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Normalizes a vector (mass-weighted if requested).
normalize.vector(x, mass=NULL)Returns the normalized vector(s).
a numeric vector or matrix to be normalized.
a numeric vector containing the atomic masses for weighting.
Lars Skjaerven
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.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
nma , inner.prod
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)
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