RNAlib-2.2.0-RC2
fold.h
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1 #ifndef VIENNA_RNA_PACKAGE_FOLD_H
2 #define VIENNA_RNA_PACKAGE_FOLD_H
3 
5 #include <ViennaRNA/params.h>
6 #include <ViennaRNA/eval.h>
7 
8 #ifdef __GNUC__
9 #define DEPRECATED(func) func __attribute__ ((deprecated))
10 #else
11 #define DEPRECATED(func) func
12 #endif
13 
14 /* make this interface backward compatible with RNAlib < 2.2.0 */
15 #define VRNA_BACKWARD_COMPAT
16 
73 float
75  char *structure);
76 
82 void
83 vrna_update_fold_params(vrna_fold_compound *vc,
84  vrna_param_t *parameters);
85 
86 plist *
87 vrna_backtrack_from_intervals(vrna_fold_compound *vc,
88  bondT *bp_stack,
89  sect bt_stack[],
90  int s);
91 
92 #ifdef VRNA_BACKWARD_COMPAT
93 
139 DEPRECATED(float
140 fold_par( const char *sequence,
141  char *structure,
142  vrna_param_t *parameters,
143  int is_constrained,
144  int is_circular));
145 
164 DEPRECATED(float fold( const char *sequence, char *structure));
165 
184 DEPRECATED(float circfold( const char *sequence, char *structure));
185 
186 
194 DEPRECATED(void free_arrays(void));
195 
196 
197 
205 DEPRECATED(void update_fold_params(void));
206 
215 DEPRECATED(void update_fold_params_par(vrna_param_t *parameters));
216 
223 DEPRECATED(void
224 export_fold_arrays( int **f5_p,
225  int **c_p,
226  int **fML_p,
227  int **fM1_p,
228  int **indx_p,
229  char **ptype_p));
230 
237 DEPRECATED(void
238 export_fold_arrays_par( int **f5_p,
239  int **c_p,
240  int **fML_p,
241  int **fM1_p,
242  int **indx_p,
243  char **ptype_p,
244  vrna_param_t **P_p));
245 
252 DEPRECATED(void
253 export_circfold_arrays( int *Fc_p,
254  int *FcH_p,
255  int *FcI_p,
256  int *FcM_p,
257  int **fM2_p,
258  int **f5_p,
259  int **c_p,
260  int **fML_p,
261  int **fM1_p,
262  int **indx_p,
263  char **ptype_p));
264 
271 DEPRECATED(void
272 export_circfold_arrays_par( int *Fc_p,
273  int *FcH_p,
274  int *FcI_p,
275  int *FcM_p,
276  int **fM2_p,
277  int **f5_p,
278  int **c_p,
279  int **fML_p,
280  int **fM1_p,
281  int **indx_p,
282  char **ptype_p,
283  vrna_param_t **P_p));
284 
285 
286 
287 /* finally moved the loop energy function declarations to this header... */
288 /* BUT: The functions only exist for backward compatibility reasons! */
289 /* You better include "loop_energies.h" and call the functions: */
290 /* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */
291 /* a pointer to the energy parameter datastructure as additional argument */
292 
297 DEPRECATED(int LoopEnergy(int n1,
298  int n2,
299  int type,
300  int type_2,
301  int si1,
302  int sj1,
303  int sp1,
304  int sq1));
305 
310 DEPRECATED(int HairpinE(int size,
311  int type,
312  int si1,
313  int sj1,
314  const char *string));
315 
322 DEPRECATED(void initialize_fold(int length));
323 
329 DEPRECATED(char *backtrack_fold_from_pair(char *sequence,
330  int i,
331  int j));
332 
333 
334 #endif
335 
336 #endif
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.
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 most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:689
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)
void update_fold_params_par(vrna_param_t *parameters)
Recalculate energy parameters.
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:45
int HairpinE(int size, int type, int si1, int sj1, const char *string)
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)
Base pair.
Definition: data_structures.h:73
Stack of partial structures for backtracking.
Definition: data_structures.h:64
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:41
void export_fold_arrays(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
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)
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. ...