bio3d (version 2.1-2)

cov.nma: 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.

Value

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

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.

References

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

See Also

nma