fold.h
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#ifndef VIENNA_RNA_PACKAGE_FOLD_H
#define VIENNA_RNA_PACKAGE_FOLD_H
#include <ViennaRNA/data_structures.h>
#include <ViennaRNA/params.h>
#include <ViennaRNA/mfe.h>
#include <ViennaRNA/eval.h>
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT
float
vrna_fold(const char *sequence,
char *structure);
float
vrna_circfold(const char *sequence,
char *structure);
#ifdef VRNA_BACKWARD_COMPAT
DEPRECATED(float
fold_par( const char *sequence,
char *structure,
vrna_param_t *parameters,
int is_constrained,
int is_circular));
DEPRECATED(float fold( const char *sequence, char *structure));
DEPRECATED(float circfold( const char *sequence, char *structure));
DEPRECATED(void free_arrays(void));
DEPRECATED(void update_fold_params(void));
DEPRECATED(void update_fold_params_par(vrna_param_t *parameters));
DEPRECATED(void
export_fold_arrays( int **f5_p,
int **c_p,
int **fML_p,
int **fM1_p,
int **indx_p,
char **ptype_p));
DEPRECATED(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));
DEPRECATED(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));
DEPRECATED(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));
/* finally moved the loop energy function declarations to this header... */
/* BUT: The functions only exist for backward compatibility reasons! */
/* You better include "loop_energies.h" and call the functions: */
/* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */
/* a pointer to the energy parameter datastructure as additional argument */
DEPRECATED(int LoopEnergy(int n1,
int n2,
int type,
int type_2,
int si1,
int sj1,
int sp1,
int sq1));
DEPRECATED(int HairpinE(int size,
int type,
int si1,
int sj1,
const char *string));
DEPRECATED(void initialize_fold(int length));
DEPRECATED(char *backtrack_fold_from_pair(char *sequence,
int i,
int j));
#endif
#endif
free_arrays
void free_arrays(void)
Free arrays for mfe folding.
HairpinE
int HairpinE(int size, int type, int si1, int sj1, const char *string)
update_fold_params_par
void update_fold_params_par(vrna_param_t *parameters)
Recalculate energy parameters.
initialize_fold
void initialize_fold(int length)
vrna_circfold
float vrna_circfold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequenc...
circfold
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence...
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
data_structures.h
params.h
vrna_fold
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence...
export_fold_arrays
void export_fold_arrays(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
fold
float fold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
export_circfold_arrays
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)
update_fold_params
void update_fold_params(void)
Recalculate energy parameters.
LoopEnergy
int LoopEnergy(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
fold_par
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.h
MFE calculations for single RNA sequences.
export_circfold_arrays_par
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)
export_fold_arrays_par
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)
eval.h
Functions and variables related to energy evaluation of sequence/structure pairs. ...