bio3d (version 2.2-4)

trim.xyz: Trim a XYZ Object of Cartesian Coordinates.

Description

Produce a new smaller XYZ object, containing a subset of atoms.

Usage

"trim"(xyz, row.inds = NULL, col.inds = NULL, ...)

Arguments

xyz

a XYZ object containing Cartesian coordinates, e.g. obtained from read.pdb, read.ncdf.

row.inds

a numeric vector specifying which rows of the xyz matrix to return.

col.inds

a numeric vector specifying which columns of the xyz matrix to return.

...

additional arguments passed to and from functions.

Value

Returns an object of class xyz with the Cartesian coordinates stored in a matrix object with dimensions M x 3N, where N is the number of atoms, and M number of frames.

Details

This function provides basic functionality for subsetting a matrix of class ‘xyz’ while also maintaining the class attribute.

References

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

See Also

read.pdb, as.xyz.

Examples

## Not run: 
# ## Read a PDB file from the RCSB online database
# pdb <- read.pdb("1bg2")
# 
# ## Select calpha atoms
# sele <- atom.select(pdb, "calpha")
# 
# ## Trim XYZ
# trim(pdb$xyz, col.inds=sele$xyz)
# 
# ## Equals to
# pdb$xyz[, sele$xyz, drop=FALSE]
# ## End(Not run)