RNAlib-2.4.4
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 
62 #include <ViennaRNA/params.h>
63 #include <ViennaRNA/part_func.h>
66 
70 extern int mirnatog;
71 
75 extern double F_monomer[2];
76 
104 vrna_pf_co_fold(const char *seq,
105  char *structure,
106  vrna_ep_t **pl);
107 
108 
113 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
114 
115 /*
116  #################################################
117  # DEPRECATED FUNCTIONS #
118  #################################################
119  */
120 
139 DEPRECATED(vrna_dimer_pf_t co_pf_fold(char *sequence,
140  char *structure),
141 "Use vrna_pf_co_fold() or vrna_pf_dimer() instead");
142 
162 DEPRECATED(vrna_dimer_pf_t co_pf_fold_par(char *sequence,
163  char *structure,
164  vrna_exp_param_t *parameters,
165  int calculate_bppm,
166  int is_constrained),
167 "Use the new API and vrna_pf_dimer() instead");
168 
174 DEPRECATED(vrna_ep_t *get_plist(vrna_ep_t *pl,
175  int length,
176  double cut_off),
177 "Use vrna_plist() and vrna_plist_from_probs() instead");
178 
198 DEPRECATED(void compute_probabilities(double FAB,
199  double FEA,
200  double FEB,
201  vrna_ep_t *prAB,
202  vrna_ep_t *prA,
203  vrna_ep_t *prB,
204  int Alength),
205 "Use vrna_pf_dimer_probs() instead");
206 
211 DEPRECATED(void init_co_pf_fold(int length),
212 "This function is obsolete");
213 
227 DEPRECATED(FLT_OR_DBL *export_co_bppm(void),
228 "Use the new API with vrna_fold_compound_t instead");
229 
237 DEPRECATED(void free_co_pf_arrays(void),
238 "This function is obsolete");
239 
250 DEPRECATED(void update_co_pf_params(int length),
251 "This function is obsolete");
252 
272 DEPRECATED(void update_co_pf_params_par(int length,
273  vrna_exp_param_t *parameters),
274 "Use the new API with vrna_fold_compound_t instead");
275 
276 #endif
277 
278 #endif
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structure_utils.h:114
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:43
void update_co_pf_params(int length)
Recalculate energy parameters.
FLT_OR_DBL * export_co_bppm(void)
Get a pointer to the base pair probability array.
Equilibrium Probability implementations.
vrna_ep_t * get_plist(vrna_ep_t *pl, int length, double cut_off)
int mirnatog
Toggles no intrabp in 2nd mol.
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
void init_co_pf_fold(int length)
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_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained)
Calculate partition function and base pair probabilities.
vrna_dimer_pf_t vrna_pf_co_fold(const char *seq, char *structure, vrna_ep_t **pl)
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers...
Partition function implementations.
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
Data structure returned by vrna_pf_dimer()
Definition: part_func.h:65
double F_monomer[2]
Free energies of the two monomers.
Concentration computations for RNA-RNA interactions.
vrna_dimer_pf_t co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.