1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
4 #ifdef DEPRECATION_WARNINGS
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
8 # define DEPRECATED(func) func
11 # define DEPRECATED(func) func
15 #define VRNA_BACKWARD_COMPAT
64 #ifdef VRNA_BACKWARD_COMPAT
177 const double *startconc,
double A0
start concentration A
Definition: part_func_co.h:100
void compute_probabilities(double FAB, double FEA, double FEB, vrna_plist_t *prAB, vrna_plist_t *prA, vrna_plist_t *prB, int Alength)
Compute Boltzmann probabilities of dimerization without homodimers.
double B0
start concentration B
Definition: part_func_co.h:101
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
double ABc
End concentration AB.
Definition: part_func_co.h:102
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.
double F0AB
Null model without DuplexInit.
Definition: part_func_co.h:89
double FA
monomer A
Definition: part_func_co.h:92
Definition: part_func_co.h:99
int mirnatog
Toggles no intrabp in 2nd mol.
vrna_plist_t * get_plist(vrna_plist_t *pl, int length, double cut_off)
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
vrna_dimer_pf_t vrna_pf_dimer(vrna_fold_compound_t *vc, char *structure)
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers...
void init_co_pf_fold(int length)
double FB
monomer B
Definition: part_func_co.h:93
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.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
void vrna_pf_dimer_probs(double FAB, double FA, double FB, vrna_plist_t *prAB, const vrna_plist_t *prA, const vrna_plist_t *prB, int Alength, const vrna_exp_param_t *exp_params)
Compute Boltzmann probabilities of dimerization without homodimers.
vrna_dimer_conc_t * vrna_pf_dimer_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...
vrna_dimer_conc_t * 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...
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
double FcAB
true hybrid states only
Definition: part_func_co.h:91
Definition: part_func_co.h:87
double F_monomer[2]
Free energies of the two monomers.
vrna_dimer_pf_t co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
double FAB
all states with DuplexInit correction
Definition: part_func_co.h:90