filter.rmsd {bio3d} | R Documentation |
RMSD Filter
Description
Identify and filter subsets of conformations at a given RMSD cutoff.
Usage
filter.rmsd(xyz = NULL, rmsd.mat = NULL, cutoff = 0.5,
fit = TRUE, verbose = TRUE, inds = NULL, method = "complete",
...)
Arguments
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. |
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’.
Value
Returns a list object with components:
ind |
indices of the conformers (rows) below the cutoff value. |
tree |
an object of class |
rmsd.mat |
a numeric matrix with all pairwise RMSD values. |
Author(s)
Barry Grant
References
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
See Also
rmsd
, read.pdb
,
read.fasta.pdb
, read.dcd
Examples
## Not run:
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)
## End(Not run)