Equilibrium Probability implementations. More...
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Functions | |
Base pair probabilities and derived computations | |
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. | |
double | vrna_mean_bp_distance (vrna_fold_compound_t *fc) |
Get the mean base pair distance in the thermodynamic ensemble. | |
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. | |
double | vrna_ensemble_defect (vrna_fold_compound_t *fc, const char *structure) |
Compute the Ensemble Defect for a given target structure. | |
double * | vrna_positional_entropy (vrna_fold_compound_t *fc) |
Compute a vector of positional entropies. | |
vrna_ep_t * | vrna_stack_prob (vrna_fold_compound_t *fc, double cutoff) |
Compute stacking probabilities. | |
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. | |
Structure probability computations | |
double | vrna_pr_structure (vrna_fold_compound_t *fc, const char *structure) |
Compute the equilibrium probability of a particular secondary structure. | |
double | vrna_pr_energy (vrna_fold_compound_t *fc, double e) |
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.