var.xyz: Pairwise Distance Variance in Cartesian Coordinates
Description
Calculate the variance of all pairwise distances in an ensemble of
Cartesian coordinates.
Usage
var.xyz(xyz, weights=TRUE)
var.pdbs(pdbs, ...)
Arguments
xyz
an object of class "xyz" containing Cartesian
coordinates in a matrix.
weights
logical, if TRUE weights are calculated based on the
pairwise distance variance.
pdbs
a pdbs object as object from function
pdbaln.
...
arguments passed to associated functions.
Value
Returns the a matrix of the pairwise distance variance, formated as
weights if weights=TRUE.
Details
This function calculates the variance of all pairwise distances in an
ensemble of Cartesian coordinates. The primary use of this function is
to calculate weights to scale the pair force constant for NMA.
References
Grant, B.J. et al. (2006) Bioinformatics22, 2695--2696.