bio3d (version 2.3-4)

normalize.vector: Mass-Weighted Normalized Vector

Description

Normalizes a vector (mass-weighted if requested).

Usage

normalize.vector(x, mass=NULL)

Arguments

x

a numeric vector or matrix to be normalized.

mass

a numeric vector containing the atomic masses for weighting.

Value

Returns the normalized vector(s).

Details

This function normalizes a vector, or alternatively, the column-wise vector elements of a matrix. If atomic masses are provided the vector is mass-weigthed.

See examples for more details.

References

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

See Also

nma , inner.prod

Examples

# NOT RUN {
x <- 1:3
y <- matrix(1:9, ncol = 3, nrow = 3)

normalize.vector(x)
normalize.vector(y)

## Application to normal modes
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

## Calculate (vibrational) normal modes
modes <- nma(pdb)

## Returns a vector
nv <- normalize.vector(modes$modes[,7])

## Returns a matrix
nv <- normalize.vector(modes$modes[,7:10])

## Mass-weighted
nv <- normalize.vector(modes$modes[,7], mass=modes$mass)
# }