bio3d (version 2.1-2)

rmsd.filter: RMSD Filter

Description

Identify and filter subsets of conformations at a given RMSD cutoff.

Usage

rmsd.filter(xyz = NULL, rmsd.mat = NULL, cutoff = 0.5,
            fit = TRUE, verbose = TRUE, inds = NULL, 
            ncore = 1, nseg.scale = 1)

Arguments

xyz

a numeric matrix or list object containing multiple coordinates for pairwise comparison, such as that obtained from read.fasta.pdb. Not used if rmsd.mat is given.

rmsd.mat

an optional matrix of RMSD values obtained from rmsd.

cutoff

a numeric rmsd cutoff value.

fit

logical, if TRUE coordinate superposition is performed prior to RMSD calculation.

verbose

logical, if TRUE progress details are printed.

inds

a vector of indices that selects the elements of xyz upon which the calculation should be based. By default, all the non-gap sites in xyz.

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.

Value

• Returns a list object with components:
• ind
  indices of the conformers (rows) below the cutoff value.
• tree
  an object of class "hclust", which describes the tree produced by the clustering process.
• rmsd.mat
  a numeric matrix with all pairwise RMSD values.

Details

This function performs hierarchical cluster analysis of a given matrix of RMSD values rmsd.mat, or an RMSD matrix calculated from a given coordinate matrix xyz, to identify conformers that fall below a given RMSD cutoff value cutoff.

References

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

See Also

rmsd, read.pdb, read.fasta.pdb, read.dcd

Examples

data(kinesin)
attach(kinesin, warn.conflicts=FALSE)
k <- rmsd.filter(xyz=pdbs,cutoff=0.5)
pdbs$id[k$ind]
plot(k$tree, ylab="RMSD")
abline(h=0.5, col="gray")

detach(kinesin)