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", ...)
a numeric matrix or list object containing multiple
coordinates for pairwise comparison, such as that obtained from
an optional matrix of RMSD values obtained from
a numeric rmsd cutoff value.
logical, if TRUE coordinate superposition is performed prior to RMSD calculation.
logical, if TRUE progress details are printed.
a vector of indices that selects the elements of
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, 2695--2696.