filter.rmsd.Rd
Identify and filter subsets of conformations at a given RMSD cutoff.
filter.rmsd(xyz = NULL, rmsd.mat = NULL, cutoff = 0.5, fit = TRUE, verbose = TRUE, inds = NULL, method = "complete", ...)
xyz  a numeric matrix or list object containing multiple
coordinates for pairwise comparison, such as that obtained from


rmsd.mat  an optional matrix of RMSD values obtained from

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

method  the agglomeration method to be used. See function

...  additional arguments passed to and from functions. 
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’.
Returns a list object with components:
indices of the conformers (rows) below the cutoff value.
an object of class "hclust"
, which describes the
tree produced by the clustering process.
a numeric matrix with all pairwise RMSD values.
Grant, B.J. et al. (2006) Bioinformatics 22, 26952696.
Barry Grant
if (FALSE) { attach(kinesin) k < filter.rmsd(xyz=pdbs,cutoff=0.5) pdbs$id[k$ind] hclustplot(k$tree, h=0.5, ylab="RMSD") abline(h=0.5, col="gray") detach(kinesin) }