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(...)
Returns the similarity coefficient(s).
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.
Lars Skjaerven
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
.