Mass-Weighted Normalized Vector

Normalizes a vector (mass-weighted if requested).

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.

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.

Value

Returns the normalized vector(s).

References

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

Author

Lars Skjaerven

See also

nma , inner.prod

Examples

x <- 1:3
y <- matrix(1:9, ncol = 3, nrow = 3)

normalize.vector(x)
#> [1] 0.2672612 0.5345225 0.8017837
normalize.vector(y)
#>           [,1]      [,2]      [,3]
#> [1,] 0.2672612 0.4558423 0.5025707
#> [2,] 0.5345225 0.5698029 0.5743665
#> [3,] 0.8017837 0.6837635 0.6461623

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

## Calculate (vibrational) normal modes
modes <- nma(pdb)
#>  Building Hessian...		Done in 0.013 seconds.
#>  Diagonalizing Hessian...	Done in 0.078 seconds.

## 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)