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");
101DEPRECATED(
float fold(
const char *sequence,
char *structure),
102"Use vrna_fold() or vrna_mfe() instead");
120DEPRECATED(
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131"This function is obsolete");
142"This function is obsolete");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241"This function is obsolete");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260"This function is obsolete");
265DEPRECATED(
char *backtrack_fold_from_pair(
char *sequence,
268"This function is obsolete. Consider using vrna_backtrack_from_intervals() instead");
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.