RNAlib-2.5.0
mfe.h
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1 #ifndef VIENNA_RNA_PACKAGE_MFE_H
2 #define VIENNA_RNA_PACKAGE_MFE_H
3 
4 #include <stdio.h>
7 
8 #ifdef VRNA_WARN_DEPRECATED
9 # if defined(__clang__)
10 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
11 # elif defined(__GNUC__)
12 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
13 # else
14 # define DEPRECATED(func, msg) func
15 # endif
16 #else
17 # define DEPRECATED(func, msg) func
18 #endif
19 
20 
97 float
99  char *structure);
100 
101 
117 DEPRECATED(float
119  char *structure),
120  "Use vrna_mfe() instead");
121 
122 
153 float
154 vrna_fold(const char *sequence,
155  char *structure);
156 
157 
180 float
181 vrna_circfold(const char *sequence,
182  char *structure);
183 
184 
206 float
207 vrna_alifold(const char **sequences,
208  char *structure);
209 
210 
235 float
236 vrna_circalifold(const char **sequences,
237  char *structure);
238 
239 
264 DEPRECATED(float
265  vrna_cofold(const char *sequence,
266  char *structure),
267  "USe vrna_fold() instead");
268 
269 
289 int
290 vrna_backtrack_from_intervals(vrna_fold_compound_t *vc,
291  vrna_bp_stack_t *bp_stack,
292  sect bt_stack[],
293  int s);
294 
295 
317 float
319  unsigned int length,
320  char *structure);
321 
322 
323 int
324 vrna_backtrack_window(vrna_fold_compound_t *fc,
325  const char *Lfold_filename,
326  long file_pos,
327  char **structure,
328  double mfe);
329 
330 
337 #endif
Various data structures and pre-processor macros.
The Basic Fold Compound API.
Base pair stack element.
Definition: basic.h:143
Stack of partial structures for backtracking.
Definition: basic.h:134
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
float vrna_backtrack5(vrna_fold_compound_t *fc, unsigned int length, char *structure)
Backtrack an MFE (sub)structure.
float vrna_circalifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence a...
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence.
float vrna_alifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
float vrna_cofold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequ...
float vrna_mfe_dimer(vrna_fold_compound_t *vc, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
float vrna_mfe(vrna_fold_compound_t *vc, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence,...
float vrna_circfold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequenc...