Compute the centroid structure
[Calculating Partition Functions and Pair Probabilities]

Collaboration diagram for Compute the centroid structure:

Functions
char *	get_centroid_struct_pl (int length, double dist, plist pl)
	Get the centroid structure of the ensemble.
char *	get_centroid_struct_pr (int length, double dist, double pr)
	Get the centroid structure of the ensemble.

Function Documentation

char* get_centroid_struct_pl	(	int	length,
		double *	dist,
		plist *	pl
	)

Get the centroid structure of the ensemble.

This function is a threadsafe replacement for centroid() with a 'plist' 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

char* get_centroid_struct_pr	(	int	length,
		double *	dist,
		double *	pr
	)

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]`	pr	A upper triangular matrix containing base pair probabilities (access via iindx get_iindx() )

Returns:: The centroid structure of the ensemble in dot-bracket notation

Compute the centroid structure [Calculating Partition Functions and Pair Probabilities]

Functions

Function Documentation

Compute the centroid structure
[Calculating Partition Functions and Pair Probabilities]