RNAlib-2.3.1
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 
59 float
60 vrna_fold(const char *sequence,
61  char *structure);
62 
85 float
86 vrna_circfold(const char *sequence,
87  char *structure);
88 
89 #ifdef VRNA_BACKWARD_COMPAT
90 
134 DEPRECATED(float
135 fold_par( const char *sequence,
136  char *structure,
137  vrna_param_t *parameters,
138  int is_constrained,
139  int is_circular));
140 
157 DEPRECATED(float fold( const char *sequence, char *structure));
158 
175 DEPRECATED(float circfold( const char *sequence, char *structure));
176 
177 
184 DEPRECATED(void free_arrays(void));
185 
186 
187 
194 DEPRECATED(void update_fold_params(void));
195 
202 DEPRECATED(void update_fold_params_par(vrna_param_t *parameters));
203 
209 DEPRECATED(void
210 export_fold_arrays( int **f5_p,
211  int **c_p,
212  int **fML_p,
213  int **fM1_p,
214  int **indx_p,
215  char **ptype_p));
216 
222 DEPRECATED(void
223 export_fold_arrays_par( int **f5_p,
224  int **c_p,
225  int **fML_p,
226  int **fM1_p,
227  int **indx_p,
228  char **ptype_p,
229  vrna_param_t **P_p));
230 
236 DEPRECATED(void
237 export_circfold_arrays( int *Fc_p,
238  int *FcH_p,
239  int *FcI_p,
240  int *FcM_p,
241  int **fM2_p,
242  int **f5_p,
243  int **c_p,
244  int **fML_p,
245  int **fM1_p,
246  int **indx_p,
247  char **ptype_p));
248 
254 DEPRECATED(void
255 export_circfold_arrays_par( int *Fc_p,
256  int *FcH_p,
257  int *FcI_p,
258  int *FcM_p,
259  int **fM2_p,
260  int **f5_p,
261  int **c_p,
262  int **fML_p,
263  int **fM1_p,
264  int **indx_p,
265  char **ptype_p,
266  vrna_param_t **P_p));
267 
268 
269 
270 /* finally moved the loop energy function declarations to this header... */
271 /* BUT: The functions only exist for backward compatibility reasons! */
272 /* You better include "loop_energies.h" and call the functions: */
273 /* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */
274 /* a pointer to the energy parameter data structure as additional argument */
275 
280 DEPRECATED(int LoopEnergy(int n1,
281  int n2,
282  int type,
283  int type_2,
284  int si1,
285  int sj1,
286  int sp1,
287  int sq1));
288 
293 DEPRECATED(int HairpinE(int size,
294  int type,
295  int si1,
296  int sj1,
297  const char *string));
298 
304 DEPRECATED(void initialize_fold(int length));
305 
309 DEPRECATED(char *backtrack_fold_from_pair(char *sequence,
310  int i,
311  int j));
312 
313 
314 #endif
315 
320 #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 vrna_circfold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequenc...
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:55
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence...
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. ...