpenMM_3D_DoubleArray_create(int size1, int size2, int size3);
 OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array, int index1, int index2, OpenMM_DoubleArray* values);
-OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy( OpenMM_3D_DoubleArray* array);"""
+OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy( OpenMM_3D_DoubleArray* array);""", file=self.out)
 
         self.writeClasses()
 
-        print >>self.out, """
+        print("""
 #if defined(__cplusplus)
 }
 #endif
 
-#endif /*AMOEBA_OPENMM_CWRAPPER_H_*/"""
+#endif /*AMOEBA_OPENMM_CWRAPPER_H_*/""", file=self.out)
 
 
 class CSourceGenerator(WrapperGenerator):
@@ -556,7 +557,7 @@ class CSourceGenerator(WrapperGenerator):
         return 'reinterpret_cast<%s>(%s)' % (type, value)
 
     def writeOutput(self):
-        print >>self.out, """
+        print("""
 #include "OpenMM.h"
 #include "OpenMMAmoeba.h"
 #include "../../../wrappers/OpenMMCWrapper.h"
@@ -634,10 +635,10 @@ OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_set(OpenMM_3D_DoubleArray* array
 
 OPENMM_EXPORT_AMOEBA void OpenMM_3D_DoubleArray_destroy( OpenMM_3D_DoubleArray* array) {
     delete reinterpret_cast<std::vector<std::vector<std::vector<double> > >*>(array);
-}"""
+}""", file=self.out)
 
         self.writeClasses()
-        print >>self.out, "}\n"
+        print("}\n", file=self.out)
 
 class FortranHeaderGenerator(WrapperGenerator):
     """This class generates the header file for the Fortran API wrappers."""
@@ -845,33 +846,33 @@ class FortranHeaderGenerator(WrapperGenerator):
         return type
 
     def writeOutput(self):
-        print >>self.out, """
+        print("""
 MODULE OpenMM_Types
     implicit none
-"""
+""", file=self.out)
         self.writeGlobalConstants()
         self.writeTypeDeclarations()
-        print >>self.out, """
+        print("""
     ! Enumerations
 
     integer*4, parameter :: OpenMM_False = 0
-    integer*4, parameter :: OpenMM_True = 1"""
+    integer*4, parameter :: OpenMM_True = 1""", file=self.out)
 
         for classNode in self._orderedClassNodes:
             self.writeEnumerations(classNode)
-        print >>self.out, """
+        print("""
 END MODULE OpenMM_Types
 
 MODULE OpenMM
     use OpenMM_Types; implicit none
     interface
-"""
+""", file=self.out)
         
         self.writeClasses()
         
-        print >>self.out, """
+        print("""
     end interface
-END MODULE OpenMM"""
+END MODULE OpenMM""", file=self.out)
 
 
 class FortranSourceGenerator(WrapperGenerator):
@@ -974,7 +975,7 @@ class FortranSourceGenerator(WrapperGenerator):
             if methodName in (shortClassName, destructorName):
                 continue
             if '~' in methodName:
-                print '***', methodName, destructorName
+                print('***', methodName, destructorName)
             if self.shouldHideMethod(methodNode):
                 continue
             isConstMethod = (methodNode.attrib['const'] == 'yes')
@@ -1143,7 +1144,7 @@ class FortranSourceGenerator(WrapperGenerator):
         return False
 
     def writeOutput(self):
-        print >>self.out, """
+        print("""
 #include "OpenMM.h"
 #include "OpenMMAmoeba.h"
 #include "../../../wrappers/OpenMMCWrapper.h"
@@ -1171,10 +1172,10 @@ static string makeString(const char* fsrc, int length) {
 }
 
 extern "C" {
-"""
+""", file=self.out)
 
         self.writeClasses()
-        print >>self.out, "}"
+        print("}", file=self.out)
 
 inputDirname = sys.argv[1]
 builder = CHeaderGenerator(inputDirname, open(os.path.join(sys.argv[2], 'AmoebaOpenMMCWrapper.h'), 'w'))

plugins/drude/serialization/include/openmm/serialization/DrudeForceProxy.h

@@ -32,8 +32,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportDrudeSerialization.h"
 #include "openmm/serialization/SerializationProxy.h"
+#include "openmm/internal/windowsExportDrude.h"
 
 namespace OpenMM {
 
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing DrudeForce objects.
  */
 
-class OPENMM_EXPORT_DRUDE_SERIALIZATION DrudeForceProxy : public SerializationProxy {
+class OPENMM_EXPORT_DRUDE DrudeForceProxy : public SerializationProxy {
 public:
     DrudeForceProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/drude/serialization/include/openmm/serialization/DrudeLangevinIntegratorProxy.h

