1 #ifndef VIENNA_RNA_PACKAGE_FOLD_H
2 #define VIENNA_RNA_PACKAGE_FOLD_H
9 #ifdef DEPRECATION_WARNINGS
11 # define DEPRECATED(func) func __attribute__ ((deprecated))
13 # define DEPRECATED(func) func
16 # define DEPRECATED(func) func
20 #define VRNA_BACKWARD_COMPAT
84 #ifdef VRNA_BACKWARD_COMPAT
152 DEPRECATED(
float fold(
const char *sequence,
char *structure));
170 DEPRECATED(
float circfold(
const char *sequence,
char *structure));
292 const char *
string));
304 DEPRECATED(
char *backtrack_fold_from_pair(
char *sequence,
void free_arrays(void)
Free arrays for mfe folding.
int HairpinE(int size, int type, int si1, int sj1, const char *string)
void update_fold_params_par(vrna_param_t *parameters)
Recalculate energy parameters.
void initialize_fold(int length)
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence...
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
float vrna_fold(const char *string, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence...
float vrna_circfold(const char *string, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequenc...
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.
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 update_fold_params(void)
Recalculate energy parameters.
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.
MFE calculations for single RNA sequences.
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_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)
Functions and variables related to energy evaluation of sequence/structure pairs. ...