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