RNAlib-2.2.7
fold.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_FOLD_H
2 #define VIENNA_RNA_PACKAGE_FOLD_H
3 
5 #include <ViennaRNA/params.h>
6 #include <ViennaRNA/mfe.h>
7 #include <ViennaRNA/eval.h>
8 
9 #ifdef DEPRECATION_WARNINGS
10 # ifdef __GNUC__
11 # define DEPRECATED(func) func __attribute__ ((deprecated))
12 # else
13 # define DEPRECATED(func) func
14 # endif
15 #else
16 # define DEPRECATED(func) func
17 #endif
18 
19 /* make this interface backward compatible with RNAlib < 2.2.0 */
20 #define VRNA_BACKWARD_COMPAT
21 
54 float
55 vrna_fold(const char *string,
56  char *structure);
57 
80 float
81 vrna_circfold(const char *string,
82  char *structure);
83 
84 #ifdef VRNA_BACKWARD_COMPAT
85 
129 DEPRECATED(float
130 fold_par( const char *sequence,
131  char *structure,
132  vrna_param_t *parameters,
133  int is_constrained,
134  int is_circular));
135 
152 DEPRECATED(float fold( const char *sequence, char *structure));
153 
170 DEPRECATED(float circfold( const char *sequence, char *structure));
171 
172 
179 DEPRECATED(void free_arrays(void));
180 
181 
182 
189 DEPRECATED(void update_fold_params(void));
190 
197 DEPRECATED(void update_fold_params_par(vrna_param_t *parameters));
198 
204 DEPRECATED(void
205 export_fold_arrays( int **f5_p,
206  int **c_p,
207  int **fML_p,
208  int **fM1_p,
209  int **indx_p,
210  char **ptype_p));
211 
217 DEPRECATED(void
218 export_fold_arrays_par( int **f5_p,
219  int **c_p,
220  int **fML_p,
221  int **fM1_p,
222  int **indx_p,
223  char **ptype_p,
224  vrna_param_t **P_p));
225 
231 DEPRECATED(void
232 export_circfold_arrays( int *Fc_p,
233  int *FcH_p,
234  int *FcI_p,
235  int *FcM_p,
236  int **fM2_p,
237  int **f5_p,
238  int **c_p,
239  int **fML_p,
240  int **fM1_p,
241  int **indx_p,
242  char **ptype_p));
243 
249 DEPRECATED(void
250 export_circfold_arrays_par( int *Fc_p,
251  int *FcH_p,
252  int *FcI_p,
253  int *FcM_p,
254  int **fM2_p,
255  int **f5_p,
256  int **c_p,
257  int **fML_p,
258  int **fM1_p,
259  int **indx_p,
260  char **ptype_p,
261  vrna_param_t **P_p));
262 
263 
264 
265 /* finally moved the loop energy function declarations to this header... */
266 /* BUT: The functions only exist for backward compatibility reasons! */
267 /* You better include "loop_energies.h" and call the functions: */
268 /* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */
269 /* a pointer to the energy parameter datastructure as additional argument */
270 
275 DEPRECATED(int LoopEnergy(int n1,
276  int n2,
277  int type,
278  int type_2,
279  int si1,
280  int sj1,
281  int sp1,
282  int sq1));
283 
288 DEPRECATED(int HairpinE(int size,
289  int type,
290  int si1,
291  int sj1,
292  const char *string));
293 
299 DEPRECATED(void initialize_fold(int length));
300 
304 DEPRECATED(char *backtrack_fold_from_pair(char *sequence,
305  int i,
306  int j));
307 
308 
309 #endif
310 
315 #endif
void free_arrays(void)
Free arrays for mfe folding.
int HairpinE(int size, int type, int si1, int sj1, const char *string)
void update_fold_params_par(vrna_param_t *parameters)
Recalculate energy parameters.
void initialize_fold(int length)
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence...
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
float vrna_fold(const char *string, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence...
float vrna_circfold(const char *string, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequenc...
void export_fold_arrays(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
float fold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
void export_circfold_arrays(int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
void update_fold_params(void)
Recalculate energy parameters.
int LoopEnergy(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
float fold_par(const char *sequence, char *structure, vrna_param_t *parameters, int is_constrained, int is_circular)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
MFE calculations for single RNA sequences.
void export_circfold_arrays_par(int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p, vrna_param_t **P_p)
void export_fold_arrays_par(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p, vrna_param_t **P_p)
Functions and variables related to energy evaluation of sequence/structure pairs. ...