inner.prod {bio3d}

Mass-weighted Inner Product

Description

Inner product of vectors (mass-weighted if requested).

Usage

inner.prod(x, y, mass=NULL)

Arguments

x

a numeric vector or matrix.

y

a numeric vector or matrix.

mass

a numeric vector containing the atomic masses for weighting.

Details

This function calculates the inner product between two vectors, or alternatively, the column-wise vector elements of matrices. If atomic masses are provided, the dot products will be mass-weighted.

See examples for more details.

Value

Returns the inner product(s).

Author(s)

Lars Skjaerven

References

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

See Also

nma , normalize.vector

Examples

## Matrix operations
x <- 1:3
y <- diag(x)
z <- matrix(1:9, ncol = 3, nrow = 3)

inner.prod(x,y)
inner.prod(y,z)


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

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

## Check for orthogonality 
inner.prod(modes$U[,7], modes$U[,8])