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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: *
* *
* 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_PERIODICPDBANDCOMWRITER_H_
#define SimTK_MOLMODEL_PERIODICPDBANDCOMWRITER_H_
#include "SimTKsimbody.h"
#include "molmodel/internal/Compound.h"
#include <iostream>
#include <iomanip>
#include <vector>
#include <list>
#include <stdio.h>
#include "RNATools/include/CenterOfMass.h"
namespace SimTK {
/// Writes atomic coordinates in PDB format to a file stream at
/// specified intervals during a simulation.
class PeriodicPdbAndCOMWriter : public PeriodicEventReporter {
public:
PeriodicPdbAndCOMWriter(
const CompoundSystem& system,
std::ostream& outputStream,
Real interval,
SimbodyMatterSubsystem & matter,//(system)
Biopolymer & myMolecule,
TinkerDuMMForceFieldSubsystem & dumm,
list<int> residueList
)
: PeriodicEventReporter(interval),
system(system),
outputStream(outputStream)
,matter(matter),
myMolecule(myMolecule),
dumm(dumm),
residueList(residueList)
{}
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::Compound::Index c(0); c < system.getNumCompounds(); ++c)
system.getCompound(c).writePdb(state, outputStream, nextAtomSerialNumber);
//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;
//
//scf added Geometric Center reporting
Vec3 helix2GC = CenterOfMass ( myMolecule , residueList, matter, state,dumm);
cout<<"REMARK Geometric Center ="<<helix2GC<<endl;
cout<<"REMARK Energy ="<<system.calcEnergy(state)<<endl;
printf ( "ATOM 1 GC GC C 1 %8.3f%8.3f%8.3f",helix2GC[0]*10,helix2GC[1]*10,helix2GC[2]*10);
char buffer [70];
sprintf (buffer,"ATOM 1 GC GC C 1 %8.3f%8.3f%8.3f",helix2GC[0]*10,helix2GC[1]*10,helix2GC[2]*10);
outputStream<<(string(buffer))<<endl;
//
outputStream << "ENDMDL" << std::endl;
++modelNumber;
}
private:
const CompoundSystem& system;
std::ostream& outputStream;
SimbodyMatterSubsystem & matter;
Biopolymer & myMolecule;
TinkerDuMMForceFieldSubsystem & dumm;
list<int> residueList ;
};
/*
*/
} // namespace SimTK
#endif // SimTK_MOLMODEL_PERIODICPDBWRITER_H_
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