1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H 2 #define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H 4 #ifdef VRNA_WARN_DEPRECATED 6 # define DEPRECATED(func) func __attribute__ ((deprecated)) 8 # define DEPRECATED(func) func 11 # define DEPRECATED(func) func 15 #define VRNA_BACKWARD_COMPAT 69 #ifdef VRNA_BACKWARD_COMPAT 189 const double *startconc,
double Bc_start
start concentration B
Definition: part_func_co.h:113
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structure_utils.h:115
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:130
double ABc
End concentration AB.
Definition: part_func_co.h:114
double Ac_start
start concentration A
Definition: part_func_co.h:112
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.
vrna_ep_t * get_plist(vrna_ep_t *pl, int length, double cut_off)
double F0AB
Null model without DuplexInit.
Definition: part_func_co.h:101
double FA
monomer A
Definition: part_func_co.h:104
void vrna_pf_dimer_probs(double FAB, double FA, double FB, vrna_ep_t *prAB, const vrna_ep_t *prA, const vrna_ep_t *prB, int Alength, const vrna_exp_param_t *exp_params)
Compute Boltzmann probabilities of dimerization without homodimers.
Data structure for concentration dependency computations.
Definition: part_func_co.h:111
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:102
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:105
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.
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
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:103
Data structure returned by vrna_pf_dimer()
Definition: part_func_co.h:99
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:102