RNAlib-2.2.0-RC3
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 
77 plist *
78 vrna_backtrack_from_intervals(vrna_fold_compound *vc,
79  bondT *bp_stack,
80  sect bt_stack[],
81  int s);
82 
83 #ifdef VRNA_BACKWARD_COMPAT
84 
130 DEPRECATED(float
131 fold_par( const char *sequence,
132  char *structure,
133  vrna_param_t *parameters,
134  int is_constrained,
135  int is_circular));
136 
155 DEPRECATED(float fold( const char *sequence, char *structure));
156 
175 DEPRECATED(float circfold( const char *sequence, char *structure));
176 
177 
185 DEPRECATED(void free_arrays(void));
186 
187 
188 
196 DEPRECATED(void update_fold_params(void));
197 
206 DEPRECATED(void update_fold_params_par(vrna_param_t *parameters));
207 
214 DEPRECATED(void
215 export_fold_arrays( int **f5_p,
216  int **c_p,
217  int **fML_p,
218  int **fM1_p,
219  int **indx_p,
220  char **ptype_p));
221 
228 DEPRECATED(void
229 export_fold_arrays_par( int **f5_p,
230  int **c_p,
231  int **fML_p,
232  int **fM1_p,
233  int **indx_p,
234  char **ptype_p,
235  vrna_param_t **P_p));
236 
243 DEPRECATED(void
244 export_circfold_arrays( int *Fc_p,
245  int *FcH_p,
246  int *FcI_p,
247  int *FcM_p,
248  int **fM2_p,
249  int **f5_p,
250  int **c_p,
251  int **fML_p,
252  int **fM1_p,
253  int **indx_p,
254  char **ptype_p));
255 
262 DEPRECATED(void
263 export_circfold_arrays_par( int *Fc_p,
264  int *FcH_p,
265  int *FcI_p,
266  int *FcM_p,
267  int **fM2_p,
268  int **f5_p,
269  int **c_p,
270  int **fML_p,
271  int **fM1_p,
272  int **indx_p,
273  char **ptype_p,
274  vrna_param_t **P_p));
275 
276 
277 
278 /* finally moved the loop energy function declarations to this header... */
279 /* BUT: The functions only exist for backward compatibility reasons! */
280 /* You better include "loop_energies.h" and call the functions: */
281 /* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */
282 /* a pointer to the energy parameter datastructure as additional argument */
283 
288 DEPRECATED(int LoopEnergy(int n1,
289  int n2,
290  int type,
291  int type_2,
292  int si1,
293  int sj1,
294  int sp1,
295  int sq1));
296 
301 DEPRECATED(int HairpinE(int size,
302  int type,
303  int si1,
304  int sj1,
305  const char *string));
306 
313 DEPRECATED(void initialize_fold(int length));
314 
320 DEPRECATED(char *backtrack_fold_from_pair(char *sequence,
321  int i,
322  int j));
323 
324 
325 #endif
326 
327 #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:698
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. ...