cov.nma: Calculate Covariance Matrix from Normal Modes

In bio3d: Biological Structure Analysis

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.

See Also

nma

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