PeriodicPdbWriter.h

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/* -------------------------------------------------------------------------- *
 *                      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) 2008 Stanford University and the Authors.           *
 * Authors: Christopher Bruns                                                 *
 * Contributors:                                                              *
 *                                                                            *
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 * copy of this software and associated documentation files (the "Software"), *
 * to deal in the Software without restriction, including without limitation  *
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 * Software is furnished to do so, subject to the following conditions:       *
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 * The above copyright notice and this permission notice shall be included in *
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#ifndef SimTK_MOLMODEL_PERIODICPDBWRITER_H_
#define SimTK_MOLMODEL_PERIODICPDBWRITER_H_

#include "SimTKsimbody.h"
#include "molmodel/internal/Compound.h"
#include <iostream>
#include <iomanip>
#include <vector>

namespace SimTK {

class PeriodicPdbWriter : public PeriodicEventReporter {
public:
    PeriodicPdbWriter(
        const CompoundSystem& system, 
        std::ostream& outputStream,
        Real interval) 
        : PeriodicEventReporter(interval), 
          system(system), 
          outputStream(outputStream) 
    {}

    void handleEvent(const State& state) const {
        static int modelNumber = 1; // increments by one at each reporting step
        int nextAtomSerialNumber = 1; // atom serial number for each compound picks up where previous compound left off

        system.realize(state, Stage::Position);

        outputStream << "MODEL     " << std::setw(4) << modelNumber << std::endl;

        for (SimTK::CompoundSystem::CompoundIndex c(0); c < system.getNumCompounds(); ++c)
            system.getCompound(c).writePdb(state, outputStream, nextAtomSerialNumber);

        outputStream << "ENDMDL" << std::endl;
    
        //scf added time reporting 
                time_t rawtime;
                struct tm * timeinfo;
                time ( &rawtime );
                timeinfo = localtime ( &rawtime );
                outputStream <<"REMARK Current time is: "<<asctime (timeinfo) <<"REMARK elapsed time: "<<(clock()/CLOCKS_PER_SEC)<<std::endl;
                //outputStream <<"REMARK Energy :"<<system.calcEnergy(state)<<std::endl;
        //
    
        ++modelNumber;
    }

private:
    const CompoundSystem& system;
    std::ostream& outputStream;
};

} // namespace SimTK

#endif // SimTK_MOLMODEL_PERIODICPDBWRITER_H_