Structure sampling from the ensemble

Overview

// global variables

int st_back

// global functions

char* vrna_pbacktrack5 (
    vrna_fold_compound_t* vc,
    int length
    )

char* vrna_pbacktrack (vrna_fold_compound_t* vc)
char* pbacktrack (char* sequence)
char* pbacktrack_circ (char* sequence)

Detailed Documentation

Global Variables

int st_back
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() .

Global 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.

SWIG Wrapper Notes This function is attached as overloaded method pbacktrack() to objects of type fold_compound

Parameters:

vc The fold compound data structure
length The length of the subsequence to consider (starting with 5’ end)

Returns:

A sampled secondary structure in dot-bracket notation (or NULL on error)

Pre-Condition

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

char* vrna_pbacktrack (vrna_fold_compound_t* vc)
Sample a secondary structure (consensus structure) from the Boltzmann ensemble according its probability.

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() .

Parameters:

vc The fold compound data structure

Returns:

A sampled secondary structure in dot-bracket notation (or NULL on error)

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

Pre-Condition

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

char* pbacktrack (char* sequence)
Sample a secondary structure from the Boltzmann ensemble according its probability.

Parameters:

sequence The RNA sequence

Returns:

A sampled secondary structure in dot-bracket notation

Pre-Condition

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

char* pbacktrack_circ (char* sequence)
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

Deprecated Use vrna_pbacktrack() instead.

Parameters:

sequence The RNA sequence

Returns:

A sampled secondary structure in dot-bracket notation

Pre-Condition

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