Merge pull request #4 from peastman/master

Most of the features to support Drude particles are now complete and functional

plugins/drude/CMakeLists.txt

@@ -205,9 +205,9 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
   SET (TEST_PATH .)
 ENDIF (EXECUTABLE_OUTPUT_PATH)
 
-#IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
-#    ADD_SUBDIRECTORY(serialization)
-#ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
+IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
+    ADD_SUBDIRECTORY(serialization)
+ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
 
 #INCLUDE(ApiDoxygen.cmake)
 

plugins/drude/platforms/cuda/src/CudaDrudeKernelFactory.cpp

 /* -------------------------------------------------------------------------- *
- *                              OpenMMAmoeba                                  *
+ *                              OpenMMDrude                                   *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

plugins/drude/platforms/opencl/src/OpenCLDrudeKernelFactory.cpp

 /* -------------------------------------------------------------------------- *
- *                              OpenMMAmoeba                                  *
+ *                              OpenMMDrude                                   *
  * -------------------------------------------------------------------------- *
  * This is part of the OpenMM molecular simulation toolkit originating from   *
  * Simbios, the NIH National Center for Physics-Based Simulation of           *

plugins/drude/platforms/reference/src/ReferenceDrudeKernelFactory.cpp

 /* -------------------------------------------------------------------------- *
- *                              OpenMMAmoeba                                  *
+ *                              OpenMMDrude                                   *
  * -------------------------------------------------------------------------- *
  * 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) 2011 Stanford University and the Authors.           *
+ * Portions copyright (c) 2011-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *

plugins/drude/serialization/CMakeLists.txt

+#---------------------------------------------------
+# OpenMMDrude Serialization Library
+#
+# Creates OpenMMDrude serializatin library, base name=OpenMMDrudeSerialization.
+# Default libraries are shared & optimized. Variants
+# are created for static (_static) and debug (_d).
+#
+# Windows:
+#   OpenMMDrudeSerialization[_d].dll
+#   OpenMMDrudeSerialization[_d].lib
+# Unix:
+#   libOpenMMDrudeSerialization[_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_DRUDE_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_DRUDE_LIBRARY_NAME OpenMMDrude)
+SET(OPENMM_SERIALIZATION_LIBRARY_NAME OpenMMSerialization)
+SET(OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME OpenMMDrudeSerialization)
+
+# 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_DRUDE_LIBRARY_NAME ${OPENMM_DRUDE_LIBRARY_NAME}_d)
+    SET(OPENMM_SERIALIZATION_LIBRARY_NAME ${OPENMM_SERIALIZATION_LIBRARY_NAME}_d)
+    SET(OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME ${OPENMM_DRUDE_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_DRUDE_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_DRUDE_SERIALIZATION_LIBRARY_NAME} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+TARGET_LINK_LIBRARIES(${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME} ${OPENMM_DRUDE_LIBRARY_NAME} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${SHARED_TARGET})
+SET_TARGET_PROPERTIES(${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME} PROPERTIES COMPILE_FLAGS "-DOPENMM_DRUDE_SERIALIZATION_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
+INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${OPENMM_DRUDE_SERIALIZATION_LIBRARY_NAME})
+
+ADD_SUBDIRECTORY(tests)

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

+#ifndef OPENMM_DRUDE_FORCE_PROXY_H_
+#define OPENMM_DRUDE_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMDrude                                 *
+ * -------------------------------------------------------------------------- *
+ * 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) 2013 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/internal/windowsExportDrudeSerialization.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing DrudeForce objects.
+ */
+
+class OPENMM_EXPORT_DRUDE_SERIALIZATION DrudeForceProxy : public SerializationProxy {
+public:
+    DrudeForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_DRUDE_FORCE_PROXY_H_*/

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

+#ifndef OPENMM_DRUDE_LANGEVIN_INTEGRATOR_PROXY_H_
+#define OPENMM_DRUDE_LANGEVIN_INTEGRATOR_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMDrude                                 *
+ * -------------------------------------------------------------------------- *
+ * 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) 2013 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/internal/windowsExportDrudeSerialization.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing DrudeLangevinIntegrator objects.
+ */
+
+class OPENMM_EXPORT_DRUDE_SERIALIZATION DrudeLangevinIntegratorProxy : public SerializationProxy {
+public:
+    DrudeLangevinIntegratorProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_DRUDE_LANGEVIN_INTEGRATOR_PROXY_H_*/

