Calculate the Bhattacharyya Coefficient as a similarity between two modes objects.
bhattacharyya(...)# S3 method for enma
bhattacharyya(enma, covs=NULL, ncore=NULL, ...)
# S3 method for array
bhattacharyya(covs, ncore=NULL, ...)
# S3 method for matrix
bhattacharyya(a, b, q=90, n=NULL, ...)
# S3 method for nma
bhattacharyya(...)
# S3 method for pca
bhattacharyya(...)
an object of class "enma" obtained from function
nma.pdbs.
an array of covariance matrices of equal dimensions.
number of CPU cores used to do the calculation.
ncore>1 requires package ‘parallel’ installed.
covariance matrix to be compared with b.
covariance matrix to be compared with a.
a numeric value (in percent) determining the number of modes to be compared.
the number of modes to be compared.
arguments passed to associated functions.
Returns the similarity coefficient(s).
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).
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.
Other similarity measures:
sip, covsoverlap, rmsip.