RNAlib-2.4.14
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 
30 #include <ViennaRNA/fold_compound.h>
31 #include <ViennaRNA/landscape/paths.h>
32 
54 int
55 vrna_path_findpath_saddle(vrna_fold_compound_t *fc,
56  const char *s1,
57  const char *s2,
58  int width);
59 
60 
87 int
88 vrna_path_findpath_saddle_ub(vrna_fold_compound_t *fc,
89  const char *s1,
90  const char *s2,
91  int width,
92  int maxE);
93 
94 
116 vrna_path_t *
117 vrna_path_findpath(vrna_fold_compound_t *fc,
118  const char *s1,
119  const char *s2,
120  int width);
121 
122 
150 vrna_path_t *
151 vrna_path_findpath_ub(vrna_fold_compound_t *fc,
152  const char *s1,
153  const char *s2,
154  int width,
155  int maxE);
156 
157 
158 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
159 
176 DEPRECATED(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 
193 DEPRECATED(void
194  free_path(vrna_path_t *path),
195  "Use vrna_path_free() instead!");
196 
197 
214 DEPRECATED(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
vrna_path_findpath_saddle_ub
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_findpath
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)
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
vrna_path_s
An element of a refolding path list.
Definition: paths.h:108
paths.h
API for computing (optimal) (re-)folding paths between secondary structures.
find_saddle
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_findpath_saddle
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)
get_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)
vrna_path_findpath_ub
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)
fold_compound.h
The Basic Fold Compound API.
free_path
void free_path(vrna_path_t *path)
Free memory allocated by get_path() function.