part_func_co.h

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#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
#define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H

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

/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT

typedef struct vrna_dimer_pf_s  vrna_dimer_pf_t;

typedef struct vrna_dimer_conc_s  vrna_dimer_conc_t;


#ifdef VRNA_BACKWARD_COMPAT

typedef struct vrna_dimer_pf_s    cofoldF;
typedef struct vrna_dimer_conc_s  ConcEnt;

#endif

#include <ViennaRNA/data_structures.h>
#include <ViennaRNA/params.h>

extern int    mirnatog;

extern double F_monomer[2];

struct vrna_dimer_pf_s {
  /* free energies for: */
  double F0AB;  
  double FAB;   
  double FcAB;  
  double FA;    
  double FB;    
};

struct vrna_dimer_conc_s {
  double A0;    
  double B0;    
  double ABc;   
  double AAc;
  double BBc;
  double Ac;
  double Bc;
};

vrna_dimer_pf_t
vrna_pf_dimer(vrna_fold_compound_t *vc,
              char *structure);

void  vrna_pf_dimer_probs(double FAB,
                          double FA,
                          double FB,
                          vrna_plist_t *prAB,
                          const vrna_plist_t *prA,
                          const vrna_plist_t *prB,
                          int Alength,
                          const vrna_exp_param_t *exp_params);

vrna_dimer_conc_t *vrna_pf_dimer_concentrations(double FcAB,
                                      double FcAA,
                                      double FcBB,
                                      double FEA,
                                      double FEB,
                                      const double *startconc,
                                      const vrna_exp_param_t *exp_params);

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

DEPRECATED(vrna_dimer_pf_t co_pf_fold( char *sequence, char *structure));

DEPRECATED(vrna_dimer_pf_t co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained));

DEPRECATED(vrna_plist_t  *get_plist( vrna_plist_t *pl,
                              int length,
                              double cut_off));

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

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

DEPRECATED(void   init_co_pf_fold(int length));

DEPRECATED(FLT_OR_DBL *export_co_bppm(void));

DEPRECATED(void free_co_pf_arrays(void));

DEPRECATED(void update_co_pf_params(int length));

DEPRECATED(void update_co_pf_params_par(int length, vrna_exp_param_t *parameters));

#endif