part_func.h

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#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_H
#define VIENNA_RNA_PACKAGE_PART_FUNC_H

typedef struct vrna_dimer_pf_s vrna_dimer_pf_t;


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

typedef struct vrna_dimer_pf_s cofoldF;

#endif


#include <ViennaRNA/datastructures/basic.h>
#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/utils/structures.h>
#include <ViennaRNA/params/basic.h>
#include <ViennaRNA/centroid.h>
#include <ViennaRNA/equilibrium_probs.h>
#include <ViennaRNA/boltzmann_sampling.h>

#ifdef VRNA_WARN_DEPRECATED
# if defined(__clang__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
# elif defined(__GNUC__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
# else
#  define DEPRECATED(func, msg) func
# endif
#else
# define DEPRECATED(func, msg) func
#endif

/*
 #################################################
 # PARTITION FUNCTION COMPUTATION                #
 #################################################
 */

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

float
vrna_pf(vrna_fold_compound_t  *vc,
        char                  *structure);


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


/* End basic global interface */
float
vrna_pf_fold(const char *sequence,
             char       *structure,
             vrna_ep_t  **pl);


float
vrna_pf_circfold(const char *sequence,
                 char       *structure,
                 vrna_ep_t  **pl);


float
vrna_pf_alifold(const char  **sequences,
                char        *structure,
                vrna_ep_t   **pl);


float
vrna_pf_circalifold(const char  **sequences,
                    char        *structure,
                    vrna_ep_t   **pl);


vrna_dimer_pf_t
vrna_pf_co_fold(const char  *seq,
                char        *structure,
                vrna_ep_t   **pl);


/* End simplified global interface */
/*
 #################################################
 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
 #################################################
 */

int
vrna_pf_float_precision(void);


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

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

extern int st_back;

DEPRECATED(float   pf_fold_par(const char       *sequence,
                               char             *structure,
                               vrna_exp_param_t *parameters,
                               int              calculate_bppm,
                               int              is_constrained,
                               int              is_circular),
           "Use the new API and vrna_pf() instead");

DEPRECATED(float   pf_fold(const char *sequence,
                           char       *structure),
           "Use vrna_pf_fold() or vrna_pf() instead");

DEPRECATED(float   pf_circ_fold(const char  *sequence,
                                char        *structure),
           "Use vrna_pf_circfold() or vrna_pf() instead");

DEPRECATED(char *pbacktrack(char *sequence), "Use vrna_pbacktrack() instead");

DEPRECATED(char *pbacktrack5(char *sequence,
                             int  length), "Use vrna_pbacktrack5() instead");

DEPRECATED(char *pbacktrack_circ(char *sequence), "Use vrna_pbacktrack() instead");

DEPRECATED(void  free_pf_arrays(void), "This function is obsolete");

DEPRECATED(void  update_pf_params(int length), "This function is obsolete");

DEPRECATED(void update_pf_params_par(int              length,
                                     vrna_exp_param_t *parameters),
           "Use the new API with vrna_fold_compound_t instead");

DEPRECATED(FLT_OR_DBL *export_bppm(void),
           "Use the new API with vrna_fold_compound_t instead");


DEPRECATED(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),
           "Use the new API with vrna_fold_compound_t instead");

DEPRECATED(double get_subseq_F(int  i,
                               int  j),
           "Use the new API with vrna_fold_compound_t instead");


DEPRECATED(double  mean_bp_distance(int length),
           "Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead");

DEPRECATED(double mean_bp_distance_pr(int         length,
                                      FLT_OR_DBL  *pr),
           "Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead");

DEPRECATED(vrna_ep_t *stackProb(double cutoff), "Use vrna_stack_prob() instead");


DEPRECATED(void init_pf_fold(int length), "This function is obsolete");

DEPRECATED(char *centroid(int     length,
                          double  *dist),
           "Use vrna_centroid() instead");

DEPRECATED(char *get_centroid_struct_gquad_pr(int     length,
                                              double  *dist),
           "Use vrna_centroid() instead");

DEPRECATED(double mean_bp_dist(int length),
           "Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead");

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),
           "");

/* this doesn't work if free_pf_arrays() is called before */
DEPRECATED(void assign_plist_gquad_from_pr(vrna_ep_t  **pl,
                                           int        length,
                                           double     cut_off),
           "Use vrna_plist_from_probs() instead");

#endif

#endif