Implemented serialization for RMSDForce

serialization/include/openmm/serialization/RMSDForceProxy.h

+#ifndef OPENMM_RMSDFORCE_PROXY_H_
+#define OPENMM_RMSDFORCE_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) 2018 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 RMSDForce objects.
+ */
+
+class OPENMM_EXPORT RMSDForceProxy : public SerializationProxy {
+public:
+    RMSDForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_RMSDFORCE_PROXY_H_*/

serialization/src/RMSDForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2018 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/RMSDForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/RMSDForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+RMSDForceProxy::RMSDForceProxy() : SerializationProxy("RMSDForce") {
+}
+
+void RMSDForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 0);
+    const RMSDForce& force = *reinterpret_cast<const RMSDForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    SerializationNode& positionsNode = node.createChildNode("ReferencePositions");
+    for (const Vec3& pos : force.getReferencePositions())
+       positionsNode.createChildNode("Position").setDoubleProperty("x", pos[0]).setDoubleProperty("y", pos[1]).setDoubleProperty("z", pos[2]);
+    SerializationNode& particlesNode = node.createChildNode("Particles");
+    for (int i : force.getParticles())
+       particlesNode.createChildNode("Particle").setIntProperty("index", i);
+}
+
+void* RMSDForceProxy::deserialize(const SerializationNode& node) const {
+    int version = node.getIntProperty("version");
+    if (version != 0)
+        throw OpenMMException("Unsupported version number");
+    RMSDForce* force = NULL;
+    try {
+        vector<Vec3> positions;
+        for (auto& pos : node.getChildNode("ReferencePositions").getChildren())
+            positions.push_back(Vec3(pos.getDoubleProperty("x"), pos.getDoubleProperty("y"), pos.getDoubleProperty("z")));
+        vector<int> particles;
+        for (auto& particle : node.getChildNode("Particles").getChildren())
+            particles.push_back(particle.getIntProperty("index"));
+        force = new RMSDForce(positions, particles);
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        return force;
+    }
+    catch (...) {
+        if (force != NULL)
+            delete force;
+        throw;
+    }
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -57,6 +57,7 @@
 #include "openmm/NonbondedForce.h"
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/RBTorsionForce.h"
+#include "openmm/RMSDForce.h"
 #include "openmm/System.h"
 #include "openmm/TabulatedFunction.h"
 #include "openmm/VariableLangevinIntegrator.h"
@@ -92,6 +93,7 @@
 #include "openmm/serialization/NonbondedForceProxy.h"
 #include "openmm/serialization/PeriodicTorsionForceProxy.h"
 #include "openmm/serialization/RBTorsionForceProxy.h"
+#include "openmm/serialization/RMSDForceProxy.h"
 #include "openmm/serialization/StateProxy.h"
 #include "openmm/serialization/SystemProxy.h"
 #include "openmm/serialization/TabulatedFunctionProxies.h"
@@ -148,6 +150,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(NonbondedForce), new NonbondedForceProxy());
     SerializationProxy::registerProxy(typeid(PeriodicTorsionForce), new PeriodicTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(RBTorsionForce), new RBTorsionForceProxy());
+    SerializationProxy::registerProxy(typeid(RMSDForce), new RMSDForceProxy());
     SerializationProxy::registerProxy(typeid(System), new SystemProxy());
     SerializationProxy::registerProxy(typeid(State), new StateProxy());
     SerializationProxy::registerProxy(typeid(VariableLangevinIntegrator), new VariableLangevinIntegratorProxy());

serialization/tests/TestSerializeRMSDForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2018 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/AssertionUtilities.h"
+#include "openmm/RMSDForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    vector<Vec3> refPos;
+    for (int i = 0; i < 10; i++)
+        refPos.push_back(Vec3(i/5.0, i*1.2, i*i/3.5));
+    vector<int> particles;
+    for (int i = 0; i < 5; i++)
+        particles.push_back(i*i);
+    RMSDForce force(refPos, particles);
+    force.setForceGroup(3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<RMSDForce>(&force, "Force", buffer);
+    RMSDForce* copy = XmlSerializer::deserialize<RMSDForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    RMSDForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.getReferencePositions().size(), force2.getReferencePositions().size());
+    for (int i = 0; i < force.getReferencePositions().size(); i++)
+        ASSERT_EQUAL_VEC(force.getReferencePositions()[i], force2.getReferencePositions()[i], 0.0);
+    ASSERT_EQUAL(force.getParticles().size(), force2.getParticles().size());
+    for (int i = 0; i < force.getParticles().size(); i++)
+        ASSERT_EQUAL(force.getParticles()[i], force2.getParticles()[i]);
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}