R: Mask a Subset of Atoms in a DCCM Object.

mask {bio3d} | R Documentation

## Mask a Subset of Atoms in a DCCM Object.

### Description

Produce a new DCCM object with selected atoms masked.

### Usage

    mask(...)

    ## S3 method for class 'dccm'
    mask(dccm, pdb = NULL, a.inds = NULL, b.inds = NULL, ...)

### Arguments

`dccm` | a DCCM structure object obtained from function `dccm`.
`pdb` | a PDB structure object obtained from `read.pdb`. Must match the dimensions of `dccm`.
`a.inds` | a numeric vector containing the indices of the elements of the DCCM matrix in which should not be masked. Alternatively, if `pdb` is provided a selection object (as obtained from `atom.select`) can be provided.
`b.inds` | a numeric vector containing the indices of the elements of the DCCM matrix in which should not be masked.
`...` | arguments not passed anywhere.

### Details

This is a basic utility function for masking a DCCM object matrix to highlight user-selected regions in the correlation network.

When both `a.inds` and `b.inds` are provided only their intersection is retained. When only `a.inds` is provided then the corresponding region to everything else is retained.

Note: The current version assumes that the input PDB corresponds to the input DCCM. In many cases this will correspond to a PDB object containing only CA atoms.

### Value

Returns a matrix list of class `"dccm"` with the indices/atoms not corresponding to the selection masked.

### Author(s)

Lars Skjaerven

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

### See Also

`dccm`, `atom.select`

### Examples

    ## Calculate DCCM
    pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
    cij <- dccm(nma(pdb))

    ## Mask DCCM matrix according to matrix indices
    cijm <- mask(cij, a.inds=40:50, b.inds=80:90)
    plot(cijm)

    ## Retain only 40:50 to everything else
    cijm <- mask(cij, a.inds=40:50)
    plot(cijm)

    ## Mask DCCM matrix according PDB selection
    pdb.ca <- trim(pdb, "calpha")
    a.inds <- atom.select(pdb.ca, resno=40:50)
    b.inds <- atom.select(pdb.ca, resno=80:90)

    # Provide pdb object correspoding to input dccm
    cijm <- mask(cij, pdb.ca, a.inds, b.inds)
    plot(cijm)

[Package bio3d version 2.3-4 Index]