RNAlib-2.4.8
Random Structure Samples from the Ensemble

Functions to draw random structure samples from the ensemble according to their equilibrium probability. More...

Detailed Description

Functions to draw random structure samples from the ensemble according to their equilibrium probability.

+ Collaboration diagram for Random Structure Samples from the Ensemble:

Modules

 Stochastic Backtracking of Structures from Distance Based Partitioning
 Contains functions related to stochastic backtracking from a specified distance class.
 

Functions

char * vrna_pbacktrack5 (vrna_fold_compound_t *vc, int length)
 Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability. More...
 
char * vrna_pbacktrack (vrna_fold_compound_t *vc)
 Sample a secondary structure (consensus structure) from the Boltzmann ensemble according its probability. More...
 
char * pbacktrack (char *sequence)
 Sample a secondary structure from the Boltzmann ensemble according its probability. More...
 
char * pbacktrack_circ (char *sequence)
 Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. More...
 

Variables

int st_back
 Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. More...
 

Function Documentation

◆ vrna_pbacktrack5()

char * vrna_pbacktrack5 ( vrna_fold_compound_t vc,
int  length 
)

#include <ViennaRNA/boltzmann_sampling.h>

Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability.

Precondition
Unique multiloop decomposition has to be active upon creation of vc with vrna_fold_compound() or similar. This can be done easily by passing vrna_fold_compound() a model details parameter with vrna_md_t.uniq_ML = 1.
vrna_pf() has to be called first to fill the partition function matrices
Parameters
vcThe fold compound data structure
lengthThe length of the subsequence to consider (starting with 5' end)
Returns
A sampled secondary structure in dot-bracket notation (or NULL on error)
SWIG Wrapper Notes:
This function is attached as overloaded method pbacktrack() to objects of type fold_compound

◆ vrna_pbacktrack()

char * vrna_pbacktrack ( vrna_fold_compound_t vc)

#include <ViennaRNA/boltzmann_sampling.h>

Sample a secondary structure (consensus structure) from the Boltzmann ensemble according its probability.

Precondition
Unique multiloop decomposition has to be active upon creation of vc with vrna_fold_compound() or similar. This can be done easily by passing vrna_fold_compound() a model details parameter with vrna_md_t.uniq_ML = 1.
vrna_pf() has to be called first to fill the partition function matrices
Note
This function is polymorphic. It accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE, and VRNA_FC_TYPE_COMPARATIVE.
The function will automagically detect cicular RNAs based on the model_details in exp_params as provided via the vrna_fold_compound_t
Parameters
vcThe fold compound data structure
Returns
A sampled secondary structure in dot-bracket notation (or NULL on error)
SWIG Wrapper Notes:
This function is attached as overloaded method pbacktrack() to objects of type fold_compound that accepts an optional length argument. Hence, it serves as a replacement for vrna_pbacktrack().

◆ pbacktrack()

char* pbacktrack ( char *  sequence)

#include <ViennaRNA/part_func.h>

Sample a secondary structure from the Boltzmann ensemble according its probability.

Precondition
st_back has to be set to 1 before calling pf_fold() or pf_fold_par()
pf_fold_par() or pf_fold() have to be called first to fill the partition function matrices
Parameters
sequenceThe RNA sequence
Returns
A sampled secondary structure in dot-bracket notation

◆ pbacktrack_circ()

char* pbacktrack_circ ( char *  sequence)

#include <ViennaRNA/part_func.h>

Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability.

This function does the same as pbacktrack() but assumes the RNA molecule to be circular

Precondition
st_back has to be set to 1 before calling pf_fold() or pf_fold_par()
pf_fold_par() or pf_circ_fold() have to be called first to fill the partition function matrices
Deprecated:
Use vrna_pbacktrack() instead.
Parameters
sequenceThe RNA sequence
Returns
A sampled secondary structure in dot-bracket notation

Variable Documentation

◆ st_back

int st_back

#include <ViennaRNA/part_func.h>

Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking.

Set this variable to 1 prior to a call of pf_fold() to ensure that all matrices needed for stochastic backtracking are filled in the forward recursions

Deprecated:
set the uniq_ML flag in vrna_md_t before passing it to vrna_fold_compound().
See also
pbacktrack(), pbacktrack_circ