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#ifndef CifOutput_h
#define CifOutput_h
#include <BiopolymerClass.h>
#include <MonoAtoms.h>
#include <iostream>
#include <fstream>
#include <string>
#include "molmodel/internal/Compound.h"
#include "PeriodicPdbAndEnergyWriter.h"
#include "SimTKsimbody.h"
#include <gemmi/align.hpp>
namespace SimTK
{
namespace CIFOut
{
class Data {
public:
using Biopolymers = std::map<const String, BiopolymerClass>;
const Biopolymers& biopolymers;
const MonoAtomsContainer& monoatoms;
Data (const Biopolymers& biopolymers, const MonoAtomsContainer& monoatoms) :
biopolymers{biopolymers},
monoatoms{monoatoms}
{}
};
void buildModel ( const State& state, gemmi::Model& gModel, const Data &data, const CompoundSystem& system, int precision );
void writeOutCif ( const gemmi::Structure& outStruct, const std::string& fileName, const std::vector < std::pair < std::string, std::string > >& remarks );
void reWriteOutCif ( const gemmi::Model& gModel, const std::string& modelName, const std::string& fileName, ParameterReader& myParameterReader, const CompoundSystem& system, bool firstInStage );
} // End namespace CIFOut
} // End namespace SimTK
#endif /* CifOutput_h */
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