RNAlib-2.6.3
 
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paths.h
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1#ifndef VIENNA_RNA_PACKAGE_PATHS_H
2#define VIENNA_RNA_PACKAGE_PATHS_H
3
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(__clang__)
6# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
7# elif defined(__GNUC__)
8# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
9# else
10# define DEPRECATED(func, msg) func
11# endif
12#else
13# define DEPRECATED(func, msg) func
14#endif
15
42typedef struct vrna_path_s vrna_path_t;
43
44
49typedef struct vrna_path_options_s *vrna_path_options_t;
50
51
52#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
53
59DEPRECATED(typedef struct vrna_path_s path_t,
60 "Use vrna_path_t instead!");
61
62#endif
63
66
72#define VRNA_PATH_TYPE_DOT_BRACKET 1U
73
79#define VRNA_PATH_TYPE_MOVES 2U
80
111 unsigned int type;
121 double en;
122 char *s;
124};
125
126
134void
136
137
145void
147
148
179 unsigned int type);
180
181
209 const char *s1,
210 const char *s2,
211 vrna_path_options_t options);
212
213
238 const char *s1,
239 const char *s2,
240 int maxE,
241 vrna_path_options_t options);
242
243
246#endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
An atomic representation of the transition / move from one structure to its neighbor.
Definition move.h:78
vrna_path_options_t vrna_path_options_findpath(int width, unsigned int type)
Create options data structure for findpath direct (re-)folding path heuristic.
vrna_path_t * vrna_path_direct_ub(vrna_fold_compound_t *fc, const char *s1, const char *s2, int maxE, vrna_path_options_t options)
Determine an optimal direct (re-)folding path between two secondary structures.
vrna_path_t * vrna_path_direct(vrna_fold_compound_t *fc, const char *s1, const char *s2, vrna_path_options_t options)
Determine an optimal direct (re-)folding path between two secondary structures.
vrna_move_t move
Move that transforms the previous structure into it's next neighbor along the path.
Definition paths.h:123
char * s
Secondary structure in dot-bracket notation.
Definition paths.h:122
unsigned int type
The type of the path element.
Definition paths.h:111
double en
Free energy of current structure.
Definition paths.h:121
void vrna_path_free(vrna_path_t *path)
Release (free) memory occupied by a (re-)folding path.
void vrna_path_options_free(vrna_path_options_t options)
Release (free) memory occupied by an options data structure for (re-)folding path implementations.
struct vrna_path_options_s * vrna_path_options_t
Options data structure for (re-)folding path implementations.
Definition paths.h:49
An element of a refolding path list.
Definition paths.h:110
Methods to operate with structural neighbors of RNA secondary structures.