ReadData.h

#ifndef READDATA_H
#define READDATA_H

#include "XMLFile.h"
#include "SmallString.h"
#include "iostream.h"
#include "SimpleList.h"
#include <stdio.h>

#include "Restrain.h"

#include "global.h"


using namespace std;

//------------------

struct Atom
{

   REAL x;
   REAL y;
   REAL z;                   int id;
   int idFrg;

   int idLoc;
  CSmallString type;       
   bool ch; 
};


class CContrELECT;

//--------------------------

class CData
{

 public:

        CData();
        ~CData();


        void Read(char *name); 

        void Delete();
        void PrintSelf();
        void Prepare(); void Postpare();        

        void CheckAllRestraints();

        int GetNumber(int id,int *idFrg,int *idLoc);    

        void EnergyFunction(int ndim, const ColumnVector& X, REAL& E, int& result);     

        void InitComputation (int ndim, ColumnVector& x);
        void SetFilenamePDBall(CSmallString &str) { strFilePDBall=str; }; 
        void SetFilenamePDBfinal(CSmallString &str) { strFilePDBfinal=str; };
        CSmallString & GetFilenamePDBall() { return strFilePDBall; };


        CSmallString & GetFilenamePDBfinal() { return strFilePDBfinal;};

        void SetFilenameEnergyGraph(CSmallString &str) { strFileEnergyGraph=str; };

        CSmallString & GetFilenameEnergyGraph() { return strFileEnergyGraph;};

//----------------------------------------


void ApplyTransformsToAllAtoms(const ColumnVector & X);

        void ExportDataPDB(const ColumnVector & X, FILE *fout); 
        void ExportDataPDB(const ColumnVector & X, char *name); 
        void ExportDataXML(const ColumnVector & X, char *name);

        int numFragments;       // number of fragments
        int *nF;                // number of atomu in each fragment
        CSmallString *idF;      // fragments Identificators

        int masterFragment;     // number of Governing Fragment

        Atom **Atoms;           // atoms in all fragments (two-dimensional array)
        int ** changingAtoms;   // references to atom that are change because of restrains
        int *cntChangeAtom;     // number of atoms that are change because 
                                // of restrains in scope of restrain


        Point **points;         // structure for computing the points
        Point *centerF;         // center of Each fragments
        REAL *chargeF;          // charge of fragment
        bool *distribF;         // distribute charges to all atoms in fragment
//----------------------

        int numRestrains;               // number of restrains
        CRestrain **restrains;          // array of CRestrains
        CContrELECT *contrEl;           

        CSmallString strFilePDBall;     // filename for all sequences
        CSmallString strFilePDBfinal;   // filename for the last frame
        CSmallString strFileEnergyGraph;        // filename for the energy graph
        
        int numIterations;              //number of Iteration (number of calling function optimize)

        void SetNumIterations(int a) { numIterations=a; };      
        void IncrementNumIterations(int a=1) { numIterations+=a; };     

 private: 
        void CreateQuickReferences();
        void CreateTableOfChangingAtoms();
        void DestructTableOfChangingAtoms();
        void PrintTableOfChangingAtoms();
        void PrintCentersOfFragments();
        void PrintPoints();

        void CenterOutFragments();
        void GetMemForPoints();

        void ComputeCenterOfFragments();
        void OpenOutputFiles();
        void CloseOutputFiles();


        FILE *fout_all_PDB,*fout_final_PDB;
        FILE *fout_EnergyGraph;
        int DataReaded;
};


class CFitting
{
public:
    CFitting();
    ~CFitting();
    void Initialize(int argc, char ** argv);
    void Run();
    void Finalize();

    CData data;
    CClock aclock;
private: 
  int nDimension;
        void Print_help(FILE *stream, int exit_code);
        void ReadParameters(int argc, char ** argv);

  char output_file[100];
  char input_file[100];
  char output_file_allPDB[100];
  char output_file_energy[100];
  char input_file_finalPDB[100];
  char program_name[100];

  OptQNewton *objfcn;
  

};

#endif

---