@@ -32,8 +32,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/internal/windowsExportDrudeSerialization.h"
 #include "openmm/serialization/SerializationProxy.h"
+#include "openmm/internal/windowsExportDrude.h"
 
 namespace OpenMM {
 
@@ -41,7 +41,7 @@ namespace OpenMM {
  * This is a proxy for serializing DrudeLangevinIntegrator objects.
  */
 
-class OPENMM_EXPORT_DRUDE_SERIALIZATION DrudeLangevinIntegratorProxy : public SerializationProxy {
+class OPENMM_EXPORT_DRUDE DrudeLangevinIntegratorProxy : public SerializationProxy {
 public:
     DrudeLangevinIntegratorProxy();
     void serialize(const void* object, SerializationNode& node) const;

plugins/drude/serialization/include/openmm/serialization/internal/windowsExportDrudeSerialization.h

-#ifndef OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_H_
-#define OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_H_
-
-/*
- * Shared libraries are messy in Visual Studio. We have to distinguish three
- * cases:
- *   (1) this header is being used to build the OpenMM shared library
- *       (dllexport)
- *   (2) this header is being used by a *client* of the OpenMM shared
- *       library (dllimport)
- *   (3) we are building the OpenMM static library, or the client is
- *       being compiled with the expectation of linking with the
- *       OpenMM static library (nothing special needed)
- * In the CMake script for building this library, we define one of the symbols
- *     OPENMM_DRUDE_SERIALIZATION_BUILDING_{SHARED|STATIC}_LIBRARY
- * Client code normally has no special symbol defined, in which case we'll
- * assume it wants to use the shared library. However, if the client defines
- * the symbol OPENMM_USE_STATIC_LIBRARIES we'll suppress the dllimport so
- * that the client code can be linked with static libraries. Note that
- * the client symbol is not library dependent, while the library symbols
- * affect only the OpenMM library, meaning that other libraries can
- * be clients of this one. However, we are assuming all-static or all-shared.
- */
-
-#ifdef _MSC_VER
-    // We don't want to hear about how sprintf is "unsafe".
-    #pragma warning(disable:4996)
-    // Keep MS VC++ quiet about lack of dll export of private members.
-    #pragma warning(disable:4251)
-    #if defined(OPENMM_DRUDE_SERIALIZATION_BUILDING_SHARED_LIBRARY)
-        #define OPENMM_EXPORT_DRUDE_SERIALIZATION __declspec(dllexport)
-    #elif defined(OPENMM_DRUDE_SERIALIZATION_BUILDING_STATIC_LIBRARY) || defined(OPENMM_DRUDE_SERIALIZATION_USE_STATIC_LIBRARIES)
-        #define OPENMM_EXPORT_DRUDE_SERIALIZATION
-    #else
-        #define OPENMM_EXPORT_DRUDE_SERIALIZATION __declspec(dllimport)   // i.e., a client of a shared library
-    #endif
-#else
-    #define OPENMM_EXPORT_DRUDE_SERIALIZATION // Linux, Mac
-#endif
-
-#endif // OPENMM_WINDOWSEXPORTDRUDESERIALIZATION_H_

plugins/drude/serialization/src/DrudeSerializationProxyRegistration.cpp

@@ -47,11 +47,10 @@
 
 #include "openmm/serialization/DrudeForceProxy.h"
 #include "openmm/serialization/DrudeLangevinIntegratorProxy.h"
-#include "openmm/serialization/internal/windowsExportDrudeSerialization.h"
 
 #if defined(WIN32)
     #include <windows.h>
-    extern "C" OPENMM_EXPORT_DRUDE_SERIALIZATION void registerDrudeSerializationProxies();
+    extern "C" OPENMM_EXPORT_DRUDE void registerDrudeSerializationProxies();
     BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
         if (ul_reason_for_call == DLL_PROCESS_ATTACH)
             registerDrudeSerializationProxies();
@@ -63,7 +62,7 @@
 
 using namespace OpenMM;
 
-extern "C" OPENMM_EXPORT_DRUDE_SERIALIZATION void registerDrudeSerializationProxies() {
+extern "C" OPENMM_EXPORT_DRUDE void registerDrudeSerializationProxies() {
     SerializationProxy::registerProxy(typeid(DrudeForce), new DrudeForceProxy());
     SerializationProxy::registerProxy(typeid(DrudeLangevinIntegrator), new DrudeLangevinIntegratorProxy());
 }

wrappers/generateWrappers.py

+from __future__ import print_function
 import sys, os
 import time
 import getopt
@@ -303,17 +304,17 @@ class CHeaderGenerator(WrapperGenerator):
         return type
 
     def writeOutput(self):
-        print >>self.out, """
+        print("""
 #ifndef OPENMM_CWRAPPER_H_
 #define OPENMM_CWRAPPER_H_
 
