RNAlib-2.4.11
equilibrium_probs.h
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1 #ifndef VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_H
2 #define VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_H
3 
6 
18 /*
19 #################################################
20 # BASE PAIR PROBABILITY RELATED FUNCTIONS #
21 #################################################
22 */
23 
24 int vrna_pairing_probs(vrna_fold_compound_t *vc, char *structure);
25 
45 double vrna_mean_bp_distance_pr(int length, FLT_OR_DBL *pr);
46 
60 
85 double
87  const char *structure);
88 
89 
102 vrna_ep_t *vrna_stack_prob(vrna_fold_compound_t *vc, double cutoff);
103 
104 /* End base pair related functions */
127 void vrna_pf_dimer_probs(double FAB,
128  double FA,
129  double FB,
130  vrna_ep_t *prAB,
131  const vrna_ep_t *prA,
132  const vrna_ep_t *prB,
133  int Alength,
134  const vrna_exp_param_t *exp_params);
135 
159 double
161  const char *structure);
162 
163 
164 double
165 vrna_pr_energy(vrna_fold_compound_t *vc,
166  double e);
167 
168 #endif
double vrna_mean_bp_distance(vrna_fold_compound_t *vc)
Get the mean base pair distance in the thermodynamic ensemble.
double vrna_pr_structure(vrna_fold_compound_t *fc, const char *structure)
Compute the equilibrium probability of a particular secondary structure.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
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_pr(int length, FLT_OR_DBL *pr)
Get the mean base pair distance in the thermodynamic ensemble from a probability matrix.
Various data structures and pre-processor macros.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:102
vrna_ep_t * vrna_stack_prob(vrna_fold_compound_t *vc, double cutoff)
Compute stacking probabilities.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
Functions to deal with sets of energy parameters.
double vrna_ensemble_defect(vrna_fold_compound_t *fc, const char *structure)
Compute the Ensemble Defect for a given target structure.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:358