delphi_datamarshal.h

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#ifndef CDELPHIDATAMARSHAL_H_
#define CDELPHIDATAMARSHAL_H_

#include <iostream>
#include <string>
#include <vector>
#include <array>
#include <memory> // std::unique_ptr for CIO

#include "../interface/interface_datacontainer.h"
#include "../interface/interface_datamarshal.h"
#include "../misc/misc_timer.h"
#include "../io/io.h"
#include "delphi_constants.h"
#include "delphi_exceptions.h"

using namespace std;

class CDelphiDataMarshal:virtual public IDataMarshal
{
   private:             
      //-----------------incl_delphimarshal_getStatement.cpp------------------//
      virtual bool getStatement(string strLineNoSpace);
      
      int yesno(string strArgument, string strStatement);

      //-----------------incl_delphimarshal_getFunction.cpp-------------------//
      virtual bool getFunction(string strLineNoSpace);   
        
      string getFile_Name_or_Format(string strArg_UpperCase,string strArg_fromInput);
      
      inline vector<string> getArguments(string strParameters);

      //----------------incl_delphimarshal_showParameters.cpp-----------------//

      void showParameters() const; 
       
   public:
      /*
       * delphi valid statements shown in user manual version 5.1
       * see the table of "index of statements and their shorthand" in the manual @ pp.19
       */

      //----------------------- set by Statements ------------------------//

      bool bAutoConverge;

      int iBndyType;

      delphi_real fPercentageFill;

      bool bFixedRelaxParam;

      bool bOutGraspSurf;

      int iConvergeFract;

      int iIterateInterval;

      bool bExitUniformDielect;

      delphi_real fExDielec;

      bool bCrgInterplateType;

      delphi_real fGridConverge;

      delphi_integer iGrid;

      delphi_real fInDielec;

      vector<delphi_real> vctfSalt;

      delphi_real fIonRadius;

      int iLinIterateNum;

      bool bLogGraph;

      bool bLogPotential;

      delphi_real fMaxc;

      int iNonIterateNum;

      vector<bool> vctbPeriodicBndy;

      bool bOutCrgDensity;

      vector<delphi_real> vctfProbeRadius;

      delphi_real fSpectralRadius;

      delphi_real fRelaxParam;

      delphi_real fRmsc;

      delphi_real fScale;

      bool bSolvePB;

      vector<int> vctiValence1;

      vector<int> vctiValence2;

      delphi_real fPotentialUpperBond;

      delphi_real fTemper;

      SGrid<delphi_real> gfPotentialDrop;

      bool bSpectralRadius;

      bool bManualRelaxParam;

      //-------------------------- io file names ------------------------//

      /* - IO type : IN
       * - F95 var.: prmnam
       * - Default : fort.10
       * - Description: \n
       * Default extension prm. Contains input parameters.
       */
      //string  strParamFile;      ///< prmnam(fort.10)
      //                           ///< input parameter file

      string strSizeFile;

      string strCrgFile;

      string strPdbFile;

      string strPhiFile;

      string strFrciFile;

      string strFrcFile;

      string strEpsFile;

      string strPhiiFile;

      string strModifiedPdbFile;

      string strUnformatPdbFile;

      string strUnformatFrcFile;

      string strGraspFile;

      string strEnergyFile;

      string strScrgFile;

      //----------------------- set by functions ------------------------//
      SGrid<delphi_real> gfOffCenter;

      SGrid<delphi_real> gfAcent;

      bool bIsAcent;

      int iPdbFormatIn;

      bool bPdbUnformatIn;

      // set by WRITE or OUT function

      bool bPhimapOut;

      int iPhiFormatOut;

      bool bBiosystemOut;

      bool bBemSrfOut;

      bool bSiteOut;

      int iFrcFormatOut;

      bool bEpsOut;

      bool bModPdbOut;

      int iModPdbFormatOut;

      bool bUnformatPdbOut;

      bool bUnformatFrcOut;

      bool bEngOut;

      bool bGridCrgOut;

      bool bHsurf2DatOut;

      bool bDbOut;

      bool bSurfEngOut;

      bool bSurfCrgOut;

      int iSurfCrgFormatOut;

      bool bGridEng;

      bool bSolvEng;

      bool bAnalySurfEng;

      bool bAnalyEng;

      bool bIonsEng;

      bool bCoulombEng;
  
      bool bAtomInSite;

      bool bCrgInSite;

      bool bGridPotentialInSite;

      bool bAtomPotentialInSite;

      bool bDebyeFractionInSite;

      bool bFieldInSite;

      bool bReactPotentialInSite;

      bool bCoulombPotentialInSite;

      bool bAtomCoordInSite;

      bool bSaltInSite;

      bool bTotalPotentialInSite;

      bool bReactForceInSite;

      bool bCoulombForceInSite;

      bool bMDInSite;

      bool bSurfCrgInSite;

      bool bTotalForceInSite;

      bool bPotentialInSite;

      bool bReactFieldInFRC;

      bool bPDB2FRCInSite;