 #ifndef OPENMM_EXPORT
 #define OPENMM_EXPORT
 #endif
-"""
+""", file=self.out)
         self.writeGlobalConstants()
         self.writeTypeDeclarations()
-        print >>self.out, """
+        print("""
 typedef struct OpenMM_Vec3Array_struct OpenMM_Vec3Array;
 typedef struct OpenMM_StringArray_struct OpenMM_StringArray;
 typedef struct OpenMM_BondArray_struct OpenMM_BondArray;
@@ -366,12 +367,12 @@ extern OPENMM_EXPORT double OpenMM_ParameterArray_get(const OpenMM_ParameterArra
 
 /* OpenMM_PropertyArray */
 extern OPENMM_EXPORT int OpenMM_PropertyArray_getSize(const OpenMM_PropertyArray* array);
-extern OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyArray* array, const char* name);"""
+extern OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyArray* array, const char* name);""", file=self.out)
 
         for type in ('double', 'int'):
             name = 'OpenMM_%sArray' % type.capitalize()
             values = {'type':type, 'name':name}
-            print >>self.out, """
+            print("""
 /* %(name)s */
 extern OPENMM_EXPORT %(name)s* %(name)s_create(int size);
 extern OPENMM_EXPORT void %(name)s_destroy(%(name)s* array);
@@ -379,19 +380,19 @@ extern OPENMM_EXPORT int %(name)s_getSize(const %(name)s* array);
 extern OPENMM_EXPORT void %(name)s_resize(%(name)s* array, int size);
 extern OPENMM_EXPORT void %(name)s_append(%(name)s* array, %(type)s value);
 extern OPENMM_EXPORT void %(name)s_set(%(name)s* array, int index, %(type)s value);
-extern OPENMM_EXPORT %(type)s %(name)s_get(const %(name)s* array, int index);""" % values
+extern OPENMM_EXPORT %(type)s %(name)s_get(const %(name)s* array, int index);""" % values, file=self.out)
 
         for type in ('int',):
             name = 'OpenMM_%sSet' % type.capitalize()
             values = {'type':type, 'name':name}
-            print >>self.out, """
+            print("""
 /* %(name)s */
 extern OPENMM_EXPORT %(name)s* %(name)s_create();
 extern OPENMM_EXPORT void %(name)s_destroy(%(name)s* set);
 extern OPENMM_EXPORT int %(name)s_getSize(const %(name)s* set);
-extern OPENMM_EXPORT void %(name)s_insert(%(name)s* set, %(type)s value);""" % values
+extern OPENMM_EXPORT void %(name)s_insert(%(name)s* set, %(type)s value);""" % values, file=self.out)
 
-        print >>self.out, """
+        print("""
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
 extern OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types, int enforcePeriodicBox);
@@ -401,16 +402,16 @@ extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeState(const OpenMM_Stat
 extern OPENMM_EXPORT char* OpenMM_XmlSerializer_serializeIntegrator(const OpenMM_Integrator* integrator);
 extern OPENMM_EXPORT OpenMM_System* OpenMM_XmlSerializer_deserializeSystem(const char* xml);
 extern OPENMM_EXPORT OpenMM_State* OpenMM_XmlSerializer_deserializeState(const char* xml);
-extern OPENMM_EXPORT OpenMM_Integrator* OpenMM_XmlSerializer_deserializeIntegrator(const char* xml);"""
+extern OPENMM_EXPORT OpenMM_Integrator* OpenMM_XmlSerializer_deserializeIntegrator(const char* xml);""", file=self.out)
 
         self.writeClasses()
 
-        print >>self.out, """
+        print("""
 #if defined(__cplusplus)
 }
 #endif
 
