RNAlib-2.3.4
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>
6 
7 
8 typedef void (vrna_mfe_window_callback)(int start,
9  int end,
10  const char *structure,
11  float en,
12  void *data);
13 
14 
15 #ifdef VRNA_WITH_SVM
16 typedef void (vrna_mfe_window_zscore_callback)(int start,
17  int end,
18  const char *structure,
19  float en,
20  float zscore,
21  void *data);
22 #endif
23 
51 float
53  char *structure);
54 
55 
68  char *structure);
69 
70 
99  FILE *file);
100 
101 
102 float vrna_mfe_window_cb(vrna_fold_compound_t *vc,
103  vrna_mfe_window_callback *cb,
104  void *data);
105 
106 
107 #ifdef VRNA_WITH_SVM
108 
136  double min_z,
137  FILE *file);
138 
139 
140 float vrna_mfe_window_zscore_cb(vrna_fold_compound_t *vc,
141  double min_z,
142  vrna_mfe_window_zscore_callback *cb,
143  void *data);
144 
145 
146 #endif
147 
148 void
149 vrna_backtrack_from_intervals(vrna_fold_compound_t *vc,
150  vrna_bp_stack_t *bp_stack,
151  sect bt_stack[],
152  int s);
153 
154 
155 #endif
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:457
Stack of partial structures for backtracking.
Definition: data_structures.h:214
Various data structures and pre-processor macros.
float vrna_mfe_window(vrna_fold_compound_t *vc, FILE *file)
Local MFE prediction using a sliding window approach.
float vrna_mfe_dimer(vrna_fold_compound_t *vc, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
Base pair stack element.
Definition: data_structures.h:223
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.
float vrna_mfe_window_zscore(vrna_fold_compound_t *vc, double min_z, FILE *file)
Local MFE prediction using a sliding window approach (with z-score cut-off)