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#ifndef PeriodicPdbSingleFrameWriter_H_
#define PeriodicPdbSingleFrameWriter_H_
/* -------------------------------------------------------------------------- *
* 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: *
* *
* 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. *
* -------------------------------------------------------------------------- */
//#ifndef SimTK_MOLMODEL_PERIODICPDBWRITER_H_
//#define SimTK_MOLMODEL_PERIODICPDBWRITER_H_
#include <cstdio>
#include "SimTKsimbody.h"
#include "molmodel/internal/Compound.h"
//#include "DistanceMatrix.h"
#include <iostream>
#include <fstream>
#include <iomanip>
#include <vector>
//using namespace std;
namespace SimTK
{
/// Writes atomic coordinates in PDB format to a file stream at
/// specified intervals during a simulation.
class PeriodicPdbAndEnergySingleFrameWriter : public PeriodicEventReporter {
public:
PeriodicPdbAndEnergySingleFrameWriter(
const CompoundSystem& system,
char* outputFrameFileName, //std::ostream& outputStream,
Real interval)
: PeriodicEventReporter(interval),
system(system),
outputFrameFileName(outputFrameFileName)
{}
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);
std::ofstream outputStream;
outputStream.open( outputFrameFileName);
//std::ostream outputStream(outputFrameFileName);
outputStream << "MODEL " << std::setw(4) << modelNumber << std::endl;
//cout<<"[PeriodicPdbAndEnergySingleFrameWriter.h] check 1"<<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.setf(ios::fixed, ios::floatfield); // set output to fixed rather than scientific format
//outputStream <<"REMARK Energy = "<<system.calcEnergy(state) <<std::endl;
outputStream.close();
++modelNumber;
}
private:
const CompoundSystem& system;
//std::ostream& outputStream;
char* outputFrameFileName;// outputStream(outputStream)
};
} // namespace SimTK
//#endif // SimTK_MOLMODEL_PERIODICPDBWRITER_H_
#endif
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