Initial serialization proxies for Amoeba

plugins/amoeba/CMakeLists.txt

@@ -195,6 +195,10 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
   SET (TEST_PATH .)
 ENDIF (EXECUTABLE_OUTPUT_PATH)
 
+IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
+    ADD_SUBDIRECTORY(serialization)
+ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
+
 #INCLUDE(ApiDoxygen.cmake)
 
 #ADD_SUBDIRECTORY(tests)

plugins/amoeba/serialization/CMakeLists.txt

+#---------------------------------------------------
+# OpenMMAmoeba Serialization Library
+#
+# Creates OpenMMAmoeba serializatin library, base name=OpenMMAmoebaSerialization.
+# Default libraries are shared & optimized. Variants
+# are created for static (_static) and debug (_d).
+#
+# Windows:
+#   OpenMMAmoebaSerialization[_d].dll
+#   OpenMMAmoebaSerialization[_d].lib
+# Unix:
+#   libOpenMMAmoebaSerialization[_d].so
+#----------------------------------------------------
+
+# The source is organized into subdirectories, but we handle them all from
+# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
+SET(OPENMM_SOURCE_SUBDIRS . ../../../serialization)
+SET(OPENMM_AMOEBA_SOURCE_SUBDIRS . )
+
+# Collect up information about the version of the OpenMM library we're building
+# and make it available to the code so it can be built into the binaries.
+
+SET(OPENMM_SERIALIZATION_LIBRARY_NAME OpenMMSerialization)
+SET(OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME OpenMMAmoebaSerialization)
+
+# Ensure that debug libraries have "_d" appended to their names.
+# CMake gets this right on Windows automatically with this definition.
+IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+    SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
+ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+
+# But on Unix or Cygwin we have to add the suffix manually
+IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME}_d)
+ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+
+
+# These are all the places to search for header files which are
+# to be part of the API.
+SET(API_INCLUDE_DIRS) # start empty
+FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
+    # append
+    SET(API_INCLUDE_DIRS ${API_INCLUDE_DIRS}
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
+ENDFOREACH(subdir)
+
+# We'll need both *relative* path names, starting with their API_INCLUDE_DIRS,
+# and absolute pathnames.
+SET(API_REL_INCLUDE_FILES)   # start these out empty
+SET(API_ABS_INCLUDE_FILES)
+
+FOREACH(dir ${API_INCLUDE_DIRS})
+    FILE(GLOB fullpaths ${dir}/*.h)	# returns full pathnames
+    SET(API_ABS_INCLUDE_FILES ${API_ABS_INCLUDE_FILES} ${fullpaths})
+
+    FOREACH(pathname ${fullpaths})
+        GET_FILENAME_COMPONENT(filename ${pathname} NAME)
+        SET(API_REL_INCLUDE_FILES ${API_REL_INCLUDE_FILES} ${dir}/${filename})
+    ENDFOREACH(pathname)
+ENDFOREACH(dir)
+
+# collect up source files
+SET(SOURCE_FILES) # empty
+SET(SOURCE_INCLUDE_FILES)
+
+FOREACH(subdir ${OPENMM_AMOEBA_SOURCE_SUBDIRS})
+    FILE(GLOB_RECURSE src_files   ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.c)
+    FILE(GLOB incl_files  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.hpp)
+    SET(SOURCE_FILES         ${SOURCE_FILES}         ${src_files})   #append
+    SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
+    INCLUDE_DIRECTORIES(BEFORE  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
+    INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../../serialization/${subdir}/include)
+ENDFOREACH(subdir)
+#Message( "API_REL_INCLUDE_FILES=${API_REL_INCLUDE_FILES}\n" )
+
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src )
+
+# Create the library
+ADD_LIBRARY(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+TARGET_LINK_LIBRARIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} ${SHARED_TARGET})
+SET_TARGET_PROPERTIES(${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
+INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME})
+INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/SerializationNode.h)
+INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/SerializationProxy.h)
+INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/XmlSerializer.h)
+
+ADD_SUBDIRECTORY(tests)

plugins/amoeba/serialization/include/openmm/serializatio

+#ifndef OPENMM_HARMONICBONDFORCE_PROXY_H_
+#define OPENMM_HARMONICBONDFORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing HarmonicBondForce objects.
+ */
+
+class OPENMM_EXPORT HarmonicBondForceProxy : public SerializationProxy {
+public:
+    HarmonicBondForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_HARMONICBONDFORCE_PROXY_H_*/

