Mass-weighted Inner Product

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

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).

References

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

Author

Lars Skjaerven

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)
#> [1] 1 4 9
inner.prod(y,z)
#> [1]  1 10 27


## 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 0.012 seconds.
#>  Diagonalizing Hessian...	Done in 0.077 seconds.

## Check for orthogonality 
inner.prod(modes$U[,7], modes$U[,8])
#> [1] -9.829387e-15