Pair List Representation of Secondary Structures

Defines

VRNA_PLIST_TYPE_BASEPAIR: #include <ViennaRNA/utils/structures.h>
A Base Pair element.

VRNA_PLIST_TYPE_GQUAD: #include <ViennaRNA/utils/structures.h>
A G-Quadruplex element.

VRNA_PLIST_TYPE_H_MOTIF: #include <ViennaRNA/utils/structures.h>
A Hairpin loop motif element.

VRNA_PLIST_TYPE_I_MOTIF: #include <ViennaRNA/utils/structures.h>
An Internal loop motif element.

VRNA_PLIST_TYPE_UD_MOTIF: #include <ViennaRNA/utils/structures.h>
An Unstructured Domain motif element.

VRNA_PLIST_TYPE_STACK: #include <ViennaRNA/utils/structures.h>
A Base Pair stack element.

VRNA_PLIST_TYPE_UNPAIRED: #include <ViennaRNA/utils/structures.h>
An unpaired base.

VRNA_PLIST_TYPE_TRIPLE: #include <ViennaRNA/utils/structures.h>
One pair of a base triplet.

Typedefs

typedef struct vrna_elem_prob_s vrna_ep_t: #include <ViennaRNA/utils/structures.h>
Convenience typedef for data structure vrna_elem_prob_s.

Functions

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

#include <ViennaRNA/utils/structures.h>

Create a vrna_ep_t from a dot-bracket string.

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

struct vrna_elem_prob_s

#include <ViennaRNA/utils/structures.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