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

+#ifndef OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing AmoebaHarmonicAngleForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaHarmonicAngleForceProxy : public SerializationProxy {
+public:
+    AmoebaHarmonicAngleForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_PROXY_H_*/

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

+#ifndef OPENMM_AMOEBA_HARMONIC_BOND_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_HARMONIC_BOND_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing AmoebaHarmonicBondForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaHarmonicBondForceProxy : public SerializationProxy {
+public:
+    AmoebaHarmonicBondForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_HARMONIC_BOND_FORCE_PROXY_H_*/

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

+#ifndef OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing AmoebaHarmonicInPlaneAngleForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForceProxy : public SerializationProxy {
+public:
+    AmoebaHarmonicInPlaneAngleForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_PROXY_H_*/

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

+#ifndef OPENMM_AMOEBA_OUT_OF_PLANE_BEND_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_OUT_OF_PLANE_BEND_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing AmoebaOutOfPlaneBendForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaOutOfPlaneBendForceProxy : public SerializationProxy {
+public:
+    AmoebaOutOfPlaneBendForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_OUT_OF_PLANE_BEND_FORCE_PROXY_H_*/

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

+#ifndef OPENMM_AMOEBA_PI_TORSION_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_PI_TORSION_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing AmoebaPiTorsionForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaPiTorsionForceProxy : public SerializationProxy {
+public:
+    AmoebaPiTorsionForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_PI_TORSION_FORCE_PROXY_H_*/

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

+#ifndef OPENMM_AMOEBA_TORSION_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_TORSION_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing AmoebaTorsionForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaTorsionForceProxy : public SerializationProxy {
+public:
+    AmoebaTorsionForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_TORSION_FORCE_PROXY_H_*/

