bhattacharyya {bio3d}

Bhattacharyya Coefficient

Description

Calculate the Bhattacharyya Coefficient as a similarity between two modes objects.

Usage

bhattacharyya(...)

## S3 method for class 'enma'
bhattacharyya(enma, covs=NULL, ncore=NULL, ...)

## S3 method for class 'array'
bhattacharyya(covs, ncore=NULL, ...)

## S3 method for class 'matrix'
bhattacharyya(a, b, q=90, n=NULL, ...)

## S3 method for class 'nma'
bhattacharyya(...)

## S3 method for class 'pca'
bhattacharyya(...)

Arguments

enma

an object of class "enma" obtained from function nma.pdbs.

covs

an array of covariance matrices of equal dimensions.

ncore

number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.

a

covariance matrix to be compared with b.

b

covariance matrix to be compared with a.

q

a numeric value (in percent) determining the number of modes to be compared.

n

the number of modes to be compared.

...

arguments passed to associated functions.

Details

Bhattacharyya coefficient provides a means to compare two covariance matrices derived from NMA or an ensemble of conformers (e.g. simulation or X-ray conformers).

Value

Returns the similarity coefficient(s).

Author(s)

Lars Skjaerven

References

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696. Fuglebakk, E. et al. (2013) JCTC 9, 5618–5628.

See Also

Other similarity measures: sip, covsoverlap, rmsip.