1 #ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__
2 #define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__
7 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #define DEPRECATED(func) func
129 const double *startconc,
231 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:456
cofoldF co_pf_fold_par(char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained)
Calculate partition function and base pair probabilities.
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 update_co_pf_params_par(int length, pf_paramT *parameters)
Recalculate energy parameters.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:225
Definition: data_structures.h:359
int mirnatog
Toggles no intrabp in 2nd mol.
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:94
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)
ConcEnt * vrna_co_pf_get_concentrations(double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const pf_paramT *exp_params)
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibri...
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
void vrna_co_pf_dimer_probs(double FAB, double FA, double FB, struct plist *prAB, const plist *prA, const plist *prB, int Alength, const pf_paramT *exp_params)
Compute Boltzmann probabilities of dimerization without homodimers.
double F_monomer[2]
Free energies of the two monomers.
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:468