Pair List Representation of Secondary Structures

Detailed Description

Collaboration diagram for Pair List Representation of Secondary Structures:

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

Macros
#define	VRNA_PLIST_TYPE_BASEPAIR   0
	A Base Pair element.
#define	VRNA_PLIST_TYPE_GQUAD   1
	A G-Quadruplex element.
#define	VRNA_PLIST_TYPE_H_MOTIF   2
	A Hairpin loop motif element.
#define	VRNA_PLIST_TYPE_I_MOTIF   3
	An Internal loop motif element.
#define	VRNA_PLIST_TYPE_UD_MOTIF   4
	An Unstructured Domain motif element.
#define	VRNA_PLIST_TYPE_STACK   5
	A Base Pair stack element.

Typedefs
typedef struct vrna_elem_prob_s	vrna_ep_t
	Convenience typedef for data structure vrna_elem_prob_s.

Functions
vrna_ep_t *	vrna_plist (const char *struc, float pr)
	Create a vrna_ep_t from a dot-bracket string. More...

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Data Structure Documentation

struct vrna_elem_prob_s

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

See also

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

Data Fields
int	i
	Start position (usually 5' nucleotide that starts the element, e.g. base pair)
int	j
	End position (usually 3' nucleotide that ends the element, e.g. base pair)
float	p
	Probability of the element.
int	type
	Type of the element.

Function Documentation

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