/* -------------------------------------------------------------------------- * * 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) 2010-2014 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/GBSAOBCForceProxy.h" #include "openmm/serialization/SerializationNode.h" #include "openmm/Force.h" #include "openmm/GBSAOBCForce.h" #include using namespace OpenMM; using namespace std; GBSAOBCForceProxy::GBSAOBCForceProxy() : SerializationProxy("GBSAOBCForce") { } void GBSAOBCForceProxy::serialize(const void* object, SerializationNode& node) const { node.setIntProperty("version", 2); const GBSAOBCForce& force = *reinterpret_cast(object); node.setIntProperty("forceGroup", force.getForceGroup()); node.setStringProperty("name", force.getName()); node.setIntProperty("method", (int) force.getNonbondedMethod()); node.setDoubleProperty("cutoff", force.getCutoffDistance()); node.setDoubleProperty("soluteDielectric", force.getSoluteDielectric()); node.setDoubleProperty("solventDielectric", force.getSolventDielectric()); node.setDoubleProperty("surfaceAreaEnergy", force.getSurfaceAreaEnergy()); SerializationNode& particles = node.createChildNode("Particles"); for (int i = 0; i < force.getNumParticles(); i++) { double charge, radius, scale; force.getParticleParameters(i, charge, radius, scale); particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("r", radius).setDoubleProperty("scale", scale); } } void* GBSAOBCForceProxy::deserialize(const SerializationNode& node) const { int version = node.getIntProperty("version"); if (version < 1 || version > 2) throw OpenMMException("Unsupported version number"); GBSAOBCForce* force = new GBSAOBCForce(); try { force->setForceGroup(node.getIntProperty("forceGroup", 0)); force->setName(node.getStringProperty("name", force->getName())); force->setNonbondedMethod((GBSAOBCForce::NonbondedMethod) node.getIntProperty("method")); force->setCutoffDistance(node.getDoubleProperty("cutoff")); force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric")); force->setSolventDielectric(node.getDoubleProperty("solventDielectric")); if (version > 1) force->setSurfaceAreaEnergy(node.getDoubleProperty("surfaceAreaEnergy")); const SerializationNode& particles = node.getChildNode("Particles"); for (auto& particle : particles.getChildren()) force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("r"), particle.getDoubleProperty("scale")); } catch (...) { delete force; throw; } return force; }