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/DrudeForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMDrude                                 *
+ * -------------------------------------------------------------------------- *
+ * 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) 2013 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/DrudeForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/DrudeForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+DrudeForceProxy::DrudeForceProxy() : SerializationProxy("DrudeForce") {
+}
+
+void DrudeForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const DrudeForce& force = *reinterpret_cast<const DrudeForce*>(object);
+    SerializationNode& particles = node.createChildNode("Particles");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        int p, p1, p2, p3, p4;
+        double charge, polarizability, aniso12, aniso34;
+        force.getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
+        particles.createChildNode("Particle").setIntProperty("p", p).setIntProperty("p1", p1).setIntProperty("p2", p2).setIntProperty("p3", p3).setIntProperty("p4", p4)
+            .setDoubleProperty("charge", charge).setDoubleProperty("polarizability", polarizability).setDoubleProperty("a12", aniso12).setDoubleProperty("a34", aniso34);
+    }
+    SerializationNode& pairs = node.createChildNode("ScreenedPairs");
+    for (int i = 0; i < force.getNumScreenedPairs(); i++) {
+        int p1, p2;
+        double thole;
+        force.getScreenedPairParameters(i, p1, p2, thole);
+        pairs.createChildNode("Pair").setIntProperty("p1", p1).setIntProperty("p2", p2).setDoubleProperty("thole", thole);
+    }
+}
+
+void* DrudeForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    DrudeForce* force = new DrudeForce();
+    try {
+        const SerializationNode& particles = node.getChildNode("Particles");
+        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
+            const SerializationNode& particle = particles.getChildren()[i];
+            force->addParticle(particle.getIntProperty("p"), particle.getIntProperty("p1"), particle.getIntProperty("p2"), particle.getIntProperty("p3"), particle.getIntProperty("p4"),
+                    particle.getDoubleProperty("charge"), particle.getDoubleProperty("polarizability"), particle.getDoubleProperty("a12"), particle.getDoubleProperty("a34"));
+        }
+        const SerializationNode& pairs = node.getChildNode("ScreenedPairs");
+        for (int i = 0; i < (int) pairs.getChildren().size(); i++) {
+            const SerializationNode& pair = pairs.getChildren()[i];
+            force->addScreenedPair(pair.getIntProperty("p1"), pair.getIntProperty("p2"), pair.getDoubleProperty("thole"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/drude/serialization/src/DrudeLangevinIntegratorProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMDrude                                 *
+ * -------------------------------------------------------------------------- *
+ * 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) 2013 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/DrudeLangevinIntegratorProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/DrudeLangevinIntegrator.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+DrudeLangevinIntegratorProxy::DrudeLangevinIntegratorProxy() : SerializationProxy("DrudeLangevinIntegrator") {
+}
+
+void DrudeLangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const DrudeLangevinIntegrator& integrator = *reinterpret_cast<const DrudeLangevinIntegrator*>(object);
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
+    node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
+    node.setDoubleProperty("temperature", integrator.getTemperature());
+    node.setDoubleProperty("friction", integrator.getFriction());
+    node.setDoubleProperty("drudeTemperature", integrator.getDrudeTemperature());
+    node.setDoubleProperty("drudeFriction", integrator.getDrudeFriction());
+    node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
+}
+
+void* DrudeLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    DrudeLangevinIntegrator *integrator = new DrudeLangevinIntegrator(node.getDoubleProperty("temperature"),
+            node.getDoubleProperty("friction"), node.getDoubleProperty("drudeTemperature"),
+            node.getDoubleProperty("drudeFriction"), node.getDoubleProperty("stepSize"));
+    integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
+    integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
+    return integrator;
+}
\ No newline at end of file

plugins/drude/serialization/src/DrudeSerializationProxyRegistration.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMDrude                                 *
+ * -------------------------------------------------------------------------- *
+ * 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) 2013 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/DrudeForce.h"
+#include "openmm/DrudeLangevinIntegrator.h"
+
+#include "openmm/serialization/SerializationProxy.h"
+
+#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();
+    BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
+        if (ul_reason_for_call == DLL_PROCESS_ATTACH)
+            registerDrudeSerializationProxies();
+        return TRUE;
+    }
+#else
+    extern "C" void __attribute__((constructor)) registerDrudeSerializationProxies();
+#endif
+
+using namespace OpenMM;
+
+extern "C" OPENMM_EXPORT_DRUDE_SERIALIZATION void registerDrudeSerializationProxies() {
+    SerializationProxy::registerProxy(typeid(DrudeForce), new DrudeForceProxy());
+    SerializationProxy::registerProxy(typeid(DrudeLangevinIntegrator), new DrudeLangevinIntegratorProxy());
+}

