RNAlib-2.4.8
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 
53 #include <ViennaRNA/params/basic.h>
54 #include <ViennaRNA/part_func.h>
57 
61 extern int mirnatog;
62 
66 extern double F_monomer[2];
67 
72 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
73 
74 /*
75  #################################################
76  # DEPRECATED FUNCTIONS #
77  #################################################
78  */
79 
100 DEPRECATED(vrna_dimer_pf_t co_pf_fold(char *sequence,
101  char *structure),
102 "Use vrna_pf_co_fold() or vrna_pf_dimer() instead");
103 
125 DEPRECATED(vrna_dimer_pf_t co_pf_fold_par(char *sequence,
126  char *structure,
127  vrna_exp_param_t *parameters,
128  int calculate_bppm,
129  int is_constrained),
130 "Use the new API and vrna_pf_dimer() instead");
131 
137 DEPRECATED(vrna_ep_t *get_plist(vrna_ep_t *pl,
138  int length,
139  double cut_off),
140 "Use vrna_plist() and vrna_plist_from_probs() instead");
141 
163 DEPRECATED(void compute_probabilities(double FAB,
164  double FEA,
165  double FEB,
166  vrna_ep_t *prAB,
167  vrna_ep_t *prA,
168  vrna_ep_t *prB,
169  int Alength),
170 "Use vrna_pf_dimer_probs() instead");
171 
177 DEPRECATED(void init_co_pf_fold(int length),
178 "This function is obsolete");
179 
195 DEPRECATED(FLT_OR_DBL *export_co_bppm(void),
196 "Use the new API with vrna_fold_compound_t instead");
197 
206 DEPRECATED(void free_co_pf_arrays(void),
207 "This function is obsolete");
208 
221 DEPRECATED(void update_co_pf_params(int length),
222 "This function is obsolete");
223 
245 DEPRECATED(void update_co_pf_params_par(int length,
246  vrna_exp_param_t *parameters),
247 "Use the new API with vrna_fold_compound_t instead");
248 
249 #endif
250 
251 #endif
void init_co_pf_fold(int length)
FLT_OR_DBL * export_co_bppm(void)
Get a pointer to the base pair probability array.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
Equilibrium Probability implementations.
vrna_ep_t * get_plist(vrna_ep_t *pl, int length, double cut_off)
Data structure returned by vrna_pf_dimer()
Definition: part_func.h:95
void update_co_pf_params(int length)
Recalculate energy parameters.
int mirnatog
Toggles no intrabp in 2nd mol.
Various data structures and pre-processor macros.
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.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:101
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.
vrna_dimer_pf_t co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
Partition function implementations.
Functions to deal with sets of energy parameters.
double F_monomer[2]
Free energies of the two monomers.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:358
Concentration computations for RNA-RNA interactions.