/* -------------------------------------------------------------------------- *
 *                      SimTK Core: SimTK Molmodel                            *
 * -------------------------------------------------------------------------- *
 * This is part of the SimTK Core biosimulation 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) 2006-7 Stanford University and the Authors.         *
 * Authors: Christopher Bruns                                                 *
 * 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 "SimTKmolmodel.h"

#include <iostream>
#include <vector>

using std::cout;
using std::endl;

using namespace SimTK;
using namespace std;

// define CREATE_VIZ_WINDOW to see animated window of simulation
// undefine for automated nightly builds
// #define CREATE_VIZ_WINDOW

void testIssue907()
{
    CompoundSystem system;
    SimbodyMatterSubsystem  matter(system);
    GeneralForceSubsystem forces(system);

    DuMMForceFieldSubsystem dumm(system);

    dumm.loadAmber99Parameters();
    dumm.setCoulombGlobalScaleFactor(0);//meterReader.globalCoulombScaleFactor);
    dumm.setBondTorsionGlobalScaleFactor(1);//meterReader.globalBondTorsionScaleFactor);
    dumm.setGbsaGlobalScaleFactor(0);//meterReader.globalGbsaScaleFactor);
    dumm.setVdwGlobalScaleFactor(0);//meterReader.globalVdwScaleFactor);
    dumm.setBondStretchGlobalScaleFactor(0);//meterReader.globalBondStretchScaleFactor);
    dumm.setBondBendGlobalScaleFactor(0);//meterReader.globalBondBendScaleFactor);
    dumm.setAmberImproperTorsionGlobalScaleFactor(0);//meterReader.globalAmberImproperTorsionScaleFactor);
     
    Biopolymer myMolecule;
    // myMolecule = Protein(    "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); //50 //ok
    myMolecule = Protein("WWGGLLAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
    // myMolecule.assignBiotypes();

    system.adoptCompound(myMolecule,Vec3(  0,0,0));
    cout<<"about to modelCompounds"<<endl;
    time_t rawtime;
    struct tm * timeinfo;
    time ( &rawtime );
    timeinfo = localtime ( &rawtime );
    cout<<" time:"<< asctime (timeinfo)   <<endl;
    system.modelCompounds();
    time ( &rawtime );
    timeinfo = localtime ( &rawtime );
    cout<<" time:"<< asctime (timeinfo)   <<endl;
    cout<<"done with modelCompounds"<<endl;
    State state = system.realizeTopology();
    system.realize(state,Stage::Position);
    VerletIntegrator study(system,.002);

    TimeStepper ts(system,study);
    ts.initialize(state);
    //# putting writeDefaultPdb here was fine to 2200 residues
    cout <<"1 about to write default pdb coords to  test.pdb"<<endl;
    myMolecule.writeDefaultPdb("test.pdb",Vec3(0));
    cout <<"1 just wrote default pdb coords to  test.pdb"<<endl;
    cout<<"[Repel.h:ConstrainedDynamics] Starting dynamics now."<<endl;
    time ( &rawtime );
    timeinfo = localtime ( &rawtime );
    cout<<" time:"<< asctime (timeinfo)   <<endl;
    //cout <<"2 about to write default pdb coords to  test.pdb"<<endl;
    //myMolecule.writeDefaultPdb("test.pdb",Vec3(0));
    //cout <<"2 just wrote default pdb coords to  test.pdb"<<endl;
    ts.stepTo(.1);

    time ( &rawtime );
    timeinfo = localtime ( &rawtime );
    cout<<" time:"<< asctime (timeinfo)   <<endl;


    cout<<"done."<<endl;
}

void testShortProtein() 
{
    // Biotype::initializePopularBiotypes();

    CompoundSystem system;
	SimbodyMatterSubsystem matter(system);
    DuMMForceFieldSubsystem dumm(system);
    DecorationSubsystem decorations(system);

    // ifstream tinkerStream("../../resources/tinker_amber99_clean.prm");
    // dumm.populateFromTinkerParameterFile(tinkerStream);
    // tinkerStream.close();
    dumm.loadAmber99Parameters();

    // Protein protein("ACDEFGHIKLMNPQRSTVWY");
    Protein protein("SPFGR");
    protein.assignBiotypes();

    protein.writeDefaultPdb(cout);

    system.adoptCompound(protein);

    system.modelCompounds();  

    State state = system.realizeTopology();
 
#ifdef CREATE_VIZ_WINDOW
    Visualizer viz(system);
    system.addEventReporter( new Visualizer::Reporter(viz, 0.005) );
#endif

    RungeKuttaMersonIntegrator study(system);

    study.initialize(state);

    int numberOfSteps = 3;

#ifdef CREATE_VIZ_WINDOW
    numberOfSteps = 1000;
#endif

    TimeStepper ts(system, study);
    ts.initialize(state);
    ts.stepTo(numberOfSteps * 0.0050);
}

int main() {
    testShortProtein();
    testIssue907();
}