plugins/drude/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_DRUDE_SERIALIZATION_LIBRARY_NAME} ${OPENMM_DRUDE_LIBRARY_NAME})
+    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
+
+ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/drude/serialization/tests/TestSerializeDrudeForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMDrude                                 *
+ * -------------------------------------------------------------------------- *
+ * 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) 2013 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/Platform.h"
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/DrudeForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+extern "C" void registerDrudeSerializationProxies();
+
+void testSerialization() {
+    // Create a Force.
+
+    DrudeForce force1;
+    force1.addParticle(0, 1, 2, 3, 4, 0.5, 1.0, 1.5, 2.0);
+    force1.addParticle(2, 3, 7, 8, 9, 0.1, 1e-4, 1.0, 0.9);
+    force1.addParticle(5, 6, -1, -1, -1, 0.2, 0.1, 1.0, 1.0);
+    force1.addScreenedPair(0, 1, 2.6);
+    force1.addScreenedPair(1, 2, 2.2);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<DrudeForce>(&force1, "Force", buffer);
+    DrudeForce* copy = XmlSerializer::deserialize<DrudeForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    DrudeForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
+    for (int i = 0; i < (int) force1.getNumParticles(); i++) {
+        int a1, a2, a3, a4, a5, b1, b2, b3, b4, b5;
+        double charge1, charge2;
+        double polar1, polar2;
+        double aa12, ba12, aa34, ba34;
+        force1.getParticleParameters(i, a1, a2, a3, a4, a5, charge1, polar1, aa12, aa34);
+        force2.getParticleParameters(i, b1, b2, b3, b4, b5, charge2, polar2, ba12, ba34);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(a3, b3);
+        ASSERT_EQUAL(a4, b4);
+        ASSERT_EQUAL(a5, b5);
+        ASSERT_EQUAL(charge1, charge2);
+        ASSERT_EQUAL(polar1, polar2);
+        ASSERT_EQUAL(aa12, ba12);
+        ASSERT_EQUAL(aa34, ba34);
+    }
+    ASSERT_EQUAL(force1.getNumScreenedPairs(), force2.getNumScreenedPairs());
+    for (int i = 0; i < (int) force1.getNumScreenedPairs(); i++) {
+        int a1, a2, b1, b2;
+        double thole1, thole2;
+        force1.getScreenedPairParameters(i, a1, a2, thole1);
+        force1.getScreenedPairParameters(i, b1, b2, thole2);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(thole1, thole2);
+    }
+}
+
+int main() {
+    try {
+        registerDrudeSerializationProxies();
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

plugins/drude/serialization/tests/TestSerializeDrudeLangevinIntegrator.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMDrude                                 *
+ * -------------------------------------------------------------------------- *
+ * 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) 2013 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/Platform.h"
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/DrudeLangevinIntegrator.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+extern "C" void registerDrudeSerializationProxies();
+
+void testSerialization() {
+    // Create an Integrator.
+
+    DrudeLangevinIntegrator integ1(301.1, 0.95, 10.5, 1.2, 0.001);
+    integ1.setRandomNumberSeed(18);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<DrudeLangevinIntegrator>(&integ1, "Integrator", buffer);
+    DrudeLangevinIntegrator* copy = XmlSerializer::deserialize<DrudeLangevinIntegrator>(buffer);
+
+    // Compare the two integrators to see if they are identical.
+    
+    DrudeLangevinIntegrator& integ2 = *copy;
+    ASSERT_EQUAL(integ1.getTemperature(), integ2.getTemperature());
+    ASSERT_EQUAL(integ1.getFriction(), integ2.getFriction());
+    ASSERT_EQUAL(integ1.getDrudeTemperature(), integ2.getDrudeTemperature());
+    ASSERT_EQUAL(integ1.getDrudeFriction(), integ2.getDrudeFriction());
+    ASSERT_EQUAL(integ1.getRandomNumberSeed(), integ2.getRandomNumberSeed());
+}
+
+int main() {
+    try {
+        registerDrudeSerializationProxies();
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

