1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
10 #define DEPRECATED(func) func
130 const double *startconc,
232 DEPRECATED(
ConcEnt *
get_concentrations(
double FEAB,
double FEAA,
double FEBB,
double FEA,
double FEB,
double *startconc));
cofoldF co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
Definition: data_structures.h:128
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.
void vrna_co_pf_dimer_probs(double FAB, double FA, double FB, struct plist *prAB, const plist *prA, const plist *prB, int Alength, const vrna_exp_param_t *exp_params)
Compute Boltzmann probabilities of dimerization without homodimers.
ConcEnt * vrna_co_pf_get_concentrations(double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const vrna_exp_param_t *exp_params)
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibri...
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:698
int mirnatog
Toggles no intrabp in 2nd mol.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:45
void init_co_pf_fold(int length)
cofoldF vrna_co_pf_fold(vrna_fold_compound *vc, char *structure)
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers...
plist * get_plist(struct plist *pl, int length, double cut_off)
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
cofoldF 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()
double F_monomer[2]
Free energies of the two monomers.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86
void compute_probabilities(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength)
Compute Boltzmann probabilities of dimerization without homodimers.
ConcEnt * get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibri...
Definition: data_structures.h:140