fold.h
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#ifndef __VIENNA_RNA_PACKAGE_FOLD_H__
#define __VIENNA_RNA_PACKAGE_FOLD_H__
#include "data_structures.h"
#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif
extern int logML;
extern int uniq_ML;
extern int cut_point;
extern int eos_debug;
float fold_par( const char *sequence,
char *structure,
paramT *parameters,
int is_constrained,
int is_circular);
float fold( const char *sequence,
char *structure);
float circfold( const char *sequence,
char *structure);
float energy_of_structure(const char *string,
const char *structure,
int verbosity_level);
float energy_of_struct_par( const char *string,
const char *structure,
paramT *parameters,
int verbosity_level);
float energy_of_circ_structure( const char *string,
const char *structure,
int verbosity_level);
float energy_of_circ_struct_par(const char *string,
const char *structure,
paramT *parameters,
int verbosity_level);
float energy_of_gquad_structure(const char *string,
const char *structure,
int verbosity_level);
float energy_of_gquad_struct_par( const char *string,
const char *structure,
paramT *parameters,
int verbosity_level);
int energy_of_structure_pt( const char *string,
short *ptable,
short *s,
short *s1,
int verbosity_level);
int energy_of_struct_pt_par(const char *string,
short *ptable,
short *s,
short *s1,
paramT *parameters,
int verbosity_level);
void free_arrays(void);
void parenthesis_structure(char *structure,
bondT *bp,
int length);
void parenthesis_zuker( char *structure,
bondT *bp,
int length);
void letter_structure(char *structure,
bondT *bp,
int length);
void update_fold_params(void);
void update_fold_params_par(paramT *parameters);
char *backtrack_fold_from_pair(char *sequence,
int i,
int j);
float energy_of_move( const char *string,
const char *structure,
int m1,
int m2);
int energy_of_move_pt(short *pt,
short *s,
short *s1,
int m1,
int m2);
int loop_energy(short *ptable,
short *s,
short *s1,
int i);
void export_fold_arrays(int **f5_p,
int **c_p,
int **fML_p,
int **fM1_p,
int **indx_p,
char **ptype_p);
void export_fold_arrays_par(int **f5_p,
int **c_p,
int **fML_p,
int **fM1_p,
int **indx_p,
char **ptype_p,
paramT **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 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,
paramT **P_p);
void assign_plist_from_db(plist **pl,
const char *struc,
float pr);
/* 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(float energy_of_struct(const char *string,
const char *structure));
DEPRECATED(int energy_of_struct_pt( const char *string,
short *ptable,
short *s,
short *s1));
DEPRECATED(float energy_of_circ_struct( const char *string,
const char *structure));
#endif