Nothing
cmap.pdb <- function(pdb, inds=NULL, verbose=FALSE, ...) {
if(!is.pdb(pdb))
stop("provide a pdb object as obtained from function 'pdb'")
if(is.null(inds)) {
inds <- atom.select(pdb, "notwater", verbose=verbose)
}
pdb <- trim.pdb(pdb, inds)
xyz <- pdb$xyz
grpby <- paste(pdb$atom$chain, pdb$atom$insert, pdb$atom$resno, sep="-")
return(cmap.xyz(xyz, grpby, ...))
}
cmap.pdbs <- function(pdbs, rm.gaps=FALSE, all.atom=FALSE, ...) {
if(!is.pdbs(pdbs))
stop("Input should be a 'pdbs' object as obtained from 'read.fasta.pdb()' or 'read.all()'.")
if(rm.gaps) {
dots <- list(...)
if("grpby" %in% names(dots) && !is.null(dots[["grpby"]])) {
if(length(unique(dots[["grpby"]])) != ncol(pdbs$ali)) {
stop("rm.gaps=TRUE not supported for non-residue wise grouping.")
}
}
}
if(!all.atom) {
# set a new default value of dcut for CA-CA contact map
cmap.default <- list(dcut=10.0, collapse=FALSE)
cmap.args <- .arg.filter(cmap.default, cmap.xyz, ...)
cm <- do.call("cmap.xyz", c(list(xyz=pdbs$xyz), cmap.args))
}
else {
# set a new default value of grpby for all-atom contact map
cmap.default <- list(grpby=pdbs$all.grpby, collapse=FALSE)
cmap.args <- .arg.filter(cmap.default, cmap.xyz, ...)
cm <- do.call("cmap.xyz", c(list(xyz=pdbs$all), cmap.args))
}
if(rm.gaps) {
gaps.res <- gap.inspect(pdbs$ali)
ndim <- length(dim(cm))
if(ndim>2) {
cm <- cm[gaps.res$f.inds, gaps.res$f.inds, ]
}
else {
cm <- cm[gaps.res$f.inds, gaps.res$f.inds]
}
}
return(cm)
}
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