structures.h

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#ifndef VIENNA_RNA_PACKAGE_STRUCT_UTILS_H
#define VIENNA_RNA_PACKAGE_STRUCT_UTILS_H

#ifdef VRNA_WARN_DEPRECATED
# if defined(__clang__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
# elif defined(__GNUC__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
# else
#  define DEPRECATED(func, msg) func
# endif
#else
# define DEPRECATED(func, msg) func
#endif

#include <stdio.h>

#include <ViennaRNA/datastructures/basic.h>

typedef struct vrna_hx_s vrna_hx_t;


typedef struct vrna_elem_prob_s vrna_ep_t;


#define VRNA_BRACKETS_ALPHA    4U


#define VRNA_BRACKETS_RND      8U


#define VRNA_BRACKETS_CLY      16U


#define VRNA_BRACKETS_ANG      32U


#define VRNA_BRACKETS_SQR      64U


#define VRNA_BRACKETS_DEFAULT  \
  (VRNA_BRACKETS_RND | \
   VRNA_BRACKETS_CLY | \
   VRNA_BRACKETS_ANG | \
   VRNA_BRACKETS_SQR)


#define VRNA_BRACKETS_ANY \
  (VRNA_BRACKETS_RND | \
   VRNA_BRACKETS_CLY | \
   VRNA_BRACKETS_ANG | \
   VRNA_BRACKETS_SQR | \
   VRNA_BRACKETS_ALPHA)


char *
vrna_db_pack(const char *struc);


char *
vrna_db_unpack(const char *packed);


void
vrna_db_flatten(char          *structure,
                unsigned int  options);


void
vrna_db_flatten_to(char         *string,
                   const char   target[3],
                   unsigned int options);


char *
vrna_db_from_ptable(short *pt);


char *
vrna_db_from_WUSS(const char *wuss);


char *
vrna_db_from_plist(vrna_ep_t    *pairs,
                   unsigned int n);


char *
vrna_db_to_element_string(const char *structure);


char *
vrna_db_pk_remove(const char *structure,
                  unsigned int options);

/* End dot-bracket interface */
short *
vrna_ptable(const char *structure);


short *
vrna_ptable_from_string(const char    *string,
                        unsigned int  options);


short *
vrna_pt_pk_get(const char *structure);


short *
vrna_ptable_copy(const short *pt);


short *
vrna_pt_ali_get(const char *structure);


short *
vrna_pt_snoop_get(const char *structure);


short *
vrna_pt_pk_remove(const short   *ptable,
                  unsigned int  options);

/* End pair table interface */
#define VRNA_PLIST_TYPE_BASEPAIR      0


#define VRNA_PLIST_TYPE_GQUAD         1


#define VRNA_PLIST_TYPE_H_MOTIF       2


#define VRNA_PLIST_TYPE_I_MOTIF       3


#define VRNA_PLIST_TYPE_UD_MOTIF      4


#define VRNA_PLIST_TYPE_STACK         5


struct vrna_elem_prob_s {
  int   i;    
  int   j;    
  float p;    
  int   type; 
};

vrna_ep_t *vrna_plist(const char  *struc,
                      float       pr);


vrna_ep_t *vrna_plist_from_probs(vrna_fold_compound_t *vc,
                                 double               cut_off);


/* End pair list interface */
struct vrna_hx_s {
  unsigned int  start;
  unsigned int  end;
  unsigned int  length;
  unsigned int  up5;
  unsigned int  up3;
};


vrna_hx_t *
vrna_hx_from_ptable(short *pt);


vrna_hx_t *
vrna_hx_merge(const vrna_hx_t *list,
              int             maxdist);


