dist.xyz: Calculate the Distances Between the Rows of Two Matrices

In bio3d: Biological Structure Analysis

Calculate the Distances Between the Rows of Two Matrices

Description

Compute the pairwise euclidean distances between the rows of two matrices.

Usage

dist.xyz(a, b = NULL, all.pairs=TRUE, ncore=1, nseg.scale=1)

Arguments

a	a ‘xyz’ object, numeric data matrix, or vector.
b	an optional second ‘xyz’ object, data matrix, or vector.
all.pairs	logical, if TRUE all pairwise distances between the rows of ‘a’ and all rows of ‘b’ are computed, if FALSE only the distances between coresponding rows of ‘a’ and ‘b’ are computed.
ncore	number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
nseg.scale	split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.

Details

This function returns a matrix of euclidean distances between each row of ‘a’ and all rows of ‘b’. Input vectors are coerced to three dimensional matrices (representing the Cartesian coordinates x, y and z) prior to distance computation. If ‘b’ is not provided then the pairwise distances between all rows of ‘a’ are computed.

Value

Returns a matrix of pairwise euclidean distances between each row of ‘a’ and all rows of ‘b’.

Note

This function will choke if ‘b’ has too many rows.

Author(s)

Barry Grant

References

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

See Also

dm, dist

Examples

 dist.xyz( c(1,1,1, 3,3,3), c(3,3,3, 2,2,2, 1,1,1))
 dist.xyz( c(1,1,1, 3,3,3), c(3,3,3, 2,2,2, 1,1,1), all.pairs=FALSE)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.