RNAlib-2.5.1
fold.h
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1#ifndef VIENNA_RNA_PACKAGE_FOLD_H
2#define VIENNA_RNA_PACKAGE_FOLD_H
3
4#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
5
8#include <ViennaRNA/mfe.h>
9#include <ViennaRNA/eval.h>
10
11#ifdef VRNA_WARN_DEPRECATED
12# if defined(__clang__)
13# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
14# elif defined(__GNUC__)
15# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
16# else
17# define DEPRECATED(func, msg) func
18# endif
19#else
20# define DEPRECATED(func, msg) func
21#endif
22
77DEPRECATED(float
78fold_par( const char *sequence,
79 char *structure,
80 vrna_param_t *parameters,
81 int is_constrained,
82 int is_circular),
83"Use the new API and vrna_mfe() instead");
84
101DEPRECATED(float fold( const char *sequence, char *structure),
102"Use vrna_fold() or vrna_mfe() instead");
103
120DEPRECATED(float circfold( const char *sequence, char *structure),
121"Use vrna_circfold() or vrna_mfe() instead");
122
123
130DEPRECATED(void free_arrays(void),
131"This function is obsolete");
132
133
134
141DEPRECATED(void update_fold_params(void),
142"This function is obsolete");
143
150DEPRECATED(void update_fold_params_par(vrna_param_t *parameters),
151"Use the new API with vrna_fold_compound_t datastructure instead");
152
158DEPRECATED(void
159export_fold_arrays( int **f5_p,
160 int **c_p,
161 int **fML_p,
162 int **fM1_p,
163 int **indx_p,
164 char **ptype_p),
165"Use the new API with vrna_fold_compound_t datastructure instead");
166
172DEPRECATED(void
173export_fold_arrays_par( int **f5_p,
174 int **c_p,
175 int **fML_p,
176 int **fM1_p,
177 int **indx_p,
178 char **ptype_p,
179 vrna_param_t **P_p),
180"Use the new API with vrna_fold_compound_t datastructure instead");
181
187DEPRECATED(void
188export_circfold_arrays( int *Fc_p,
189 int *FcH_p,
190 int *FcI_p,
191 int *FcM_p,
192 int **fM2_p,
193 int **f5_p,
194 int **c_p,
195 int **fML_p,
196 int **fM1_p,
197 int **indx_p,
198 char **ptype_p),
199"Use the new API with vrna_fold_compound_t datastructure instead");
200
206DEPRECATED(void
208 int *FcH_p,
209 int *FcI_p,
210 int *FcM_p,
211 int **fM2_p,
212 int **f5_p,
213 int **c_p,
214 int **fML_p,
215 int **fM1_p,
216 int **indx_p,
217 char **ptype_p,
218 vrna_param_t **P_p),
219"Use the new API with vrna_fold_compound_t datastructure instead");
220
221
222
223/* finally moved the loop energy function declarations to this header... */
224/* BUT: The functions only exist for backward compatibility reasons! */
225/* You better include "loop_energies.h" and call the functions: */
226/* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */
227/* a pointer to the energy parameter data structure as additional argument */
228
233DEPRECATED(int LoopEnergy(int n1,
234 int n2,
235 int type,
236 int type_2,
237 int si1,
238 int sj1,
239 int sp1,
240 int sq1),
241"This function is obsolete");
242
247DEPRECATED(int HairpinE(int size,
248 int type,
249 int si1,
250 int sj1,
251 const char *string),
252"Use E_Hairpin() instead");
253
259DEPRECATED(void initialize_fold(int length),
260"This function is obsolete");
261
265DEPRECATED(char *backtrack_fold_from_pair(char *sequence,
266 int i,
267 int j),
268"This function is obsolete. Consider using vrna_backtrack_from_intervals() instead");
269
270
271#endif
272
277#endif
Various data structures and pre-processor macros.
Functions and variables related to energy evaluation of sequence/structure pairs.
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
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_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 free_arrays(void)
Free arrays for mfe folding.
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.
void update_fold_params(void)
Recalculate energy parameters.
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.
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 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.
int HairpinE(int size, int type, int si1, int sj1, const char *string)
void initialize_fold(int length)
void update_fold_params_par(vrna_param_t *parameters)
Recalculate energy parameters.
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
Functions to deal with sets of energy parameters.