Compute the Centroid Structure
Functions
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char *vrna_centroid(vrna_fold_compound_t *fc, 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
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 (
NULLon error)
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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
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 (
NULLon error)
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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
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 (
NULLon error)
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char *vrna_centroid(vrna_fold_compound_t *fc, double *dist)