wrappers/python/simtk/openmm/app/modeller.py

@@ -33,11 +33,12 @@ from __future__ import division
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-from simtk.openmm.app import Topology, PDBFile
-from simtk.openmm.app.forcefield import HAngles
+from simtk.openmm.app import Topology, PDBFile, ForceField
+from simtk.openmm.app.forcefield import HAngles, _createResidueSignature, _matchResidue, DrudeGenerator
+from simtk.openmm.app.topology import Residue
 from simtk.openmm.vec3 import Vec3
 from simtk.openmm import System, Context, NonbondedForce, VerletIntegrator, LocalEnergyMinimizer
-from simtk.unit import nanometer, molar, elementary_charge, amu, gram, liter, degree, sqrt, acos, is_quantity, dot, norm
+from simtk.unit import nanometer, molar, elementary_charge, amu, gram, liter, degree, sqrt, acos, is_quantity, dot, norm, sum
 import element as elem
 import os
 import random
@@ -516,7 +517,7 @@ class Modeller(object):
                     terminal = hydrogen.attrib['terminal']
                 data.hydrogens.append(Modeller._Hydrogen(hydrogen.attrib['name'], hydrogen.attrib['parent'], maxph, atomVariants, terminal))
     
-    def addHydrogens(self, forcefield, pH=7.0, variants=None, hydrogenDefinitions=None):
+    def addHydrogens(self, forcefield, pH=7.0, variants=None):
         """Add missing hydrogens to the model.
         
