1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H 2 #define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H 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))) 10 # define DEPRECATED(func, msg) func 13 # define DEPRECATED(func, msg) func 113 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 141 "Use vrna_pf_co_fold() or vrna_pf_dimer() instead");
167 "Use the new API and vrna_pf_dimer() instead");
177 "Use vrna_plist() and vrna_plist_from_probs() instead");
205 "Use vrna_pf_dimer_probs() instead");
212 "This function is obsolete");
228 "Use the new API with vrna_fold_compound_t instead");
238 "This function is obsolete");
251 "This function is obsolete");
274 "Use the new API with vrna_fold_compound_t instead");
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.