Nothing
print.prmtop <- function(x, printseq=TRUE, ...) {
if(!is.null(x$SOLVENT_POINTER))
sbox <- TRUE
else
sbox <- FALSE
cn <- class(x)
natom <- x$POINTERS[1]
##nca <- length(which(x$ATOM_NAME=="CA" & x$AMBER_ATOM_TYPE=="CX"))
if(sbox) {
nres.total <- x$POINTERS[12]
nres.solute <- x$SOLVENT_POINTER[1]
nmol.total <- x$SOLVENT_POINTER[2]
nmol.solute <- x$SOLVENT_POINTER[3]-1
natom.per.mol <- x$ATOMS_PER_MOLECULE[1:nmol.solute]
box.dim <- x$BOX_DIMENSIONS
}
else {
nres.total <- x$POINTERS[12]
nres.solute <- nres.total
nmol.total <- length(which(x$ATOM_NAME=="OXT"))
nmol.solute <- nmol.total
}
cat("\n Call:\n ", paste(deparse(x$call), sep = "\n", collapse = "\n"),
"\n\n", sep = "")
cat(" Class:\n ", paste(cn, collapse=", "),
"\n\n", sep = "")
cat(" System information:", "\n")
cat(" Total number of atoms: ", natom, "\n", sep="")
if(nres.solute!=nres.total) {
cat(" Solute residues: ", nres.solute, " (of ", nres.total, ")\n", sep="")
cat(" Solute molecules: ", nmol.solute, " (of ", nmol.total, ")\n", sep="")
}
else {
cat(" Solute residues: ", nres.solute, "\n", sep="")
cat(" Solute molecules: ", nmol.solute, "\n", sep="")
}
if(sbox)
cat(" Box dimensions: ", paste(round(box.dim,2), collapse=" x "), "\n", sep="")
if(printseq) {
aa <- aa321(x$RESIDUE_LABEL[1:nres.solute])
if(nres.solute > 225) {
## Trim long sequences before output
aa <- c(aa[1:225], "...<cut>...", aa[(nres.solute-3):nres.solute])
}
aa <- paste(" ", gsub(" ","",
strwrap( paste(aa,collapse=" "),
width=120, exdent=0) ), collapse="\n")
cat("\n")
cat(" Sequence:\n", aa, "\n", sep="")
## other residues
if(nres.total>nres.solute) {
unq.res <- unique(x$RESIDUE_LABEL[(nres.solute+1):length(x$RESIDUE_LABEL)])
unq.res <- paste(" ", gsub(" ","",
strwrap( paste(unq.res,collapse=" "),
width=120, exdent=0) ), collapse="\n")
cat("\n")
cat(" Residues in solvent:\n", unq.res, "\n", sep="")
}
}
cat("\n")
#i <- paste( attributes(x)$names, collapse=", ")
#cat(strwrap(paste(" + attr:",i,"\n"),width=45, exdent=8), sep="\n")
invisible( c(natom=natom, nres=nres.total, nres.solute=nres.solute,
nmol=nmol.total, nmol.solute=nmol.solute) )
}
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