src/corrtype.h

   1 #ifndef CORRTYPE_H
   2 #define CORRTYPE_H
   3
   4 #include <iostream>
   5 #include <vector>
   6 #include <cfloat>
   7
   8 #include <gromacs/trajectoryanalysis.h>
   9 // #include <gromacs/trajectoryanalysis/topologyinformation.h>
  10
  11 #include "/home/titov_ai/Develop/gromacs-original/src/gromacs/trajectoryanalysis/topologyinformation.h"
  12
  13 #include "newfit.h"
  14
  15 using namespace gmx;
  16
  17 using gmx::RVec;
  18
  19
  20 class correlationType {
  21
  22     public:
  23
  24         // деструктор класса
  25         ~correlationType();
  26
  27         // конструктор класса для инициализации
  28         correlationType();
  29
  30         correlationType(std::vector< RVec > ref, int wnd, int taau, int tau_st, float crlUp, float effRad, int mod, std::string out, std::vector< std::vector < std::vector < unsigned int > > > sels, std::vector< std::string > rsNames);
  31
  32         void setDefaults(std::vector< RVec > ref, int wnd, int taau, int tau_st, float crlUp, float effRad, int mod, std::string out, std::vector< std::vector < std::vector < unsigned int > > > sels, std::vector< std::string > rsNames);
  33
  34         void update(int frame, std::vector< RVec > curFrame);
  35
  36         void printData();
  37
  38     private:
  39
  40         std::vector< std::vector< std::vector< double > > >                                     matrixes;
  41         std::vector< std::vector< RVec > >                                                      trajectory;
  42         std::vector< std::vector< RVec > >                                                      frankensteinTrajectory;
  43         std::vector< std::vector< std::vector< RVec > > >                                       fitTrajectory;
  44         std::vector< RVec >                                                                     reference;
  45         int                                                                                     window      = 1000;         // selectable
  46         int                                                                                     tau         = window / 2;   // selectable
  47         int                                                                                     tauStep     = window / 10;  // selectable
  48         float                                                                                   crlUpBorder = 0.5;          // selectable
  49         float                                                                                   effRadius   = 1.5;          // selectable
  50         int                                                                                     mode        = 0;            // selectable
  51         std::string                                                                             outputName  = "";           // selectable
  52         std::vector< int >                                                                      index;
  53         std::vector< std::string >                                                              resNames;
  54         std::vector< std::vector < std::vector < unsigned int > > >                             selections;
  55         int                                                                                     count       = 0;
  56
  57         std::vector< std::vector< std::pair< double, int > > >                                  graph;
  58         std::vector< std::vector< unsigned int > >                                              subGraphPoints;
  59         std::vector< std::vector< std::pair< unsigned int, unsigned int > > >                   subGraphRbr;
  60         std::vector< std::vector< std::vector< std::pair< unsigned int, unsigned int > > > >    subGraphRouts;
  61
  62         void trajectoryPartition();
  63
  64         void readWriteCorrelations(int rwMode);
  65
  66         void correlationEval();
  67
  68         void graphCalculations(unsigned int tauStart, unsigned int tauEnd);
  69
  70         static bool myComparisonFunction (const std::pair< int, double > i, const std::pair< int, double > j);
  71
  72         void graphBackBoneEvaluation();
  73
  74         void printOutputData();
  75 };
  76
  77 #endif // CORRTYPE_H