Calculate Covariance Matrix from Normal Modes

Calculate the covariance matrix from a normal mode object.

# S3 method for nma
cov(nma)
# S3 method for enma
cov(enma, ncore=NULL)

Arguments

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

Details

This function calculates the covariance matrix from a nma object as obtained from function nma.pdb or covariance matrices from a enma object as obtain from function nma.pdbs.

Value

Returns the calculated covariance matrix (function cov.nma), or covariance matrices (function cov.enma).

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. Fuglebakk, E. et al. (2013) JCTC 9, 5618--5628.

Author