RNAlib-2.5.0
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 
62 int
63 vrna_pairing_probs(vrna_fold_compound_t *vc,
64  char *structure);
65 
66 
82 double
84  FLT_OR_DBL *pr);
85 
86 
101 double
103 
104 
127 double
129  const short *pt);
130 
131 
155 double
157  const char *structure);
158 
159 
182 double *
184 
185 
196 vrna_ep_t *
198  double cutoff);
199 
200 
201 /* End base pair related functions */
227 void
229  double FA,
230  double FB,
231  vrna_ep_t *prAB,
232  const vrna_ep_t *prA,
233  const vrna_ep_t *prB,
234  int Alength,
235  const vrna_exp_param_t *exp_params);
236 
237 
238 /* End multimer probability related functions */
268 double
270  const char *structure);
271 
272 
273 double
275  double e);
276 
277 
278 /* End structure probability related functions */
281 /* End thermodynamics */
284 #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:103
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:459
vrna_ep_t * vrna_stack_prob(vrna_fold_compound_t *vc, double cutoff)
Compute stacking probabilities.
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_positional_entropy(vrna_fold_compound_t *fc)
Compute a vector of positional entropies.
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_mean_bp_distance(vrna_fold_compound_t *vc)
Get the mean base pair distance in the thermodynamic ensemble.
double vrna_pr_energy(vrna_fold_compound_t *vc, double e)
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.
Functions to deal with sets of energy parameters.
Various utility- and helper-functions for secondary structure parsing, converting,...