Nothing
"aa321" <-
function (aa) {
# convert three-letters amino-acid code into
# one-letter IUPAC code, for instance "ALA" into "A".
# new residues should be added to through the util/make_aatable.R script
aa1 <- c("-", ".", "X", bio3d::aa.table$aa1)
aa3 <- c("---", "---","UNK", bio3d::aa.table$aa3)
convert <- function(x) {
if(is.na(x)) return(NA)
if (all(x != aa3)) {
warning(paste("Unknown 3-letters code for aminoacid:",x))
return("X") # mask unk
}
else {
return(aa1[which(x == aa3)])
}
}
return(as.vector(unlist(sapply(aa, convert))))
}
".aa321.na" <-
function (aa) {
# convert three-letters amino-acid code into
# one-letter IUPAC code, for instance "ALA" into "A".
aa1 <- c("-",".","X",
"C", "G", "T", "A", "U", "I",
"C", "G", "T"," A", "U", "I")
aa3 <- c("---", "---","UNK",
"DC", "DG", "DT", "DA", "DU", "DI",
"C", "G", "T", "A", "U", "I")
convert <- function(x) {
if(is.na(x)) return(NA)
if (all(x != aa3)) {
warning(paste("Unknown 3-letters code for residue:",x))
return("X") # mask unk
}
else {
return(aa1[which(x == aa3)])
}
}
return(as.vector(unlist(sapply(aa, convert))))
}
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