-#endif /*OPENMM_CWRAPPER_H_*/"""
+#endif /*OPENMM_CWRAPPER_H_*/""", file=self.out)
 
 
 class CSourceGenerator(WrapperGenerator):
@@ -630,7 +631,7 @@ class CSourceGenerator(WrapperGenerator):
         return 'reinterpret_cast<%s>(%s)' % (type, value)
 
     def writeOutput(self):
-        print >>self.out, """
+        print("""
 #include "OpenMM.h"
 #include "OpenMMCWrapper.h"
 #include <cstdlib>
@@ -742,12 +743,12 @@ OPENMM_EXPORT const char* OpenMM_PropertyArray_get(const OpenMM_PropertyArray* a
     if (iter == params->end())
         throw OpenMMException("OpenMM_PropertyArray_get: No such property");
     return iter->second.c_str();
-}"""
+}""", file=self.out)
 
         for type in ('double', 'int'):
             name = 'OpenMM_%sArray' % type.capitalize()
             values = {'type':type, 'name':name}
-            print >>self.out, """
+            print("""
 /* %(name)s */
 OPENMM_EXPORT %(name)s* %(name)s_create(int size) {
     return reinterpret_cast<%(name)s*>(new vector<%(type)s>(size));
@@ -769,12 +770,12 @@ OPENMM_EXPORT void %(name)s_set(%(name)s* array, int index, %(type)s value) {
 }
 OPENMM_EXPORT %(type)s %(name)s_get(const %(name)s* array, int index) {
     return (*reinterpret_cast<const vector<%(type)s>*>(array))[index];
-}""" % values
+}""" % values, file=self.out)
 
         for type in ('int',):
             name = 'OpenMM_%sSet' % type.capitalize()
             values = {'type':type, 'name':name}
-            print >>self.out, """
+            print("""
 /* %(name)s */
 OPENMM_EXPORT %(name)s* %(name)s_create() {
     return reinterpret_cast<%(name)s*>(new set<%(type)s>());
@@ -787,9 +788,9 @@ OPENMM_EXPORT int %(name)s_getSize(const %(name)s* s) {
 }
 OPENMM_EXPORT void %(name)s_insert(%(name)s* s, %(type)s value) {
     reinterpret_cast<set<%(type)s>*>(s)->insert(value);
-}""" % values
+}""" % values, file=self.out)
 
-        print >>self.out, """
+        print("""
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
 OPENMM_EXPORT OpenMM_State* OpenMM_Context_getState(const OpenMM_Context* target, int types, int enforcePeriodicBox) {
@@ -836,9 +837,9 @@ OPENMM_EXPORT OpenMM_Integrator* OpenMM_XmlSerializer_deserializeIntegrator(cons
     string input(xml);
     stringstream stream(input);
     return reinterpret_cast<OpenMM_Integrator*>(OpenMM::XmlSerializer::deserialize<OpenMM::Integrator>(stream));
-}"""
+}""", file=self.out)
         self.writeClasses()
-        print >>self.out, "}\n"
+        print("}\n", file=self.out)
 
 class FortranHeaderGenerator(WrapperGenerator):
     """This class generates the header file for the Fortran API wrappers."""
@@ -1049,13 +1050,13 @@ class FortranHeaderGenerator(WrapperGenerator):
         return type
 
     def writeOutput(self):
-        print >>self.out, """
+        print("""
 MODULE OpenMM_Types
     implicit none
-"""
+""", file=self.out)
         self.writeGlobalConstants()
         self.writeTypeDeclarations()
-        print >>self.out, """
+        print("""
     type OpenMM_Vec3Array
         integer*8 :: handle = 0
     end type
@@ -1091,10 +1092,10 @@ MODULE OpenMM_Types
     ! Enumerations
 
     integer*4, parameter :: OpenMM_False = 0
-    integer*4, parameter :: OpenMM_True = 1"""
+    integer*4, parameter :: OpenMM_True = 1""", file=self.out)
         for classNode in self._orderedClassNodes:
             self.writeEnumerations(classNode)
-        print >>self.out, """
+        print("""
 END MODULE OpenMM_Types
 
 MODULE OpenMM
@@ -1250,12 +1251,12 @@ MODULE OpenMM
             type (OpenMM_PropertyArray) target
             character(*) name
             character(*) result
-        end subroutine"""
+        end subroutine""", file=self.out)
 
         arrayTypes = {'OpenMM_DoubleArray':'real*8', 'OpenMM_IntArray':'integer*4'}
         for name in arrayTypes:
             values = {'type':arrayTypes[name], 'name':name}
-            print >>self.out, """
+            print("""
         ! %(name)s
         subroutine %(name)s_create(result, size)
             use OpenMM_Types; implicit none
@@ -1292,9 +1293,9 @@ MODULE OpenMM
             type (%(name)s) target
             integer*4 index
             %(type)s result
-        end subroutine""" % values
+        end subroutine""" % values, file=self.out)
         
-        print >>self.out, """
+        print("""
         ! These methods need to be handled specially, since their C++ APIs cannot be directly translated to Fortran.
         ! Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself.
         subroutine OpenMM_Context_getState(target, types, enforcePeriodicBox, result)
@@ -1341,11 +1342,11 @@ MODULE OpenMM
             use OpenMM_Types; implicit none
             character(*) xml
             type(OpenMM_Integrator) result
-        end subroutine"""
+        end subroutine""", file=self.out)
         
         self.writeClasses()
         
