H/part_func_co.h

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/* functions from part_func.c */
/* calculate partition function and base pair probabilities */
#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__
#define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__

#include "data_structures.h"

#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif

extern int    mirnatog;

extern double F_monomer[2];

cofoldF co_pf_fold( char *sequence,
                    char *structure);

cofoldF co_pf_fold_par( char *sequence,
                        char *structure,
                        pf_paramT *parameters,
                        int calculate_bppm,
                        int is_constrained);

FLT_OR_DBL *export_co_bppm(void);

void    free_co_pf_arrays(void);

void    update_co_pf_params(int length);

void    update_co_pf_params_par(int length,
                                pf_paramT *parameters);

void    compute_probabilities(double FAB,
                              double FEA,
                              double FEB,
                              struct plist  *prAB,
                              struct plist  *prA,
                              struct plist  *prB,
                              int Alength);

ConcEnt *get_concentrations(double FEAB,
                            double FEAA,
                            double FEBB,
                            double FEA,
                            double FEB,
                            double *startconc);

/*
#################################################
# DEPRECATED FUNCTIONS                          #
#################################################
*/

DEPRECATED(plist  *get_plist( struct plist *pl,
                              int length,
                              double cut_off));
DEPRECATED(void   init_co_pf_fold(int length));

#endif

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