R: Calculate Covariance Matrix from Normal Modes

cov.nma {bio3d}

R Documentation

Calculate Covariance Matrix from Normal Modes

Description

Calculate the covariance matrix from a normal mode object.

Usage

## S3 method for class 'nma'
cov(nma)
## S3 method for class '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).

Author(s)

Lars Skjaerven

References

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