Pair List Representation of Secondary Structures

Defines

VRNA_PLIST_TYPE_BASEPAIR

A Base Pair element. 

#include <ViennaRNA/structures/problist.h>
VRNA_PLIST_TYPE_GQUAD

A G-Quadruplex element. 

#include <ViennaRNA/structures/problist.h>
VRNA_PLIST_TYPE_H_MOTIF

A Hairpin loop motif element. 

#include <ViennaRNA/structures/problist.h>
VRNA_PLIST_TYPE_I_MOTIF

An Internal loop motif element. 

#include <ViennaRNA/structures/problist.h>
VRNA_PLIST_TYPE_UD_MOTIF

An Unstructured Domain motif element. 

#include <ViennaRNA/structures/problist.h>
VRNA_PLIST_TYPE_STACK

A Base Pair stack element. 

#include <ViennaRNA/structures/problist.h>
VRNA_PLIST_TYPE_UNPAIRED

An unpaired base. 

#include <ViennaRNA/structures/problist.h>
VRNA_PLIST_TYPE_TRIPLE

One pair of a base triplet. 

#include <ViennaRNA/structures/problist.h>

Typedefs

typedef struct vrna_elem_prob_s vrna_ep_t

Convenience typedef for data structure vrna_elem_prob_s. 

#include <ViennaRNA/structures/problist.h>

Functions

vrna_ep_t *vrna_plist(const char *struc, float pr)

Create a vrna_ep_t from a dot-bracket string. 

#include <ViennaRNA/structures/problist.h>

The dot-bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.

The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries

Parameters:

  • struc – The secondary structure in dot-bracket notation

  • pr – The probability for each base pair used in the plist

Returns:

The plist array

int vrna_plist_append(vrna_ep_t **target, const vrna_ep_t *list)
#include <ViennaRNA/structures/problist.h>
struct vrna_elem_prob_s
#include <ViennaRNA/structures/problist.h>

Data structure representing a single entry of an element probability list (e.g. list of pair probabilities).

VRNA_PLIST_TYPE_BASEPAIR, VRNA_PLIST_TYPE_GQUAD, VRNA_PLIST_TYPE_H_MOTIF, VRNA_PLIST_TYPE_I_MOTIF, VRNA_PLIST_TYPE_UD_MOTIF, VRNA_PLIST_TYPE_STACK

See also

vrna_plist(), vrna_plist_from_probs(), vrna_db_from_plist(),

Public Members

int i

Start position (usually 5’ nucleotide that starts the element, e.g. base pair). 

#include <ViennaRNA/structures/problist.h>
int j

End position (usually 3’ nucleotide that ends the element, e.g. base pair). 

#include <ViennaRNA/structures/problist.h>
float p

Probability of the element. 

#include <ViennaRNA/structures/problist.h>
int type

Type of the element. 

#include <ViennaRNA/structures/problist.h>