RNAlib-2.4.11
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Functions to draw random structure samples from the ensemble according to their equilibrium probability. More...
Functions to draw random structure samples from the ensemble according to their equilibrium probability.
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_nr (vrna_fold_compound_t *vc, int num_samples) |
Samples multiple secondary structures non-redundantly 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... | |
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.
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. vc | The fold compound data structure |
length | The length of the subsequence to consider (starting with 5' end) |
char * vrna_pbacktrack_nr | ( | vrna_fold_compound_t * | vc, |
int | num_samples | ||
) |
#include <ViennaRNA/boltzmann_sampling.h>
Samples multiple secondary structures non-redundantly from the Boltzmann ensemble according its probability.
vc | The fold compound data structure |
num_samples | The number of desired non-redundant samples |
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.
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. vc | The fold compound data structure |
length
argument. Hence, it serves as a replacement for vrna_pbacktrack(). char* pbacktrack | ( | char * | sequence | ) |
#include <ViennaRNA/part_func.h>
Sample a secondary structure from the Boltzmann ensemble according its probability.
sequence | The RNA sequence |
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
sequence | The RNA sequence |
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