plugins/amoeba/serialization/src/AmoebaHarmonicAngleForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/AmoebaHarmonicAngleForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaHarmonicAngleForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaHarmonicAngleForceProxy::AmoebaHarmonicAngleForceProxy() : SerializationProxy("AmoebaHarmonicAngleForce") {
+}
+
+void AmoebaHarmonicAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaHarmonicAngleForce& force = *reinterpret_cast<const AmoebaHarmonicAngleForce*>(object);
+    node.setDoubleProperty("HarmonicAngleCubic", force.getAmoebaGlobalHarmonicAngleCubic());
+    node.setDoubleProperty("HarmonicAngleQuartic", force.getAmoebaGlobalHarmonicAngleQuartic());
+    node.setDoubleProperty("HarmonicAnglePentic", force.getAmoebaGlobalHarmonicAnglePentic());
+    node.setDoubleProperty("HarmonicAngleSextic", force.getAmoebaGlobalHarmonicAngleSextic());
+    SerializationNode& bonds = node.createChildNode("Angles");
+    for (int i = 0; i < force.getNumAngles(); i++) {
+        int particle1, particle2, particle3;
+        double distance, k;
+        force.getAngleParameters(i, particle1, particle2, particle3, distance, k);
+        bonds.createChildNode("Angle").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setDoubleProperty("d", distance).setDoubleProperty("k", k);
+    }
+}
+
+void* AmoebaHarmonicAngleForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    AmoebaHarmonicAngleForce* force = new AmoebaHarmonicAngleForce();
+    try {
+        force->setAmoebaGlobalHarmonicAngleCubic(node.getDoubleProperty("HarmonicAngleCubic"));
+        force->setAmoebaGlobalHarmonicAngleQuartic(node.getDoubleProperty("HarmonicAngleQuartic"));
+        force->setAmoebaGlobalHarmonicAnglePentic(node.getDoubleProperty("HarmonicAnglePentic"));
+        force->setAmoebaGlobalHarmonicAngleSextic(node.getDoubleProperty("HarmonicAngleSextic"));
+        const SerializationNode& bonds = node.getChildNode("Angles");
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            force->addAngle(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/amoeba/serialization/src/AmoebaHarmonicBondForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/AmoebaHarmonicBondForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaHarmonicBondForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaHarmonicBondForceProxy::AmoebaHarmonicBondForceProxy() : SerializationProxy("AmoebaHarmonicBondForce") {
+}
+
+void AmoebaHarmonicBondForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaHarmonicBondForce& force = *reinterpret_cast<const AmoebaHarmonicBondForce*>(object);
+    node.setDoubleProperty("HarmonicBondCubic", force.getAmoebaGlobalHarmonicBondCubic());
+    node.setDoubleProperty("HarmonicBondQuartic", force.getAmoebaGlobalHarmonicBondQuartic());
+    SerializationNode& bonds = node.createChildNode("Bonds");
+    for (int i = 0; i < force.getNumBonds(); i++) {
+        int particle1, particle2;
+        double distance, k;
+        force.getBondParameters(i, particle1, particle2, distance, k);
+        bonds.createChildNode("Bond").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("d", distance).setDoubleProperty("k", k);
+    }
+}
+
+void* AmoebaHarmonicBondForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    AmoebaHarmonicBondForce* force = new AmoebaHarmonicBondForce();
+    try {
+        force->setAmoebaGlobalHarmonicBondCubic(node.getDoubleProperty("HarmonicBondCubic"));
+        force->setAmoebaGlobalHarmonicBondQuartic(node.getDoubleProperty("HarmonicBondQuartic"));
+        const SerializationNode& bonds = node.getChildNode("Bonds");
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/amoeba/serialization/src/AmoebaHarmonicInPlaneAngleForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/AmoebaHarmonicInPlaneAngleForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaHarmonicInPlaneAngleForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaHarmonicInPlaneAngleForceProxy::AmoebaHarmonicInPlaneAngleForceProxy() : SerializationProxy("AmoebaHarmonicInPlaneAngleForce") {
+}
+
+void AmoebaHarmonicInPlaneAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaHarmonicInPlaneAngleForce& force = *reinterpret_cast<const AmoebaHarmonicInPlaneAngleForce*>(object);
