io.h

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#ifndef CIO_H_
#define CIO_H_

#include <iostream>
#include <iomanip>
#include <fstream>
#include <string>   // std::string
#include <vector>   // std::vector
#include <locale>
#include <stdlib.h> // atof
#include <cmath>

#include "../interface/environment.h"
#include "../misc/misc_grid.h"
#include "io_datatype.h"
#include "io_exceptions.h"

using namespace std;

const int SIZEFILE   = 1;
const int CHARGEFILE = 2;

const int STDPDB     = 10;
const int MODPDB     = 20;
const int PQRPDB     = 21;
const int MOD4PDB    = 30;
const int PQR4PDB    = 31;

class CIO
{
   protected:
      const delphi_real fDielec;

      const delphi_real fEPKT;

      /*
       * ******************** miscellany functions defined in io_misc.cpp *******************
       */

      string toUpperCase(const string& strLine);

      string removeSpace(const string& strLine);

      bool checkFileFormat(const string& strFile);
                 
      /*
       * ******************* for reading atom force (radii/size and charge) file *******************
       * ********** these static attributes are declared here and defined in io_force.cpp **********
       */

      static delphi_integer iRadiusNum;

      static vector<CForce> prgas;

      static delphi_integer iCrgNum;

      static vector<CForce> prgac;

      void readFileInNotPKFormat(ifstream& ifFileStream, const int& iFileType);

      void readFileInPKFormat(ifstream& ifFileStream, const int& iFileType);

#ifdef DEBUG_IO_FORCE

      void printForce(const int& iFileType, const vector<CForce>& prgaf);
#endif

      delphi_integer FindRecordIndex(const string& strAtom,const string& strResidue,const string& strResidueNum,
                                     const string& strChain,const delphi_integer& iRecordNum,vector<CForce>* prgaf);

      delphi_integer FindRecord(const string& strAtom,const string& strResidue,const string& strResidueNum,
                                const string& strChain,const int& iFileType, delphi_real& fValue);

      //void checkCharge(const bool& bSurfCrgInSite);

      /*
       * ********** functions defined in io_pdb.cpp for reading PDB file in various formats ********
       */

      delphi_integer iObjectMediaNum;

      void readStdPdbFile(ifstream& ifPdbFileStream);

      void readModFile1(ifstream& ifPdbFileStream);

      void readModFile4(ifstream& ifPdbFileStream);

      void readPqrFile(ifstream& ifPdbFileStream);

      void readMod4File(ifstream& ifPdbFileStream);

      void readPqr4File(ifstream& ifPdbFileStream);

      void readUnformattedPdb(const string& strPdbFile,ifstream& ifPdbFileStream,bool& bPostProcess);
                              
#ifdef DEBUG_IO_PDB

      void printPDB();                        
#endif
           
      bool    bExistRadiiInfo;

      vector<delphi_integer> prgiObjectMediaNum;

   public:     

      delphi_integer    iMediaNum;

      delphi_integer    iObjectNum;

      delphi_integer    iAtomNum;

      delphi_integer    iResidueNum;

      bool       bOnlyMolecule;

      vector<CAtomPdb> vctapAtomPdb;

      vector<delphi_real>    vctfMediaEps;

      vector<string>  vctstrObject;

      vector<delphi_integer> vctiAtomMediaNum;

      CIO():fDielec(4.0),fEPKT(167100.9162872952/297.3342119)
      {     
#ifdef DEBUG_OBJECT
         cout << endl;
         cout << "****************************************************************\n";
         cout << "*                     CIO is constructed                       *\n";
         cout << "****************************************************************\n";
#endif

         //iRadiusNum      = 0;
         //iCrgNum         = 0;
         iMediaNum       = 1;
         iObjectNum      = 1;  
         iAtomNum        = 0;
         iObjectMediaNum = 1;
         bOnlyMolecule   = true;
         bExistRadiiInfo = false;
         iResidueNum     = 0;        
      };

      CIO(delphi_real fDielecIn,delphi_real fEPKTIn):fDielec(fDielecIn),fEPKT(fEPKTIn)
      {
#ifdef DEBUG_OBJECT
         cout << endl;
         cout << "****************************************************************\n";
         cout << "*                     CIO is constructed                       *\n";
         cout << "****************************************************************\n";
#endif

         //iRadiusNum      = 0;
         //iCrgNum         = 0;
         iMediaNum       = 1;
         iObjectNum      = 1;  
         iAtomNum        = 0;
         iObjectMediaNum = 1;
         bOnlyMolecule   = true;
         bExistRadiiInfo = false;
         iResidueNum     = 0;        
      };
      
      ~CIO()
      {
#ifdef DEBUG_OBJECT
         cout << endl;
         cout << "****************************************************************\n";
         cout << "*                      CIO is destroyed                        *\n";
         cout << "****************************************************************\n";
#endif
      };


      void readForceFile(const string& strFile);

      void readPdbFile(const string& strPdbFile,const int& iPdbFormat,const bool& bPdbUnformat);

      void writeUnformatPdb(const string& strPdbFile);

      void writeModifiedPdb(const string& strPdbFile,const int& iModPdbFormatOut);
                       
      /*
       * miscellany
       */

      void setDelphiAtom(const bool& bSolvePB,const bool& bSurfCrgInSite,const string& strSizeFile,
                         const string& strCrgFile,const string& strPdbFile,const int& iPdbFormat,
                         const bool& bPdbUnformat);
                                                 
      SGrid<delphi_real> readFrcFile(const string& strFrcFile,const SGrid<delphi_real>& fgOffCenter,
                                     const delphi_real& fScale);

      void writeEpsMap(const delphi_integer& iAtomNumIn,const delphi_integer& iObjectNumIn,
                       const delphi_integer& iGrid,const delphi_real& fScale,const SGrid<delphi_real>& fgBoxCenter,
                       const vector< SGrid<delphi_integer> >& vctigEpsMap,const vector<bool>& vctbDielecMap,
                       const string& strEpsFile);
      
      /*
       * for reading/writing PHI file
       */

      /*
       *for writing ENERGY file
       */

      /*
       * for writing HSURF2 file
       */

      /*
       *for writing SURFEN file
       */

      /*
       * for writing SCRG file
       */

};

#endif // CIO_H_