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