+    node.setDoubleProperty("HarmonicInPlaneAngleCubic", force.getAmoebaGlobalHarmonicInPlaneAngleCubic());
+    node.setDoubleProperty("HarmonicInPlaneAngleQuartic", force.getAmoebaGlobalHarmonicInPlaneAngleQuartic());
+    node.setDoubleProperty("HarmonicInPlaneAnglePentic", force.getAmoebaGlobalHarmonicInPlaneAnglePentic());
+    node.setDoubleProperty("HarmonicInPlaneAngleSextic", force.getAmoebaGlobalHarmonicInPlaneAngleSextic());
+    SerializationNode& bonds = node.createChildNode("InPlaneAngles");
+    for (int i = 0; i < force.getNumAngles(); i++) {
+        int particle1, particle2, particle3, particle4;
+        double distance, k;
+        force.getAngleParameters(i, particle1, particle2, particle3, particle4, distance, k);
+        bonds.createChildNode("InPlaneAngle").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setDoubleProperty("d", distance).setDoubleProperty("k", k);
+    }
+}
+
+void* AmoebaHarmonicInPlaneAngleForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    AmoebaHarmonicInPlaneAngleForce* force = new AmoebaHarmonicInPlaneAngleForce();
+    try {
+        force->setAmoebaGlobalHarmonicInPlaneAngleCubic(node.getDoubleProperty("HarmonicInPlaneAngleCubic"));
+        force->setAmoebaGlobalHarmonicInPlaneAngleQuartic(node.getDoubleProperty("HarmonicInPlaneAngleQuartic"));
+        force->setAmoebaGlobalHarmonicInPlaneAnglePentic(node.getDoubleProperty("HarmonicInPlaneAnglePentic"));
+        force->setAmoebaGlobalHarmonicInPlaneAngleSextic(node.getDoubleProperty("HarmonicInPlaneAngleSextic"));
+        const SerializationNode& bonds = node.getChildNode("InPlaneAngles");
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            force->addAngle(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"),  bond.getIntProperty("p4"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/AmoebaOutOfPlaneBendForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaOutOfPlaneBendForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaOutOfPlaneBendForceProxy::AmoebaOutOfPlaneBendForceProxy() : SerializationProxy("AmoebaOutOfPlaneBendForce") {
+}
+
+void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaOutOfPlaneBendForce& force = *reinterpret_cast<const AmoebaOutOfPlaneBendForce*>(object);
+    node.setDoubleProperty("OutOfPlaneBendCubic", force.getAmoebaGlobalOutOfPlaneBendCubic());
+    node.setDoubleProperty("OutOfPlaneBendQuartic", force.getAmoebaGlobalOutOfPlaneBendQuartic());
+    node.setDoubleProperty("OutOfPlaneBendPentic", force.getAmoebaGlobalOutOfPlaneBendPentic());
+    node.setDoubleProperty("OutOfPlaneBendSextic", force.getAmoebaGlobalOutOfPlaneBendSextic());
+    SerializationNode& bonds = node.createChildNode("OutOfPlaneBend");
+    for (int i = 0; i < force.getNumOutOfPlaneBends(); i++) {
+        int particle1, particle2, particle3, particle4;
+        double k;
+        force.getOutOfPlaneBendParameters(i, particle1, particle2, particle3, particle4, k);
+        bonds.createChildNode("OutOfPlaneBend").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setDoubleProperty("k", k);
+    }
+}
+
+void* AmoebaOutOfPlaneBendForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    AmoebaOutOfPlaneBendForce* force = new AmoebaOutOfPlaneBendForce();
+    try {
+        force->setAmoebaGlobalOutOfPlaneBendCubic(node.getDoubleProperty("OutOfPlaneBendCubic"));
+        force->setAmoebaGlobalOutOfPlaneBendQuartic(node.getDoubleProperty("OutOfPlaneBendQuartic"));
+        force->setAmoebaGlobalOutOfPlaneBendPentic(node.getDoubleProperty("OutOfPlaneBendPentic"));
+        force->setAmoebaGlobalOutOfPlaneBendSextic(node.getDoubleProperty("OutOfPlaneBendSextic"));
+        const SerializationNode& bonds = node.getChildNode("OutOfPlaneBend");
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            force->addOutOfPlaneBend(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"),  bond.getIntProperty("p4"), bond.getDoubleProperty("k"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/AmoebaPiTorsionForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaPiTorsionForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaPiTorsionForceProxy::AmoebaPiTorsionForceProxy() : SerializationProxy("AmoebaPiTorsionForce") {
+}
+
+void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
