Bhattacharyya Coefficient

Usage

bhattacharyya(...)


"bhattacharyya"(enma, covs=NULL, ncore=NULL, ...)


"bhattacharyya"(covs, ncore=NULL, ...)


"bhattacharyya"(a, b, q=90, n=NULL, ...)


"bhattacharyya"(...)


"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.

Description

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

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).

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.

Author

Lars Skjaerven