RNAlib-2.4.17
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 char *structure);
130 
131 
154 double *
156 
157 
168 vrna_ep_t *
170  double cutoff);
171 
172 
173 /* End base pair related functions */
199 void
201  double FA,
202  double FB,
203  vrna_ep_t *prAB,
204  const vrna_ep_t *prA,
205  const vrna_ep_t *prB,
206  int Alength,
207  const vrna_exp_param_t *exp_params);
208 
209 
210 /* End multimer probability related functions */
240 double
242  const char *structure);
243 
244 
245 double
247  double e);
248 
249 
250 /* End structure probability related functions */
253 /* End thermodynamics */
256 #endif
vrna_positional_entropy
double * vrna_positional_entropy(vrna_fold_compound_t *fc)
Compute a vector of positional entropies.
vrna_elem_prob_s
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453
vrna_ensemble_defect
double vrna_ensemble_defect(vrna_fold_compound_t *fc, const char *structure)
Compute the Ensemble Defect for a given target structure.
vrna_mean_bp_distance
double vrna_mean_bp_distance(vrna_fold_compound_t *vc)
Get the mean base pair distance in the thermodynamic ensemble.
FLT_OR_DBL
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
vrna_exp_param_s
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
basic.h
Various data structures and pre-processor macros.
vrna_stack_prob
vrna_ep_t * vrna_stack_prob(vrna_fold_compound_t *vc, double cutoff)
Compute stacking probabilities.
pr
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
vrna_pf_dimer_probs
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.
vrna_pr_structure
double vrna_pr_structure(vrna_fold_compound_t *fc, const char *structure)
Compute the equilibrium probability of a particular secondary structure.
vrna_mean_bp_distance_pr
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.
fold_compound.h
The Basic Fold Compound API.
vrna_pr_energy
double vrna_pr_energy(vrna_fold_compound_t *vc, double e)
basic.h
Functions to deal with sets of energy parameters.
structures.h
Various utility- and helper-functions for secondary structure parsing, converting,...