+    SerializationNode& bonds = node.createChildNode("PiTorsion");
+    for (int i = 0; i < force.getNumPiTorsions(); i++) {
+        int particle1, particle2, particle3, particle4, particle5, particle6;
+        double k;
+        force.getPiTorsionParameters(i, particle1, particle2, particle3, particle4, particle5, particle6, k);
+        bonds.createChildNode("PiTorsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setIntProperty("p5", particle5).setIntProperty("p6", particle6).setDoubleProperty("k", k);
+    }
+}
+
+void* AmoebaPiTorsionForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    AmoebaPiTorsionForce* force = new AmoebaPiTorsionForce();
+    try {
+        const SerializationNode& bonds = node.getChildNode("PiTorsion");
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            force->addPiTorsion(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"),  bond.getIntProperty("p4"), bond.getIntProperty("p5"),  bond.getIntProperty("p6"),bond.getDoubleProperty("k"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/amoeba/serialization/src/AmoebaSerializationProxyRegistration.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#ifdef WIN32
+#include <windows.h>
+#include <sstream>
+#else
+#include <dlfcn.h>
+#include <dirent.h>
+#include <cstdlib>
+#endif
+
+#include "openmm/OpenMMException.h"
+#include "openmm/AmoebaHarmonicBondForce.h"
+#include "openmm/AmoebaHarmonicAngleForce.h"
+#include "openmm/AmoebaHarmonicInPlaneAngleForce.h"
+#include "openmm/AmoebaOutOfPlaneBendForce.h"
+#include "openmm/AmoebaPiTorsionForce.h"
+#include "openmm/AmoebaTorsionForce.h"
+
+#include "openmm/serialization/SerializationProxy.h"
+#include "openmm/serialization/AmoebaHarmonicBondForceProxy.h"
+#include "openmm/serialization/AmoebaHarmonicAngleForceProxy.h"
+#include "openmm/serialization/AmoebaHarmonicInPlaneAngleForceProxy.h"
+#include "openmm/serialization/AmoebaOutOfPlaneBendForceProxy.h"
+#include "openmm/serialization/AmoebaPiTorsionForceProxy.h"
+#include "openmm/serialization/AmoebaTorsionForceProxy.h"
+
+#if defined(WIN32)
+    #include <windows.h>
+    extern "C" void registerAmoebaSerializationProxies();
+    BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
+        if (ul_reason_for_call == DLL_PROCESS_ATTACH)
+            registerAmoebaSerializationProxies();
+        return TRUE;
+    }
+#else
+    extern "C" void __attribute__((constructor)) registerAmoebaSerializationProxies();
+#endif
+
+using namespace OpenMM;
+
+extern "C" void registerAmoebaSerializationProxies() {
+
+    // force libOpenMMSerialization to load before libOpenMMSerialization
+    // required in order guarantee initialization of
+    //    map<const string, const SerializationProxy*> SerializationProxy::proxiesByType;
+    //    map<const string, const SerializationProxy*> SerializationProxy::proxiesByName;
+
+    // is there a cleaner solution?
+
+    std::string file = "libOpenMMSerialization.so";
+#ifdef WIN32
+    // Tell Windows not to bother the user with ugly error boxes.
+    const UINT oldErrorMode = SetErrorMode(SEM_FAILCRITICALERRORS);
+    HMODULE handle = LoadLibrary(file.c_str());
+    SetErrorMode(oldErrorMode); // Restore previous error mode.
+    if (handle == NULL) {
+        string message;
+        stringstream(message) << "Error loading library " << file << ": " << GetLastError();
+        throw OpenMMException(message);
+    }   
+#else
+    void *handle = dlopen(file.c_str(), RTLD_LAZY | RTLD_GLOBAL);
+    if (handle == NULL)
+        throw OpenMMException("Error loading library "+file+": "+dlerror());
+
+#endif
+
+    SerializationProxy::registerProxy(typeid(AmoebaHarmonicBondForce), new AmoebaHarmonicBondForceProxy());
+    SerializationProxy::registerProxy(typeid(AmoebaHarmonicAngleForce), new AmoebaHarmonicAngleForceProxy());
+    SerializationProxy::registerProxy(typeid(AmoebaHarmonicInPlaneAngleForce), new AmoebaHarmonicInPlaneAngleForceProxy());
+    SerializationProxy::registerProxy(typeid(AmoebaOutOfPlaneBendForce), new AmoebaOutOfPlaneBendForceProxy());
+    SerializationProxy::registerProxy(typeid(AmoebaPiTorsionForce), new AmoebaPiTorsionForceProxy());
+    SerializationProxy::registerProxy(typeid(AmoebaTorsionForce), new AmoebaTorsionForceProxy());
+}