-        print >>self.out, """
+        print("""
     end interface
 
 contains
@@ -1404,7 +1405,7 @@ contains
         end do
     end subroutine
 
-END MODULE OpenMM"""
+END MODULE OpenMM""", file=self.out)
 
 
 class FortranSourceGenerator(WrapperGenerator):
@@ -1505,7 +1506,7 @@ class FortranSourceGenerator(WrapperGenerator):
             if methodName in (shortClassName, destructorName):
                 continue
             if '~' in methodName:
-                print '***', methodName, destructorName
+                print('***', methodName, destructorName)
             if self.shouldHideMethod(methodNode):
                 continue
             isConstMethod = (methodNode.attrib['const'] == 'yes')
@@ -1674,7 +1675,7 @@ class FortranSourceGenerator(WrapperGenerator):
         return False
 
     def writeOutput(self):
-        print >>self.out, """
+        print("""
 #include "OpenMM.h"
 #include "OpenMMCWrapper.h"
 #include <cstring>
@@ -1883,12 +1884,12 @@ OPENMM_EXPORT const char* openmm_propertyarray_get_(const OpenMM_PropertyArray*
 }
 OPENMM_EXPORT const char* OPENMM_PROPERTYARRAY_GET(const OpenMM_PropertyArray* const& array, const char* name, int length) {
     return OpenMM_PropertyArray_get(array, makeString(name, length).c_str());
-}"""
+}""", file=self.out)
 
         for type in ('double', 'int'):
             name = 'OpenMM_%sArray' % type.capitalize()
             values = {'type':type, 'name':name, 'name_lower':name.lower(), 'name_upper':name.upper()}
-            print >>self.out, """
+            print("""
 /* %(name)s */
 OPENMM_EXPORT void %(name_lower)s_create_(%(name)s*& result, const int& size) {
     result = %(name)s_create(size);
@@ -1933,12 +1934,12 @@ OPENMM_EXPORT void %(name_lower)s_get_(const %(name)s* const& array, const int&
 }
 OPENMM_EXPORT void %(name_upper)s_GET(const %(name)s* const& array, const int& index, %(type)s& result) {
     result = %(name)s_get(array, index-1);
-}""" % values
+}""" % values, file=self.out)
 
         for type in ('int', ):
             name = 'OpenMM_%sSet' % type.capitalize()
             values = {'type':type, 'name':name, 'name_lower':name.lower(), 'name_upper':name.upper()}
-            print >>self.out, """
+            print("""
 /* %(name)s */
 OPENMM_EXPORT void %(name_lower)s_create_(%(name)s*& result) {
     result = %(name)s_create();
@@ -1965,9 +1966,9 @@ OPENMM_EXPORT void %(name_lower)s_insert_(%(name)s* const& array, const %(type)s
 }
 OPENMM_EXPORT void %(name_upper)s_INSERT(%(name)s* const& array, const %(type)s& value) {
     %(name)s_insert(array, value);
-}""" % values
+}""" % values, file=self.out)
 
-        print >>self.out, """
+        print("""
 /* These methods need to be handled specially, since their C++ APIs cannot be directly translated to C.
    Unlike the C++ versions, the return value is allocated on the heap, and you must delete it yourself. */
 OPENMM_EXPORT void openmm_context_getstate_(const OpenMM_Context*& target, int const& types, int const& enforcePeriodicBox, OpenMM_State*& result) {
@@ -2017,10 +2018,10 @@ OPENMM_EXPORT void openmm_xmlserializer_deserializeintegrator_(const char* xml,
 }
 OPENMM_EXPORT void OPENMM_XMLSERIALIZER_DESERIALIZEINTEGRATOR(const char* xml, OpenMM_Integrator*& result, int length) {
     result = OpenMM_XmlSerializer_deserializeIntegrator(makeString(xml, length).c_str());
-}"""
+}""", file=self.out)
 
         self.writeClasses()
-        print >>self.out, "}"
+        print("}", file=self.out)
 
 inputDirname = sys.argv[1]
 builder = CHeaderGenerator(inputDirname, open(os.path.join(sys.argv[2], 'OpenMMCWrapper.h'), 'w'))

wrappers/python/src/swig_doxygen/doxygen/Doxyfile.in

@@ -600,7 +600,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a 
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = 
+EXCLUDE                = *Impl.h
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
 # directories that are symbolic links (a Unix filesystem feature) are excluded