Detailed Description

Collaboration diagram for Compute the Centroid Structure:

Functions
char *	vrna_centroid (vrna_fold_compound_t vc, double dist)
	Get the centroid structure of the ensemble. More...

char *	vrna_centroid_from_plist (int length, double dist, vrna_ep_t pl)
	Get the centroid structure of the ensemble. More...

char *	vrna_centroid_from_probs (int length, double dist, FLT_OR_DBL probs)
	Get the centroid structure of the ensemble. More...

Function Documentation

char* vrna_centroid	(	vrna_fold_compound_t *	vc,
		double *	dist
	)

#include <ViennaRNA/centroid.h>

Get the centroid structure of the ensemble.

The centroid is the structure with the minimal average distance to all other structures
$<d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}$
Thus, the centroid is simply the structure containing all pairs with $p_ij>0.5$ The distance of the centroid to the ensemble is written to the memory adressed by dist.

Parameters

[in]	vc	The fold compound data structure
[out]	dist	A pointer to the distance variable where the centroid distance will be written to

Returns: The centroid structure of the ensemble in dot-bracket notation (NULL on error)

char* vrna_centroid_from_plist	(	int	length,
		double *	dist,
		vrna_ep_t *	pl
	)

#include <ViennaRNA/centroid.h>

Get the centroid structure of the ensemble.

This function is a threadsafe replacement for centroid() with a vrna_ep_t input

The centroid is the structure with the minimal average distance to all other structures
$<d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}$
Thus, the centroid is simply the structure containing all pairs with $p_ij>0.5$ The distance of the centroid to the ensemble is written to the memory adressed by dist.

Parameters

[in]	length	The length of the sequence
[out]	dist	A pointer to the distance variable where the centroid distance will be written to
[in]	pl	A pair list containing base pair probability information about the ensemble

Returns: The centroid structure of the ensemble in dot-bracket notation (NULL on error)

char* vrna_centroid_from_probs	(	int	length,
		double *	dist,
		FLT_OR_DBL *	probs
	)

#include <ViennaRNA/centroid.h>

Get the centroid structure of the ensemble.

This function is a threadsafe replacement for centroid() with a probability array input

The centroid is the structure with the minimal average distance to all other structures
$<d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}$
Thus, the centroid is simply the structure containing all pairs with $p_ij>0.5$ The distance of the centroid to the ensemble is written to the memory adressed by dist.

Parameters

[in]	length	The length of the sequence
[out]	dist	A pointer to the distance variable where the centroid distance will be written to
[in]	probs	An upper triangular matrix containing base pair probabilities (access via iindx vrna_idx_row_wise() )

Returns: The centroid structure of the ensemble in dot-bracket notation (NULL on error)

Detailed Description

Functions

Function Documentation