- separated corr type into (cpp/h) combo

[alexxy/gromacs-spacetimecorr.git] / src / corrtype.h

diff --git a/src/corrtype.h b/src/corrtype.h
index fb8a41b6cddb39a1532acb69d2d57538d75491e9..1b09062135e5c9b34a75b781df45ec1aa70c22cf 100644 (file)
--- a/src/corrtype.h
+++ b/src/corrtype.h
@@ -1,11 +1,77 @@
 #ifndef CORRTYPE_H
 #define CORRTYPE_H
 
+#include <iostream>
+#include <vector>
+#include <cfloat>
 
-class corrtype
-{
-public:
-    corrtype();
+#include <gromacs/trajectoryanalysis.h>
+// #include <gromacs/trajectoryanalysis/topologyinformation.h>
+
+#include "/home/titov_ai/Develop/gromacs-original/src/gromacs/trajectoryanalysis/topologyinformation.h"
+
+#include "newfit.h"
+
+using namespace gmx;
+
+using gmx::RVec;
+
+
+class correlationType {
+
+    public:
+
+        // деструктор класса
+        ~correlationType();
+
+        // конструктор класса для инициализации
+        correlationType();
+
+        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);
+
+        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);
+
+        void update(int frame, std::vector< RVec > curFrame);
+
+        void printData();
+
+    private:
+
+        std::vector< std::vector< std::vector< double > > >                                     matrixes;
+        std::vector< std::vector< RVec > >                                                      trajectory;
+        std::vector< std::vector< RVec > >                                                      frankensteinTrajectory;
+        std::vector< std::vector< std::vector< RVec > > >                                       fitTrajectory;
+        std::vector< RVec >                                                                     reference;
+        int                                                                                     window      = 1000;         // selectable
+        int                                                                                     tau         = window / 2;   // selectable
+        int                                                                                     tauStep     = window / 10;  // selectable
+        float                                                                                   crlUpBorder = 0.5;          // selectable
+        float                                                                                   effRadius   = 1.5;          // selectable
+        int                                                                                     mode        = 0;            // selectable
+        std::string                                                                             outputName  = "";           // selectable
+        std::vector< int >                                                                      index;
+        std::vector< std::string >                                                              resNames;
+        std::vector< std::vector < std::vector < unsigned int > > >                             selections;
+        int                                                                                     count       = 0;
+
+        std::vector< std::vector< std::pair< double, int > > >                                  graph;
+        std::vector< std::vector< unsigned int > >                                              subGraphPoints;
+        std::vector< std::vector< std::pair< unsigned int, unsigned int > > >                   subGraphRbr;
+        std::vector< std::vector< std::vector< std::pair< unsigned int, unsigned int > > > >    subGraphRouts;
+
+        void trajectoryPartition();
+
+        void readWriteCorrelations(int rwMode);
+
+        void correlationEval();
+
+        void graphCalculations(unsigned int tauStart, unsigned int tauEnd);
+
+        static bool myComparisonFunction (const std::pair< int, double > i, const std::pair< int, double > j);
+
+        void graphBackBoneEvaluation();
+
+        void printOutputData();
 };
 
 #endif // CORRTYPE_H