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gdatastruct.h

Go to the documentation of this file.

#ifndef DATASTRUCT
#define DATASTRUCT



/* typedef struct _Epar_set{ */
/* typedef int tstack[NBPAIRS+1][NBPAIRS+1] _stack; */
/* typedef int[NBPAIRS+1][5][5] _mismatchI; */
/* typedef int[NBPAIRS+1][5][5] _mismatchH; */
/* typedef int[NBPAIRS+1][5] _dangle5; */
/* typedef int[NBPAIRS+1][5] _dangle3; */
/* typedef int[NBPAIRS+1][NBPAIRS+1][5][5] _Sint2; */
/* typedef int[11][2] _deep; */
/* typedef int[11][2] _shallow; */


typedef struct _baum{
  int nummer; /* of base in sequence */
  char looptype;
  int int_bps;
  int pk_flag;
  int pk_com;
  int no_dang;
  int deng;
  int col;
  unsigned short base; /* 0<->unknown, 1<->A, 2<->C, 3<->G, 4<->U */
  struct _baum *up;
  struct _baum *down;
  struct _baum *next[2];
  struct _baum *prev[2];
  struct _baum *next_bp[2];
  struct _baum *prev_bp[2];
}baum;

typedef struct _F_set{
  float startE;
  float stopE;
  double elotime;
  int elostep;
  int startlen;  
  double smt; 
  int smn;
  short starT ;/* 0 start structure is open chain, 1 specified start structure */
  short stoP ;     /* 1 specified stop structure */
  short noS ;     /* no structure output */
  short allS;
  short pS ;
  short mC ; /* 0 kawasaki rule, 1 metropolis rule */
}F_set;

typedef struct _E_set{
  short tetra_loop; 
  short james_rule; 
  short energy_set; 
  short logML;
  short new_ninio;
  short stack_bulge;
  int  dangles ; 
  
  
  /* _stack stack; */
  int **stack;
  int *hairpin;
  int *bulge;
  int *internal_loop;
  int ***mismatchI; 
  int ***mismatchH; 
  int **dangle5 ; 
  int **dangle3; 
  int ****Sint2; 
  int *F_ninio;
  double lxc;
  int MLbase;
  int MLintern;
  int MLclosing;
  int *TETRA_ENERGY;
  /* int Triloop_E[40]; */
  /* char *Triloops=Triloops_37; */
  char *Tetraloops;
  int MAX_NINIO;
  int Coax_const;
  int **deep; 
  int **shallow; 
}E_set;

typedef struct _M_set{
  short noGU ;  
  short no_closingGU ;  
  short do_pk;
  short do_flip;  
  short myturn;
}M_set;


typedef struct _mol{
  baum *vroot;
  char *seq;
  char *struc;

  char *currform;
  char *oldform;
  char *startform; /* array for start structure */
  char **stopform; /* array for stop structure */
  short *nei_list;
  double *bmf_list;
  int nei_cnt;

  E_set *e_info;
  M_set *m_info;
  F_set *f_info;

  float E1 ;
  double Zeit;
  int round ;
  int len ;   
  float temperature ;
  
}mol;

#endif

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