Trim a XYZ Object of Cartesian Coordinates.
Produce a new smaller XYZ object, containing a subset of atoms.
## S3 method for class 'xyz' trim(xyz, row.inds = NULL, col.inds = NULL, ...)
xyz |
a XYZ object containing Cartesian coordinates,
e.g. obtained from |
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. |
This function provides basic functionality for subsetting a matrix of class ‘xyz’ while also maintaining the class attribute.
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.
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## 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]
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