RNAlib-2.5.1
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
97float
99 char *structure);
100
101
117DEPRECATED(float
119 char *structure),
120 "Use vrna_mfe() instead");
121
122
153float
154vrna_fold(const char *sequence,
155 char *structure);
156
157
180float
181vrna_circfold(const char *sequence,
182 char *structure);
183
184
206float
207vrna_alifold(const char **sequences,
208 char *structure);
209
210
235float
236vrna_circalifold(const char **sequences,
237 char *structure);
238
239
264DEPRECATED(float
265 vrna_cofold(const char *sequence,
266 char *structure),
267 "USe vrna_fold() instead");
268
269
289int
290vrna_backtrack_from_intervals(vrna_fold_compound_t *vc,
291 vrna_bp_stack_t *bp_stack,
292 sect bt_stack[],
293 int s);
294
295
317float
319 unsigned int length,
320 char *structure);
321
322
323int
324vrna_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:148
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...