Calculate Covariance Matrix from Normal Modes

Usage

"cov"(nma)
"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.

Description

Calculate the covariance matrix from a normal mode object.

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.

See also

nma

Author

Lars Skjaerven