Pairwise Distance Variance in 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.

Description

Calculate the variance of all pairwise distances in an ensemble of Cartesian coordinates.

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.

Value

Returns the a matrix of the pairwise distance variance, formated as weights if ‘weights=TRUE’.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See also

nma.pdbs

Author

Lars Skjaerven