Calculate the covariance overlap obtained from NMA.

covsoverlap(...)

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

# S3 method for nma
covsoverlap(a, b, subset=NULL, ...)

## Arguments

enma an object of class "enma" obtained from function nma.pdbs. number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed. 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. 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. 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).

## 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.

## Author

Lars Skjaerven

Other similarity measures: sip, covsoverlap, bhattacharyya.