R: RMSD Filter

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 `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.

### 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 `"hclust"`, which describes the tree produced by the clustering process.
`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)

[Package bio3d version 2.4-0 Index]