text: ///////////////////////////////////////////////////////////////////////////////////////////////
  //         Copyright (C) Regents of the University of Michigan - All Rights Reserved         //
  //          Unauthorized copying of this file, via any medium is strictly prohibited         //
  //                                                                                           //
  //                          Author: Robin Pearce <robpearc@umich.edu>                        //
  //                                                                                           //
  ///////////////////////////////////////////////////////////////////////////////////////////////
  
  #ifndef FRAGMENTS_H
  #define FRAGMENTS_H
  
  #include "CommonPara.h"
  #include "InputData.h"
  
  class Fragments
  {
    public:
      Fragments();
      virtual ~Fragments();   
  
      bool loadPISCES(char *selfile);
      bool loadSS2(char *ss2file,ssef *sssef,int seqlength);
      void normpSS2();
      void calcfragdh(int seqlength,char *outname,int segleng,int cuttop);
      void scoreFragments(seginfo **seginfall,int seqlength,InputData inputInfo,
                          char *dbfile,int segleng,int topleng,double *wtterm);
      bool generateFragments(char *dataDir,char *listName,InputData inputInfo,char *mtxDbName,
                             char *dbFeatName,char *outName,int fragSize);
      void calcfragdh(char *dataDir,int seqlength,char *outname,
                      int segleng,int cuttop);
      bool loadfragd(int numseq,int seglength,int ntop,char *filename);
  
    private:
      int numsel;
      int numhomo;
      int *homolist;
      int *dhcennum;
      point3f **fragcont[20];
      dihedral *fragdh[nosegdh];
      namep *namepdb;
      int oldseglength;
  };
  
  #endif
  