R: Mass-weighted Inner Product

inner.prod {bio3d} | R Documentation

## 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])

[Package bio3d version 2.3-3 Index]