RNAlib-2.6.3
 
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equilibrium_probs.h
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1#ifndef VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_H
2#define VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_H
3
8
20/*
21 #################################################
22 # BASE PAIR PROBABILITY RELATED FUNCTIONS #
23 #################################################
24 */
25
26
70int
71vrna_pairing_probs(vrna_fold_compound_t *fc,
72 char *structure);
73
74
92double
94 FLT_OR_DBL *pr);
95
96
113double
115
116
141double
143 const short *pt);
144
145
171double
173 const char *structure);
174
175
200double *
202
203
214vrna_ep_t *
216 double cutoff);
217
218
219/* End base pair related functions */
245void
247 double FA,
248 double FB,
249 vrna_ep_t *prAB,
250 const vrna_ep_t *prA,
251 const vrna_ep_t *prB,
252 int Alength,
253 const vrna_exp_param_t *exp_params);
254
255
256/* End multimer probability related functions */
290double
292 const char *structure);
293
294
295double
297 double e);
298
299
300/* End structure probability related functions */
303/* End thermodynamics */
306#endif
Various data structures and pre-processor macros.
The Basic Fold Compound API.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition basic.h:43
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition basic.h:110
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition structures.h:486
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.
vrna_ep_t * vrna_stack_prob(vrna_fold_compound_t *fc, double cutoff)
Compute stacking probabilities.
double * vrna_positional_entropy(vrna_fold_compound_t *fc)
Compute a vector of positional entropies.
double vrna_pr_energy(vrna_fold_compound_t *fc, double e)
double vrna_pr_structure(vrna_fold_compound_t *fc, const char *structure)
Compute the equilibrium probability of a particular secondary structure.
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.
double vrna_ensemble_defect(vrna_fold_compound_t *fc, const char *structure)
Compute the Ensemble Defect for a given target 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.
double vrna_mean_bp_distance(vrna_fold_compound_t *fc)
Get the mean base pair distance in the thermodynamic ensemble.
Functions to deal with sets of energy parameters.
Various utility- and helper-functions for secondary structure parsing, converting,...