RNAlib-2.4.14
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>
5 #include <ViennaRNA/datastructures/basic.h>
6 #include <ViennaRNA/fold_compound.h>
7 
83 float
84 vrna_mfe(vrna_fold_compound_t *vc,
85  char *structure);
86 
87 
97 float
98 vrna_mfe_dimer(vrna_fold_compound_t *vc,
99  char *structure);
100 
101 
132 float
133 vrna_fold(const char *sequence,
134  char *structure);
135 
136 
159 float
160 vrna_circfold(const char *sequence,
161  char *structure);
162 
163 
185 float
186 vrna_alifold(const char **sequences,
187  char *structure);
188 
189 
214 float
215 vrna_circalifold(const char **sequences,
216  char *structure);
217 
218 
239 float
240 vrna_cofold(const char *sequence,
241  char *structure);
242 
243 
263 int
264 vrna_backtrack_from_intervals(vrna_fold_compound_t *vc,
265  vrna_bp_stack_t *bp_stack,
266  sect bt_stack[],
267  int s);
268 
269 
291 float
292 vrna_backtrack5(vrna_fold_compound_t *fc,
293  unsigned int length,
294  char *structure);
295 
296 
303 #endif
vrna_mfe_dimer
float vrna_mfe_dimer(vrna_fold_compound_t *vc, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
vrna_fold
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence...
vrna_alifold
float vrna_alifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
vrna_sect_s
Stack of partial structures for backtracking.
Definition: basic.h:134
basic.h
Various data structures and pre-processor macros.
vrna_mfe
float vrna_mfe(vrna_fold_compound_t *vc, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence, or RNA sequence alignment.
vrna_circfold
float vrna_circfold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequenc...
vrna_circalifold
float vrna_circalifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence a...
vrna_backtrack5
float vrna_backtrack5(vrna_fold_compound_t *fc, unsigned int length, char *structure)
Backtrack an MFE (sub)structure.
vrna_bp_stack_s
Base pair stack element.
Definition: basic.h:143
fold_compound.h
The Basic Fold Compound API.
vrna_cofold
float vrna_cofold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequ...