RNAlib-2.2.0RC0
fold.h
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1 #ifndef __VIENNA_RNA_PACKAGE_FOLD_H__
2 #define __VIENNA_RNA_PACKAGE_FOLD_H__
3 
5 #include <ViennaRNA/eval.h>
6 
7 #ifdef __GNUC__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #else
10 #define DEPRECATED(func) func
11 #endif
12 
96 DEPRECATED(float
97 fold_par( const char *sequence,
98  char *structure,
99  paramT *parameters,
100  int is_constrained,
101  int is_circular));
102 
142 float
144  char *structure);
145 
166 DEPRECATED(float fold( const char *sequence, char *structure));
167 
186 DEPRECATED(float circfold( const char *sequence, char *structure));
187 
188 
195 DEPRECATED(void free_arrays(void));
196 
197 
198 
206 DEPRECATED(void update_fold_params(void));
207 
216 DEPRECATED(void update_fold_params_par(paramT *parameters));
217 
223 void
224 vrna_update_fold_params(vrna_fold_compound *vc,
225  paramT *parameters);
226 
232 char *backtrack_fold_from_pair(char *sequence,
233  int i,
234  int j);
235 
236 plist *
237 vrna_backtrack_from_intervals(vrna_fold_compound *vc,
238  bondT *bp_stack,
239  sect bt_stack[],
240  int s);
241 
247 DEPRECATED(void
248 export_fold_arrays( int **f5_p,
249  int **c_p,
250  int **fML_p,
251  int **fM1_p,
252  int **indx_p,
253  char **ptype_p));
254 
260 DEPRECATED(void
261 export_fold_arrays_par( int **f5_p,
262  int **c_p,
263  int **fML_p,
264  int **fM1_p,
265  int **indx_p,
266  char **ptype_p,
267  paramT **P_p));
268 
274 DEPRECATED(void
275 export_circfold_arrays( int *Fc_p,
276  int *FcH_p,
277  int *FcI_p,
278  int *FcM_p,
279  int **fM2_p,
280  int **f5_p,
281  int **c_p,
282  int **fML_p,
283  int **fM1_p,
284  int **indx_p,
285  char **ptype_p));
286 
292 DEPRECATED(void
293 export_circfold_arrays_par( int *Fc_p,
294  int *FcH_p,
295  int *FcI_p,
296  int *FcM_p,
297  int **fM2_p,
298  int **f5_p,
299  int **c_p,
300  int **fML_p,
301  int **fM1_p,
302  int **indx_p,
303  char **ptype_p,
304  paramT **P_p));
305 
306 
307 
308 /* finally moved the loop energy function declarations to this header... */
309 /* BUT: The functions only exist for backward compatibility reasons! */
310 /* You better include "loop_energies.h" and call the functions: */
311 /* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */
312 /* a pointer to the energy parameter datastructure as additional argument */
313 
318 DEPRECATED(int LoopEnergy(int n1,
319  int n2,
320  int type,
321  int type_2,
322  int si1,
323  int sj1,
324  int sp1,
325  int sq1));
326 
331 DEPRECATED(int HairpinE(int size,
332  int type,
333  int si1,
334  int sj1,
335  const char *string));
336 
342 DEPRECATED(void initialize_fold(int length));
343 
344 #endif
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence...
void update_fold_params(void)
Recalculate energy parameters.
float fold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
The datastructure that contains temperature scaled energy parameters.
Definition: data_structures.h:180
Definition: data_structures.h:359
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
int LoopEnergy(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:94
void update_fold_params_par(paramT *parameters)
Recalculate energy parameters.
int HairpinE(int size, int type, int si1, int sj1, const char *string)
Base pair.
Definition: data_structures.h:122
Stack of partial structures for backtracking.
Definition: data_structures.h:113
float fold_par(const char *sequence, char *structure, paramT *parameters, int is_constrained, int is_circular)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
float vrna_fold(vrna_fold_compound *vc, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
void free_arrays(void)
Free arrays for mfe folding.
void initialize_fold(int length)
Functions and variables related to energy evaluation of sequence/structure pairs. ...