Nothing
"write.pir" <-
function(alignment = NULL,
ids = NULL,
seqs = alignment$ali,
pdb.file = NULL,
chain.first = NULL,
resno.first = NULL,
chain.last = NULL,
resno.last = NULL,
file,
append = FALSE) {
if (is.null(seqs))
stop("write.pir: please provide a 'seqs' or 'alignment' input object")
if (!is.null(alignment)) {
if (is.null(alignment$id) | is.null(alignment$ali)) {
stop("write.pir: 'alignment' should be a list with '$id' and '$ali'components")
}
if (is.null(ids)) {
ids=alignment$id
}
} else {
if (is.null(ids)) {
n.ids <- nrow(seqs)
if(is.null(n.ids)) { n.ids=1 }
ids=seq( 1, length=n.ids )
}
}
if(is.null(pdb.file)) pdb.file = rep("", nrow(seqs))
if(is.null(chain.first)) chain.first = rep("", nrow(seqs))
if(is.null(resno.first)) resno.first = rep("", nrow(seqs))
if(is.null(chain.last)) chain.last = rep("", nrow(seqs))
if(is.null(resno.last)) resno.last = rep("", nrow(seqs))
if (!append) {
##file.remove(file, showWarnings = FALSE)
suppressWarnings( file.remove(file) )
}
nseqs <- length(ids)
if (nseqs == 1) {
head = "sequence"
if(pdb.file!="") {
head = "structureX"
if(chain.first == "") chain.first = "@"
if(resno.first == "") resno.first = "FIRST"
if(resno.last == "") resno.last = paste("+", sum(!is.gap(seqs)), sep="")
}
head = paste(head, pdb.file, resno.first, chain.first,
resno.last, chain.last, "", "", "", "", sep=":")
# change for shortening lines (<=60) - Xinqiu
cat(">P1;", ids, "\n", file = file, append = TRUE, sep = "")
cat(head, "\n", file = file, append = TRUE)
cat(seqs, "*", file = file, append = TRUE, sep = "", fill = 60)
}
else {
for (i in 1:nseqs) {
head = "sequence"
if(pdb.file[i]!="") {
head = "structureX"
if(chain.first[i] == "") chain.first[i] = "@"
if(resno.first[i] == "") resno.first[i] = "FIRST"
if(resno.last[i] == "") resno.last[i] = paste("+", sum(!is.gap(seqs[i,])), sep="")
}
head = paste(head, pdb.file[i], resno.first[i], chain.first[i],
resno.last[i], chain.last[i], "", "", "", "", sep=":")
cat(">P1;", ids[i], "\n", file = file, append = TRUE, sep = "")
cat(head, "\n", file = file, append = TRUE)
cat(seqs[i,], "*", file = file, append = TRUE, sep = "", fill = 60)
}
}
}
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