Compute the Centroid Structure

Functions

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

Get the centroid structure of the ensemble. 

#include <ViennaRNA/structures/centroid.h>

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:

  • fc – [in] The fold compound data structure

  • dist – [out] 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)

Get the centroid structure of the ensemble. 

#include <ViennaRNA/structures/centroid.h>

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:

  • length – [in] The length of the sequence

  • dist – [out] A pointer to the distance variable where the centroid distance will be written to

  • pl – [in] 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)

Get the centroid structure of the ensemble. 

#include <ViennaRNA/structures/centroid.h>

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:

  • length – [in] The length of the sequence

  • dist – [out] A pointer to the distance variable where the centroid distance will be written to

  • probs – [in] 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)