      SExtrema<delphi_integer> eiBuffz;

      bool bIsBuffz;

      int iTypeSurf;

      //---------------------------- statements -------------------------//
      array<string,iStatementNum> rgstrStatement_ShortForm, rgstrStatement_2lAbbre;

      //------------------------------ functions ------------------------//
      array<string,iFunctionNum_FullName>   rgstrFunction_FullForm;
      array<string,iFunctionNum_ShortName>  rgstrFunction_ShortForm;

      //------------------------------ DelPhi ---------------------------//
      delphi_real fDebyeLength;

      delphi_real fEpsOut;

      SGrid<delphi_real> gfCoordinateRange;

      SGrid<delphi_real> gfGeometricCenter;

      SGrid<delphi_real> gfBoxCenter;

      delphi_real fIonStrength;

      delphi_real fTaylorCoeff1;

      delphi_real fTaylorCoeff2;

      delphi_real fTaylorCoeff3;

      delphi_real fTaylorCoeff4;

      delphi_real fTaylorCoeff5;

      bool bNonlinearEng;

      delphi_real fEPKT;

      delphi_real fEpsIn;

      bool bFrcUnformatIn;

      int iDirectEpsMap;

      delphi_integer iMoleculeNum;

      delphi_real fMaxRadius;

      bool bUniformDielec;

      vector< SExtrema<delphi_real> > vctefExtrema;

      vector< SGrid<delphi_real> > vctgfAtomCoordA;

      vector< SGrid<delphi_real> > vctgfAtomCoordG;

      //-------------------------------- IO -----------------------------//

      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;

      //------------------------------ Surface --------------------------//

      delphi_integer iCrgGridNum;

      delphi_real fNetCrg;

      delphi_real fMinusCrg;

      delphi_real fPlusCrg;

      SGrid<delphi_real> gfPlusCrgCenter;

      SGrid<delphi_real> gfMinusCrgCenter;

      SGrid<delphi_real> gfMinCoordinate;

      SGrid<delphi_real> gfMaxCoordinate;

      delphi_integer iBndyGridNum;

      vector< SGrid<delphi_integer> > vctgiEpsMap;

      vector<bool> vctbDielecMap;

      vector< SGrid<delphi_integer> > vctgiBndyGrid;

      delphi_integer iCrg2GridNum;

      vector< SGridValue<delphi_real> > vctgvfCrg2Grid;

      vector<delphi_integer> vctiCrg2GridMap;

      vector< SGridValue<delphi_real> > vctgvfAtomCrg;

      vector< SGrid<delphi_real> > vctgfCrgPoseA;

      vector< SGrid<delphi_real> > vctgfSurfCrgA;

      vector<delphi_integer> vctiCrgAt;

      vector<delphi_integer> vctiAtSurf;

      vector<delphi_integer> vctiAtNdx;

      vector< SGrid<delphi_real> > vctgfSurfCrgE;

      vector<delphi_real> vctfAtomEps;

      //------------------------------ Solver ---------------------------//

      delphi_integer iDielecBndySum;

      delphi_integer iCrgedGridSum;

      vector<delphi_real> vctfGridCrg;

      vector< SGrid<delphi_integer> > vctgiGridCrgPose;

      delphi_integer iCrgBdyGrid;

      vector<SDoubleGridValue> vctdgvCrgBndyGrid;

      vector<delphi_real> vctfPhiMap;

      //------------------------------ Energy ---------------------------//

      vector<delphi_real> vctfSurfCrgE;

      delphi_real fEngGrid;

      delphi_real fEngCoul;

      delphi_real fEngCorrect;

      delphi_real fEngReact;

      delphi_real fEngIons;

      //------------------------- NOT TO BE MAPPED ----------------------//  

      string strCentFile;

      delphi_real   fMaxDimension;

      shared_ptr<CTimer> pTimer;   //pointer to an object of CTimer class
         
      CDelphiDataMarshal(int argc,char* argv[],shared_ptr<CTimer> pt):IDataMarshal(argc,argv),pTimer(pt)
      {
#ifdef DEBUG_OBJECT
         cout << endl;
         cout << "****************************************************************\n";
         cout << "*             CDelphiDataMarshal is constructed                *\n";
         cout << "****************************************************************\n";
#endif

         setDefault();
      };

      CDelphiDataMarshal(shared_ptr<CTimer> pt):IDataMarshal(),pTimer(pt)
      {
#ifdef DEBUG_OBJECT
         cout << endl;
         cout << "****************************************************************\n";
         cout << "*             CDelphiDataMarshal is constructed                *\n";
         cout << "****************************************************************\n";
#endif

         setDefault();
      };

      ~CDelphiDataMarshal()
      {
#ifdef DEBUG_OBJECT
         cout << endl;
         cout << "****************************************************************\n";
         cout << "*                CDelphiDataMarshal is destroyed               *\n";
         cout << "****************************************************************\n";
#endif
      };

      void setDefault();

      virtual void updateParameters();
};

#endif // CDELPHIDATAMARSHAL_H_