RNAlib-2.5.1
findpath.h
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1#ifndef VIENNA_RNA_PACKAGE_FIND_PATH_H
2#define VIENNA_RNA_PACKAGE_FIND_PATH_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
32
54int
56 const char *s1,
57 const char *s2,
58 int width);
59
60
87int
89 const char *s1,
90 const char *s2,
91 int width,
92 int maxE);
93
94
118 const char *s1,
119 const char *s2,
120 int width);
121
122
152 const char *s1,
153 const char *s2,
154 int width,
155 int maxE);
156
157
158#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
159
176DEPRECATED(int
177 find_saddle(const char *seq,
178 const char *s1,
179 const char *s2,
180 int width),
181 "Use vrna_path_findpath_saddle() instead!");
182
183
193DEPRECATED(void
194 free_path(vrna_path_t *path),
195 "Use vrna_path_free() instead!");
196
197
214DEPRECATED(vrna_path_t *
215 get_path(const char *seq,
216 const char *s1,
217 const char *s2,
218 int width),
219 "Use vrna_path_findpath() instead!");
220
221
222#endif
223
228#endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
int find_saddle(const char *seq, const char *s1, const char *s2, int width)
Find energy of a saddle point between 2 structures (search only direct path)
vrna_path_t * get_path(const char *seq, const char *s1, const char *s2, int width)
Find refolding path between 2 structures (search only direct path)
void free_path(vrna_path_t *path)
Free memory allocated by get_path() function.
vrna_path_t * vrna_path_findpath(vrna_fold_compound_t *fc, const char *s1, const char *s2, int width)
Find refolding path between 2 structures (search only direct path)
int vrna_path_findpath_saddle_ub(vrna_fold_compound_t *fc, const char *s1, const char *s2, int width, int maxE)
Find energy of a saddle point between 2 structures (search only direct path)
vrna_path_t * vrna_path_findpath_ub(vrna_fold_compound_t *fc, const char *s1, const char *s2, int width, int maxE)
Find refolding path between 2 structures (search only direct path)
int vrna_path_findpath_saddle(vrna_fold_compound_t *fc, const char *s1, const char *s2, int width)
Find energy of a saddle point between 2 structures (search only direct path)
An element of a refolding path list.
Definition: paths.h:108
API for computing (optimal) (re-)folding paths between secondary structures.