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bio3d (version 2.2-4)

covsoverlap: Covariance Overlap

Description

Calculate the covariance overlap obtained from NMA.

Usage

covsoverlap(...)


"covsoverlap"(enma, ncore=NULL, ...)


"covsoverlap"(a, b, subset=NULL, ...)

Arguments

enma
an object of class "enma" obtained from function nma.pdbs.
ncore
number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
a
a list object with elements ‘U’ and ‘L’ (e.g. as obtained from function nma) containing the eigenvectors and eigenvalues, respectively, to be compared with b.
b
a list object with elements ‘U’ and ‘L’ (e.g. as obtained from function nma) containing the eigenvectors and eigenvalues, respectively, to be compared with a.
subset
the number of modes to consider.
...
arguments passed to associated functions.

Value

Returns the similarity coefficient(s).

Details

Covariance overlap is a measure for the similarity between two covariance matrices, e.g. obtained from NMA.

References

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. Romo, T.D. et al. (2011) Proteins 79, 23--34.

See Also

Other similarity measures: sip, covsoverlap, bhattacharyya.