rmsd.filter {bio3d} | R Documentation |
Identify and filter subsets of conformations at a given RMSD cutoff.
rmsd.filter(xyz = NULL, rmsd.mat = NULL, cutoff = 0.5, fit = TRUE, verbose = TRUE)
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. |
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:
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. |
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
rmsd
, read.pdb
,
read.fasta.pdb
, read.dcd
## Not run: data(kinesin) k <- rmsd.filter(pdbs,cutoff=0.5) aln$id[k$ind] plot(k$tree, ylab="RMSD") abline(h=0.5, col="gray") ## End(Not run)