         Some residues can exist in multiple forms depending on the pH and properties of the local environment.  These
@@ -763,3 +764,160 @@ class Modeller(object):
         self.topology = newTopology
         self.positions = context.getState(getPositions=True).getPositions()
         return actualVariants
+    
+    def addExtraParticles(self, forcefield):
+        """Add missing extra particles to the model that are required by a force field.
+        
+        Some force fields use "extra particles" that do not represent actual atoms, but still need to be included in
+        the System.  Examples include lone pairs, Drude particles, and the virtual sites used in some water models
+        to adjust the charge distribution.  Extra particles can be recognized by the fact that their element is None.
+        
+        This method is primarily used to add extra particles, but it can also remove them.  It tries to match every
+        residue in the Topology to a template in the force field.  If there is no match, it will both add and remove
+        extra particles as necessary to make it match.
+        
+        Parameters:
+         - forcefield (ForceField) the ForceField defining what extra particles should be present
+        """
+        # Create copies of all residue templates that have had all extra points removed.
+        
+        templatesNoEP = {}
+        for resName, template in forcefield._templates.iteritems():
+            if any(atom.element is None for atom in template.atoms):
+                index = 0
+                newIndex = {}
+                newTemplate = ForceField._TemplateData(resName)
+                for i, atom in enumerate(template.atoms):
+                    if atom.element is not None:
+                        newIndex[i] = index
+                        index += 1
+                        newTemplate.atoms.append(ForceField._TemplateAtomData(atom.name, atom.type, atom.element))
+                for b1, b2 in template.bonds:
+                    if b1 in newIndex and b2 in newIndex:
+                        newTemplate.bonds.append((newIndex[b1], newIndex[b2]))
+                        newTemplate.atoms[newIndex[b1]].bondedTo.append(newIndex[b2])
+                        newTemplate.atoms[newIndex[b2]].bondedTo.append(newIndex[b1])
+                for b in template.externalBonds:
+                    if b in newIndex:
+                        newTemplate.externalBonds.append(newIndex[b])
+                templatesNoEP[template] = newTemplate
+        
+        # Record which atoms are bonded to each other atom, with and without extra particles.
+        
+        bondedToAtom = []
+        bondedToAtomNoEP = []
+        for atom in self.topology.atoms():
+            bondedToAtom.append(set())
+            if atom.element is not None:
+                bondedToAtomNoEP.append(set())
+        for atom1, atom2 in self.topology.bonds():
+            bondedToAtom[atom1.index].add(atom2.index)
+            bondedToAtom[atom2.index].add(atom1.index)
+            if atom1.element is not None and atom2.element is not None:
+                bondedToAtomNoEP[atom1.index].add(atom2.index)
+                bondedToAtomNoEP[atom2.index].add(atom1.index)
+        
+        # If the force field has a DrudeForce, record the types of Drude particles and their parents since we'll
+        # need them for picking particle positions.
+        
+        drudeTypeMap = {}
+        for force in forcefield._forces:
+            if isinstance(force, DrudeGenerator):
+                for type in force.typeMap:
+                    drudeTypeMap[type] = force.typeMap[type][0]
+        
+        # Create the new Topology.
+        
+        newTopology = Topology()
+        newTopology.setUnitCellDimensions(deepcopy(self.topology.getUnitCellDimensions()))
+        newAtoms = {}
+        newPositions = []*nanometer
+        for chain in self.topology.chains():
+            newChain = newTopology.addChain()
+            for residue in chain.residues():
+                newResidue = newTopology.addResidue(residue.name, newChain)
+                
+                # Look for a matching template.
+                
+                matchFound = False
+                signature = _createResidueSignature([atom.element for atom in residue.atoms()])
+                if signature in forcefield._templateSignatures:
+                    for t in forcefield._templateSignatures[signature]:
+                        if _matchResidue(residue, t, bondedToAtom) is not None:
+                            matchFound = True
+                if matchFound:
+                    # Just copy the residue over.
+                    
+                    for atom in residue.atoms():
+                        newAtom = newTopology.addAtom(atom.name, atom.element, newResidue)
+                        newAtoms[atom] = newAtom
+                        newPositions.append(deepcopy(self.positions[atom.index]))
+                else:
+                    # There's no matching template.  Try to find one that matches based on everything except
+                    # extra points.
+                    
+                    template = None
+                    residueNoEP = Residue(residue.name, residue.index, residue.chain)
+                    residueNoEP._atoms = [atom for atom in residue.atoms() if atom.element is not None]
+                    if signature in forcefield._templateSignatures:
+                        for t in forcefield._templateSignatures[signature]:
+                            if t in templatesNoEP:
+                                matches = _matchResidue(residueNoEP, templatesNoEP[t], bondedToAtomNoEP)
+                                if matches is not None:
+                                    template = t;
+                                    # Record the corresponding atoms.
+                                    matchingAtoms = {}
+                                    for atom, match in zip(residueNoEP.atoms(), matches):
+                                        templateAtomName = t.atoms[match].name
+                                        for templateAtom in template.atoms:
+                                            if templateAtom.name == templateAtomName:
+                                                matchingAtoms[templateAtom] = atom
+                                    break
+                    if template is None:
+                        raise ValueError('Residue %d (%s) does not match any template defined by the ForceField.' % (residue.index+1, residue.name))
+                    
+                    # Add the regular atoms.
+                    
+                    for atom in residue.atoms():
+                        if atom.element is not None:
+                            newAtoms[atom] = newTopology.addAtom(atom.name, atom.element, newResidue)
+                            newPositions.append(deepcopy(self.positions[atom.index]))
+                    
+                    # Add the extra points.
+                    
+                    templateAtomPositions = len(template.atoms)*[None]
+                    for index, atom in enumerate(template.atoms):
+                        if atom in matchingAtoms:
+                            templateAtomPositions[index] = self.positions[matchingAtoms[atom].index]
+                    for index, atom in enumerate(template.atoms):
+                        if atom.element is None:
+                            newTopology.addAtom(atom.name, None, newResidue)
+                            position = None
+                            for site in template.virtualSites:
+                                if site.index == index:
+                                    # This is a virtual site.  Compute its position by the correct rule.
+                                    
+                                    if site.type == 'average2':
+                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]]
+                                    elif site.type == 'average3':
+                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] + site.weights[2]*templateAtomPositions[index+site.atoms[2]]
+                                    elif site.type == 'outOfPlane':
+                                        position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] + site.weights[2]*templateAtomPositions[index+site.atoms[2]]
+                            if position is None and atom.type in drudeTypeMap:
+                                # This is a Drude particle.  Put it on top of its parent atom.
+                                
+                                for atom2, pos in zip(template.atoms, templateAtomPositions):
+                                    if atom2.type in drudeTypeMap[atom.type]:
+                                        position = deepcopy(pos)
+                            if position is None:
+                                # We couldn't figure out the correct position.  As a wild guess, just put it at the center of the residue
+                                # and hope that energy minimization will fix it.
+                                
+                                knownPositions = [x for x in templateAtomPositions if x is not None]
+                                position = sum(knownPositions)/len(knownPositions)
+                            newPositions.append(position)
+        for bond in self.topology.bonds():
+            if bond[0] in newAtoms and bond[1] in newAtoms:
+                newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
+        self.topology = newTopology
+        self.positions = newPositions
\ No newline at end of file