/* End helix list interface */
int *
vrna_loopidx_from_ptable(const short *pt);


int
vrna_bp_distance(const char *str1,
                 const char *str2);


double
vrna_dist_mountain(const char   *str1,
                   const char   *str2,
                   unsigned int p);


unsigned int *
vrna_refBPcnt_matrix(const short  *reference_pt,
                     unsigned int turn);


unsigned int *
vrna_refBPdist_matrix(const short   *pt1,
                      const short   *pt2,
                      unsigned int  turn);


char *
vrna_db_from_probs(const FLT_OR_DBL *pr,
                   unsigned int     length);


char
vrna_bpp_symbol(const float *x);


char *
vrna_db_from_bp_stack(vrna_bp_stack_t *bp,
                      unsigned int    length);


void
vrna_letter_structure(char            *structure,
                      vrna_bp_stack_t *bp,
                      unsigned int    length);


#define   VRNA_STRUCTURE_TREE_HIT             1U


#define   VRNA_STRUCTURE_TREE_SHAPIRO_SHORT   2U


#define   VRNA_STRUCTURE_TREE_SHAPIRO         3U


#define   VRNA_STRUCTURE_TREE_SHAPIRO_EXT     4U


#define   VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT  5U

#define   VRNA_STRUCTURE_TREE_EXPANDED        6U


char *
vrna_db_to_tree_string(const char   *structure,
                       unsigned int type);


char *
vrna_tree_string_unweight(const char *structure);


char *
vrna_tree_string_to_db(const char *tree);


/* End tree representations */
#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

/*###########################################*/
/*# deprecated functions below              #*/
/*###########################################*/

DEPRECATED(void assign_plist_from_db(vrna_ep_t  **pl,
                                     const char *struc,
                                     float      pr),
           "Use vrna_plist() instead");

DEPRECATED(char *pack_structure(const char *struc),
           "Use vrna_db_pack() instead");

DEPRECATED(char *unpack_structure(const char *packed),
           "Use vrna_db_unpack() instead");

DEPRECATED(short *make_pair_table(const char *structure),
           "Use vrna_ptable() instead");

DEPRECATED(short *make_pair_table_pk(const char *structure),
           "Use vrna_ptable_from_string() instead");

DEPRECATED(short *copy_pair_table(const short *pt),
           "Use vrna_ptable_copy() instead");

DEPRECATED(short *alimake_pair_table(const char *structure),
           "Use vrna_pt_ali_get() instead");

DEPRECATED(short *make_pair_table_snoop(const char *structure),
           "Use vrna_pt_snoop_get() instead");

DEPRECATED(int *make_loop_index_pt(short *pt),
           "Use vrna_loopidx_from_ptable() instead");

DEPRECATED(int bp_distance(const char *str1,
                           const char *str2),
           "Use vrna_bp_distance() instead");

DEPRECATED(unsigned int *make_referenceBP_array(short         *reference_pt,
                                                unsigned int  turn),
           "Use vrna_refBPcnt_matrix() instead");

DEPRECATED(unsigned int *compute_BPdifferences(short        *pt1,
                                               short        *pt2,
                                               unsigned int turn),
           "Use vrna_refBPdist_matrix() instead");

DEPRECATED(void  assign_plist_from_pr(vrna_ep_t   **pl,
                                      FLT_OR_DBL  *probs,
                                      int         length,
                                      double      cutoff),
           "Use vrna_plist_from_probs() instead");

DEPRECATED(void parenthesis_structure(char            *structure,
                                      vrna_bp_stack_t *bp,
                                      int             length),
           "Use vrna_parenthesis_structure() instead");

DEPRECATED(void parenthesis_zuker(char            *structure,
                                  vrna_bp_stack_t *bp,
                                  int             length),
           "Use vrna_parenthesis_zuker() instead");

DEPRECATED(void letter_structure(char             *structure,
                                 vrna_bp_stack_t  *bp,
                                 int              length),
           "Use vrna_letter_structure() instead");

DEPRECATED(void  bppm_to_structure(char         *structure,
                                   FLT_OR_DBL   *pr,
                                   unsigned int length),
           "Use vrna_db_from_probs() instead");

DEPRECATED(char    bppm_symbol(const float *x),
           "Use vrna_bpp_symbol() instead");

#endif

#endif