CIF.h

#ifndef _OBJCRYST_CIF_H
#define _OBJCRYST_CIF_H

#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <list>
#include <map>
#include <set>

#include "ObjCryst/Quirks/ci_string.h"
namespace ObjCryst
{// Forward declaration
   class CIF;
}
#include "ObjCryst/ObjCryst/PowderPattern.h" // For CreatePowderPatternFromCIF only.
#include "ObjCryst/ObjCryst/DiffractionDataSingleCrystal.h" // For CreateSingleCrystalDataFromCIF only.
#include "ObjCryst/ObjCryst/Crystal.h" // For CreateCrystalFromCIF only.
#include "ObjCryst/ObjCryst/General.h" // TO identify wavelength type in CIFData::ExtractPowderPattern.

namespace ObjCryst
{
REAL CIFNumeric2REAL(const std::string &s);
int CIFNumeric2Int(const std::string &s);

class CIFData
{
   public:
      CIFData();

      void ExtractAll(const bool verbose=false);
      void ExtractName(const bool verbose=false);
      void ExtractUnitCell(const bool verbose=false);
      void ExtractSpacegroup(const bool verbose=false);
      void ExtractAtomicPositions(const bool verbose=false);
      //  may be extracted in ExtractAtomicPositions. This takes prescedent.
      void ExtractAnisotropicADPs(const bool verbose=false);
      void ExtractPowderPattern(const bool verbose=false);
      void ExtractSingleCrystalData(const bool verbose=false);
      void Cartesian2FractionalCoord();
      void Fractional2CartesianCoord();
      void f2c(REAL &x,REAL &y, REAL &z);
      void c2f(REAL &x,REAL &y, REAL &z);
      void CalcMatrices(const bool verbose=false);
      std::list<std::string> mvComment;
      std::map<ci_string,std::string> mvItem;
      std::map<std::set<ci_string>,std::map<ci_string,std::vector<std::string> > > mvLoop;
      std::vector<REAL> mvLatticePar;
      std::string mSpacegroupNumberIT;
      std::string mSpacegroupSymbolHall;
      std::string mSpacegroupHermannMauguin;
      std::set<string> mvSymmetry_equiv_pos_as_xyz;
      std::string mName;
      std::string mFormula;
      struct CIFAtom
      {
         CIFAtom();
         std::string mLabel;
         std::string mSymbol;
         std::vector<REAL> mCoordFrac;
         std::vector<REAL> mCoordCart;
         REAL mOccupancy;

         std::vector<REAL> mBeta;

         REAL mBiso;
      };
      std::vector<CIFAtom> mvAtom;
      REAL mOrthMatrix[3][3];
      REAL mOrthMatrixInvert[3][3];
      std::vector<REAL> mPowderPatternObs,mPowderPatternX,mPowderPatternSigma;
      CrystVector_long mH,mK,mL;
      CrystVector_REAL mIobs,mSigma;
      WavelengthType mDataType;
      REAL mWavelength;
};

class CIF
{
   public:
      CIF(std::istream &in, const bool interpret=true,const bool verbose=false);
   //private:
      void Parse(std::stringstream &in);
      std::map<std::string,CIFData> mvData;
      std::list<std::string> mvComment;
};

// Forward declarations
class Crystal;
class PowderPattern;

Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose=true,const bool checkSymAsXYZ=true);

Crystal* CreateCrystalFromCIF(CIF &cif,const bool verbose,const bool checkSymAsXYZ, const bool oneScatteringPowerPerElement, const bool connectAtoms);

PowderPattern* CreatePowderPatternFromCIF(CIF &cif);

DiffractionDataSingleCrystal* CreateSingleCrystalDataFromCIF(CIF &cif, Crystal *pryst=0);

}

#endif