covsoverlap: Covariance Overlap

In bio3d: Biological Structure Analysis

Covariance Overlap

Description

Calculate the covariance overlap obtained from NMA.

Usage

covsoverlap(...)

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

## S3 method for class 'nma'
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.

Details

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

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. Romo, T.D. et al. (2011) Proteins 79, 23–34.

See Also

Other similarity measures: sip, covsoverlap, bhattacharyya.

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.