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.
method
the agglomeration method to be used. See function
hclust for more information.
…
additional arguments passed to and from functions.
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) Bioinformatics22, 2695--2696.