Produce a new DCCM object with selected atoms masked.
mask(...)# S3 method for dccm
mask(dccm, pdb = NULL, a.inds = NULL, b.inds = NULL, ...)
Returns a matrix list of class "dccm" with the indices/atoms
not corresponding to the selection masked.
a DCCM structure object obtained from function
dccm.
a PDB structure object obtained from
read.pdb. Must match the dimensions of dccm.
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.
a numeric vector containing the indices of the elements of the DCCM matrix in which should not be masked.
arguments not passed anywhere.
Lars Skjaerven
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.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
dccm, atom.select
## 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)
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