RNAlib-2.5.1

Equilibrium Probability implementations. More...

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Functions

Base pair probabilities and derived computations
int vrna_pairing_probs (vrna_fold_compound_t *vc, char *structure)
 
double vrna_mean_bp_distance_pr (int length, FLT_OR_DBL *pr)
 Get the mean base pair distance in the thermodynamic ensemble from a probability matrix. More...
 
double vrna_mean_bp_distance (vrna_fold_compound_t *vc)
 Get the mean base pair distance in the thermodynamic ensemble. More...
 
double vrna_ensemble_defect_pt (vrna_fold_compound_t *fc, const short *pt)
 Compute the Ensemble Defect for a given target structure provided as a vrna_ptable. More...
 
double vrna_ensemble_defect (vrna_fold_compound_t *fc, const char *structure)
 Compute the Ensemble Defect for a given target structure. More...
 
double * vrna_positional_entropy (vrna_fold_compound_t *fc)
 Compute a vector of positional entropies. More...
 
vrna_ep_tvrna_stack_prob (vrna_fold_compound_t *vc, double cutoff)
 Compute stacking probabilities. More...
 
Multimer probabilities computations
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. More...
 
Structure probability computations
double vrna_pr_structure (vrna_fold_compound_t *fc, const char *structure)
 Compute the equilibrium probability of a particular secondary structure. More...
 
double vrna_pr_energy (vrna_fold_compound_t *vc, double e)
 

Detailed Description

Equilibrium Probability implementations.

This file includes various implementations for equilibrium probability computations based on the partition function of an RNA sequence, two concatenated sequences, or a sequence alignment.