bio3d (version 2.2-4)

layout.cna: Protein Structure Network Layout

Description

Determine protein structure network layout in 2D and 3D from the geometric center of each community.

Usage

layout.cna(x, pdb, renumber=TRUE, k=2, full=FALSE)

Arguments

x

A protein structure network object as obtained from the ‘cna’ function.

pdb

A pdb class object as obtained from the ‘read.pdb’ function.

renumber

Logical, if TRUE the input ‘pdb’ will be re-numbered starting at residue number one before community coordinate averages are calculated.

k

A single element numeric vector between 1 and 3 specifying the returned coordinate dimensions.

full

Logical, if TRUE the full all-Calpha atom network coordinates will be returned rather than the default clustered network community coordinates.

Value

A numeric matrix of Nxk, where N is the number of communities and k the number of dimensions requested.

Details

This function calculates the geometric center for each community from the atomic position of it's Calpha atoms taken from a corresponding PDB file. Care needs to be taken to ensure the PDB residue numbers and the community vector names/length match.

The community residue membership are typically taken from the input network object but can be supplied as a list object with 'x$communities$membership'.

See Also

plot.cna, plot.communities, igraph.plotting, plot.igraph

Examples

# Load the correlation network
attach(hivp)

# Read the starting PDB file to determine atom correspondence
pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
pdb <- read.pdb(pdbfile)

# Plot will be slow
#xy <- plot.cna(net)
#plot3d.cna(net, pdb)

layout.cna(net, pdb, k=3)
layout.cna(net, pdb)

# can be used as input to plot.cna and plot3d.cna....
# plot.cna( net, layout=layout.cna(net, pdb) )
# plot3d.cna(net, pdb, layout=layout.cna(net, pdb, k=3))

detach(hivp)