Nothing
mask <- function(...)
UseMethod("mask")
mask.dccm <- function(dccm, pdb=NULL, a.inds=NULL, b.inds=NULL, ...) {
x <- dccm
dims <- dim(x)
if(is.null(a.inds))
stop("'a.inds' must be provided")
if(is.null(b.inds))
b.inds <- 1:nrow(dccm)
if(!is.null(pdb)) {
if(!is.pdb(pdb))
stop("If provided, 'pdb' must be a pdb object as obtained from 'read.pdb'")
if(nrow(pdb$atom) != dims[1])
stop("If provided, 'pdb' must match the dimensions of 'x'")
if(!all(pdb$atom$elety == "CA"))
warning("Non all-CA pdb detected. Ensure that provided 'pdb' match 'x'")
if(is.select(a.inds))
a.inds = a.inds$atom
if(is.select(b.inds))
b.inds = b.inds$atom
}
else {
if(is.select(a.inds) | is.select(b.inds))
stop("a.inds/b.inds should only be a 'select' object(s) when 'pdb' is provided")
}
if(!is.null(a.inds)) {
tmp <- x
tmp[ a.inds, b.inds ] = 666
tmp[ b.inds, a.inds ] = 666
inds.rm <- which(tmp != 666)
x[inds.rm] = 0
}
return(x)
}
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