plugins/amoeba/serialization/src/AmoebaTorsionForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/AmoebaTorsionForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaTorsionForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaTorsionForceProxy::AmoebaTorsionForceProxy() : SerializationProxy("AmoebaTorsionForce") {
+}
+
+static void addTorsionValues( SerializationNode& torsion, std::vector<double>& torsionValues ){
+    for (int j = 0; j < torsionValues.size(); j++) {
+        torsion.createChildNode("Value").setDoubleProperty("v", torsionValues[j]);
+    }
+}
+
+static void loadTorsionValues( SerializationNode& torsion, std::vector<double>& torsionValues ){
+    for (int j = 0; j < torsionValues.size(); j++) {
+        torsion.createChildNode("Value").setDoubleProperty("v", torsionValues[j]);
+    }
+}
+
+void AmoebaTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaTorsionForce& force = *reinterpret_cast<const AmoebaTorsionForce*>(object);
+    SerializationNode& bonds = node.createChildNode("Torsion");
+    for (int i = 0; i < force.getNumTorsions(); i++) {
+        int particle1, particle2, particle3, particle4;
+        std::vector<double> torsion1;
+        std::vector<double> torsion2;
+        std::vector<double> torsion3;
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3);
+        bonds.createChildNode("Torsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4);
+        SerializationNode& torsion = bonds.createChildNode("Torsion1").setIntProperty("size", torsion1.size());
+        addTorsionValues( torsion, torsion1 );
+        torsion = bonds.createChildNode("Torsion2").setIntProperty("size", torsion2.size());
+        addTorsionValues( torsion, torsion2 );
+        torsion = bonds.createChildNode("Torsion3").setIntProperty("size", torsion3.size());
+        addTorsionValues( torsion, torsion3 );
+    }
+}
+
+void* AmoebaTorsionForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    AmoebaTorsionForce* force = new AmoebaTorsionForce();
+/*
+    try {
+        const SerializationNode& bonds = node.getChildNode("Torsion");
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            //force->addTorsion(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"),  bond.getIntProperty("p4") );
+            std::vector<double> torsion1, std::vector<double> torsion2, std::vector<double> torsion3;
+            const SerializationNode& torsion = bond.getChildNode("Torsion1");
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+*/
+    return force;
+}

