part_func.h
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#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_H__
#define __VIENNA_RNA_PACKAGE_PART_FUNC_H__
#include "data_structures.h"
#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif
extern int st_back;
/*
#################################################
# PARTITION FUNCTION COMPUTATION #
#################################################
*/
float pf_fold_par( const char *sequence,
char *structure,
pf_paramT *parameters,
int calculate_bppm,
int is_constrained,
int is_circular);
float pf_fold(const char *sequence,
char *structure);
float pf_circ_fold( const char *sequence,
char *structure);
char *pbacktrack(char *sequence);
char *pbacktrack_circ(char *sequence);
void free_pf_arrays(void);
void update_pf_params(int length);
void update_pf_params_par(int length, pf_paramT *parameters);
FLT_OR_DBL *export_bppm(void);
/*
#################################################
# OTHER PARTITION FUNCTION RELATED DECLARATIONS #
#################################################
*/
void assign_plist_from_pr( plist **pl,
FLT_OR_DBL *probs,
int length,
double cutoff);
/* this doesn't work if free_pf_arrays() is called before */
void assign_plist_gquad_from_pr(plist **pl,
int length,
double cut_off);
char *get_centroid_struct_gquad_pr(int length,
double *dist);
int get_pf_arrays(short **S_p,
short **S1_p,
char **ptype_p,
FLT_OR_DBL **qb_p,
FLT_OR_DBL **qm_p,
FLT_OR_DBL **q1k_p,
FLT_OR_DBL **qln_p);
double get_subseq_F(int i, int j);
char *get_centroid_struct_pl(int length,
double *dist,
plist *pl);
char *get_centroid_struct_pr(int length,
double *dist,
FLT_OR_DBL *pr);
double mean_bp_distance(int length);
double mean_bp_distance_pr(int length,
FLT_OR_DBL *pr);
void bppm_to_structure(char *structure,
FLT_OR_DBL *pr,
unsigned int length);
plist *stackProb(double cutoff);
char bppm_symbol(const float *x);
/*
#################################################
# DEPRECATED FUNCTIONS #
#################################################
*/
DEPRECATED(void init_pf_fold(int length));
DEPRECATED(char *centroid(int length,
double *dist)); /* mean pair distance of ensemble */
DEPRECATED(double mean_bp_dist(int length));
DEPRECATED(double expLoopEnergy(int u1,
int u2,
int type,
int type2,
short si1,
short sj1,
short sp1,
short sq1));
DEPRECATED(double expHairpinEnergy( int u,
int type,
short si1,
short sj1,
const char *string));
#endif