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fold.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_FOLD_H
2 #define VIENNA_RNA_PACKAGE_FOLD_H
3
4 #include <ViennaRNA/data_structures.h>
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 *sequence,
56 char *structure);
57
80 float
81 vrna_circfold(const char *sequence,
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
free_arrays
void free_arrays(void)
Free arrays for mfe folding.
HairpinE
int HairpinE(int size, int type, int si1, int sj1, const char *string)
update_fold_params_par
void update_fold_params_par(vrna_param_t *parameters)
Recalculate energy parameters.
initialize_fold
void initialize_fold(int length)
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...
circfold
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence...
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
data_structures.h
params.h
vrna_fold
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence...
export_fold_arrays
void export_fold_arrays(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
fold
float fold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
export_circfold_arrays
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)
update_fold_params
void update_fold_params(void)
Recalculate energy parameters.
LoopEnergy
int LoopEnergy(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
fold_par
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.h
MFE calculations for single RNA sequences.
export_circfold_arrays_par
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)
export_fold_arrays_par
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)
eval.h
Functions and variables related to energy evaluation of sequence/structure pairs. ...