plugins/amoeba/serialization/tests/CMakeLists.txt

+#
+# Testing
+#
+
+ENABLE_TESTING()
+
+# Automatically create tests using files named "Test*.cpp"
+FILE(GLOB TEST_PROGS "*Test*.cpp")
+FOREACH(TEST_PROG ${TEST_PROGS})
+    GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
+
+    # All tests use shared libraries
+    ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
+    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${OPENMM_AMOEBA_SERIALIZATION_LIBRARY_NAME} OpenMMAmoeba)
+    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
+
+ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicAngleForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "openmm/AmoebaHarmonicAngleForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaHarmonicAngleForce force;
+    force.setAmoebaGlobalHarmonicAngleCubic( 12.3 );
+    force.setAmoebaGlobalHarmonicAngleQuartic( 98.7 );
+    force.setAmoebaGlobalHarmonicAnglePentic( 91.7 );
+    force.setAmoebaGlobalHarmonicAngleSextic( 93.7 );
+    force.addAngle(0, 1, 3, 1.0, 2.0);
+    force.addAngle(0, 2, 3, 2.0, 2.1);
+    force.addAngle(2, 3, 5, 3.0, 2.2);
+    force.addAngle(5, 1, 8, 4.0, 2.3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaHarmonicAngleForce>(&force, "Force", buffer);
+    AmoebaHarmonicAngleForce* copy = XmlSerializer::deserialize<AmoebaHarmonicAngleForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    AmoebaHarmonicAngleForce& force2 = *copy;
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicAngleCubic(), force2.getAmoebaGlobalHarmonicAngleCubic());
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicAngleQuartic(), force2.getAmoebaGlobalHarmonicAngleQuartic());
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicAnglePentic(), force2.getAmoebaGlobalHarmonicAnglePentic());
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicAngleSextic(), force2.getAmoebaGlobalHarmonicAngleSextic());
+    ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
+    for (int i = 0; i < force.getNumAngles(); i++) {
+        int a1, a2, a3, b1, b2, b3;
+        double da, db, ka, kb;
+        force.getAngleParameters(i, a1, a2, a3, da, ka);
+        force2.getAngleParameters(i, b1, b2, b3, db, kb);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(a3, b3);
+        ASSERT_EQUAL(da, db);
+        ASSERT_EQUAL(ka, kb);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicBondForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "openmm/AmoebaHarmonicBondForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaHarmonicBondForce force;
+    force.setAmoebaGlobalHarmonicBondCubic( 12.3 );
+    force.setAmoebaGlobalHarmonicBondQuartic( 98.7 );
+    force.addBond(0, 1, 1.0, 2.0);
+    force.addBond(0, 2, 2.0, 2.1);
+    force.addBond(2, 3, 3.0, 2.2);
+    force.addBond(5, 1, 4.0, 2.3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaHarmonicBondForce>(&force, "Force", buffer);
+    AmoebaHarmonicBondForce* copy = XmlSerializer::deserialize<AmoebaHarmonicBondForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    AmoebaHarmonicBondForce& force2 = *copy;
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicBondCubic(), force2.getAmoebaGlobalHarmonicBondCubic());
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicBondQuartic(), force2.getAmoebaGlobalHarmonicBondQuartic());
+    ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
+    for (int i = 0; i < force.getNumBonds(); i++) {
+        int a1, a2, b1, b2;
+        double da, db, ka, kb;
+        force.getBondParameters(i, a1, a2, da, ka);
+        force2.getBondParameters(i, b1, b2, db, kb);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(da, db);
+        ASSERT_EQUAL(ka, kb);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicInPlaneAngleForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "openmm/AmoebaHarmonicInPlaneAngleForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaHarmonicInPlaneAngleForce force;
+    force.setAmoebaGlobalHarmonicInPlaneAngleCubic( 12.3 );
+    force.setAmoebaGlobalHarmonicInPlaneAngleQuartic( 98.7 );
+    force.setAmoebaGlobalHarmonicInPlaneAnglePentic( 91.7 );
+    force.setAmoebaGlobalHarmonicInPlaneAngleSextic( 93.7 );
+    force.addAngle(0, 1, 3, 4, 1.0, 2.0);
+    force.addAngle(0, 2, 3, 5, 2.0, 2.1);
+    force.addAngle(2, 3, 5, 6, 3.0, 2.2);
+    force.addAngle(5, 1, 8, 8, 4.0, 2.3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaHarmonicInPlaneAngleForce>(&force, "Force", buffer);
+    AmoebaHarmonicInPlaneAngleForce* copy = XmlSerializer::deserialize<AmoebaHarmonicInPlaneAngleForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    AmoebaHarmonicInPlaneAngleForce& force2 = *copy;
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicInPlaneAngleCubic(), force2.getAmoebaGlobalHarmonicInPlaneAngleCubic());
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicInPlaneAngleQuartic(), force2.getAmoebaGlobalHarmonicInPlaneAngleQuartic());
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicInPlaneAnglePentic(), force2.getAmoebaGlobalHarmonicInPlaneAnglePentic());
+    ASSERT_EQUAL(force.getAmoebaGlobalHarmonicInPlaneAngleSextic(), force2.getAmoebaGlobalHarmonicInPlaneAngleSextic());
+    ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
+    for (int i = 0; i < force.getNumAngles(); i++) {
+        int a1, a2, a3, a4, b1, b2, b3, b4;
+        double da, db, ka, kb;
+        force.getAngleParameters(i, a1, a2, a3, a4, da, ka);
+        force2.getAngleParameters(i, b1, b2, b3, b4, db, kb);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(a3, b3);
+        ASSERT_EQUAL(a4, b4);
+        ASSERT_EQUAL(da, db);
+        ASSERT_EQUAL(ka, kb);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+