Go to the documentation of this file. 1 #ifndef VIENNA_RNA_PACKAGE_FOLD_H
2 #define VIENNA_RNA_PACKAGE_FOLD_H
4 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
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)))
17 # define DEPRECATED(func, msg) func
20 # define DEPRECATED(func, msg) func
83 "Use the new API and vrna_mfe() instead");
101 DEPRECATED(
float fold(
const char *sequence,
char *structure),
102 "Use vrna_fold() or vrna_mfe() instead");
120 DEPRECATED(
float circfold(
const char *sequence,
char *structure),
121 "Use vrna_circfold() or vrna_mfe() instead");
131 "This function is obsolete");
142 "This function is obsolete");
151 "Use the new API with vrna_fold_compound_t datastructure instead");
165 "Use the new API with vrna_fold_compound_t datastructure instead");
180 "Use the new API with vrna_fold_compound_t datastructure instead");
199 "Use the new API with vrna_fold_compound_t datastructure instead");
219 "Use the new API with vrna_fold_compound_t datastructure instead");
241 "This function is obsolete");
252 "Use E_Hairpin() instead");
260 "This function is obsolete");
265 DEPRECATED(
char *backtrack_fold_from_pair(
char *sequence,
268 "This function is obsolete. Consider using vrna_backtrack_from_intervals() instead");
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)
int HairpinE(int size, int type, int si1, int sj1, const char *string)
void export_fold_arrays(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.
float fold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
void update_fold_params(void)
Recalculate energy parameters.
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 initialize_fold(int length)
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)
Various data structures and pre-processor macros.
Functions and variables related to energy evaluation of sequence/structure pairs.
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)
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.
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.