CustomBondForceProxy.cpp

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
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 * 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.               *
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 * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
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#include "openmm/serialization/CustomBondForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/CustomBondForce.h"
#include <sstream>

using namespace OpenMM;
using namespace std;

CustomBondForceProxy::CustomBondForceProxy() : SerializationProxy("CustomBondForce") {
}

void CustomBondForceProxy::serialize(const void* object, SerializationNode& node) const {
    node.setIntProperty("version", 3);
    const CustomBondForce& force = *reinterpret_cast<const CustomBondForce*>(object);
    node.setIntProperty("forceGroup", force.getForceGroup());
    node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
    node.setStringProperty("energy", force.getEnergyFunction());
    SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
        perBondParams.createChildNode("Parameter").setStringProperty("name", force.getPerBondParameterName(i));
    }
    SerializationNode& globalParams = node.createChildNode("GlobalParameters");
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
    }
    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
    }
    SerializationNode& bonds = node.createChildNode("Bonds");
    for (int i = 0; i < force.getNumBonds(); i++) {
        int p1, p2;
        vector<double> params;
        force.getBondParameters(i, p1, p2, params);
        SerializationNode& bond = bonds.createChildNode("Bond").setIntProperty("p1", p1).setIntProperty("p2", p2);
        for (int j = 0; j < (int) params.size(); j++) {
            stringstream key;
            key << "param";
            key << j+1;
            bond.setDoubleProperty(key.str(), params[j]);
        }
    }
}

void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
    int version = node.getIntProperty("version");
    if (version < 1 || version > 3)
        throw OpenMMException("Unsupported version number");
    CustomBondForce* force = NULL;
    try {
        CustomBondForce* force = new CustomBondForce(node.getStringProperty("energy"));
        force->setForceGroup(node.getIntProperty("forceGroup", 0));
        if (version > 1)
            force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
        const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
        for (auto& parameter : perBondParams.getChildren())
            force->addPerBondParameter(parameter.getStringProperty("name"));
        const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
        for (auto& parameter : globalParams.getChildren())
            force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
        if (version > 2) {
            const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
            for (auto& parameter : energyDerivs.getChildren())
                force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
        }
        const SerializationNode& bonds = node.getChildNode("Bonds");
        vector<double> params(force->getNumPerBondParameters());
        for (auto& bond : bonds.getChildren()) {
            for (int j = 0; j < (int) params.size(); j++) {
                stringstream key;
                key << "param";
                key << j+1;
                params[j] = bond.getDoubleProperty(key.str());
            }
            force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), params);
        }
        return force;
    }
    catch (...) {
        if (force != NULL)
            delete force;
        throw;
    }
}