RNAlib-2.5.1
part_func_co.h
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1#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
2#define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
3
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(__clang__)
6# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
7# elif defined(__GNUC__)
8# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
9# else
10# define DEPRECATED(func, msg) func
11# endif
12#else
13# define DEPRECATED(func, msg) func
14#endif
15
54#include <ViennaRNA/part_func.h>
58
62extern int mirnatog;
63
67extern double F_monomer[2];
68
73#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
74
75/*
76 #################################################
77 # DEPRECATED FUNCTIONS #
78 #################################################
79 */
80
101DEPRECATED(vrna_dimer_pf_t co_pf_fold(char *sequence,
102 char *structure),
103"Use vrna_pf_co_fold() or vrna_pf_dimer() instead");
104
126DEPRECATED(vrna_dimer_pf_t co_pf_fold_par(char *sequence,
127 char *structure,
128 vrna_exp_param_t *parameters,
129 int calculate_bppm,
130 int is_constrained),
131"Use the new API and vrna_pf_dimer() instead");
132
138DEPRECATED(vrna_ep_t *get_plist(vrna_ep_t *pl,
139 int length,
140 double cut_off),
141"Use vrna_plist() and vrna_plist_from_probs() instead");
142
164DEPRECATED(void compute_probabilities(double FAB,
165 double FEA,
166 double FEB,
167 vrna_ep_t *prAB,
168 vrna_ep_t *prA,
169 vrna_ep_t *prB,
170 int Alength),
171"Use vrna_pf_dimer_probs() instead");
172
178DEPRECATED(void init_co_pf_fold(int length),
179"This function is obsolete");
180
196DEPRECATED(FLT_OR_DBL *export_co_bppm(void),
197"Use the new API with vrna_fold_compound_t instead");
198
207DEPRECATED(void free_co_pf_arrays(void),
208"This function is obsolete");
209
222DEPRECATED(void update_co_pf_params(int length),
223"This function is obsolete");
224
246DEPRECATED(void update_co_pf_params_par(int length,
247 vrna_exp_param_t *parameters),
248"Use the new API with vrna_fold_compound_t instead");
249
250#endif
251
252#endif
Concentration computations for RNA-RNA interactions.
Various data structures and pre-processor macros.
Equilibrium Probability implementations.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
void update_co_pf_params(int length)
Recalculate energy parameters.
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
void compute_probabilities(double FAB, double FEA, double FEB, vrna_ep_t *prAB, vrna_ep_t *prA, vrna_ep_t *prB, int Alength)
Compute Boltzmann probabilities of dimerization without homodimers.
FLT_OR_DBL * export_co_bppm(void)
Get a pointer to the base pair probability array.
void init_co_pf_fold(int length)
vrna_dimer_pf_t co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained)
Calculate partition function and base pair probabilities.
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
vrna_dimer_pf_t co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
Data structure returned by vrna_pf_dimer()
Definition: part_func.h:98
double F_monomer[2]
Free energies of the two monomers.
int mirnatog
Toggles no intrabp in 2nd mol.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:482
Functions to deal with sets of energy parameters.
Partition function implementations.
vrna_ep_t * get_plist(vrna_ep_t *pl, int length, double cut_off)
Various utility- and helper-functions for secondary structure parsing, converting,...