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GUI commands to call for a protein from protein data bank

5 messages · Amitoj S. Chopra, j verzani

Original
Amitoj S. Chopra
# 
What I am trying to do is use GUI function, traitr, and to call for a pdb
file and save it and then display it. I want to call for it by taking it
from the user and then displaying it on the screen. I am having problems
with that. The line pdb <- read.pdb(""ProteinCode) where proteincode should
be the name of the protein, for example 1ly2, but it always ends up being
protein. My question is how to you make the input for read.pdb actually be
the input by the user and not protein code. I want to be able to type 1ly2,
and for the program to actually display the contents of 1ly2. Thanks!




Code:

dlg <- aDialog(items=list(
ProteinCode=stringItem("")
),
OK_handler=function(.) { # . is reference to dlg object
values <- .$to_R()
f <- function(ProteinCode)
pdb <- read.pdb("ProteinCode")
do.call(f, values)
}
)
dlg$make_gui()
j verzani
# 
Amitoj S. Chopra <amitojc <at> gmail.com> writes:
I'm just guessing, but you might try this for your OK_handler:

OK_handler=function(.) {
  pdb <- read.pdb(.$get_ProteinCode())
}

(Or use yours, but drop the quotes around "ProteinCode".)

That doesn't modify pdb outside the scope of the handler, so likely you need to
do something else with it.

--John
j verzani
# 
Amitoj S. Chopra <amitojc <at> gmail.com> writes:
Not sure why this makes a difference, but if it does great. As to
programattically closing a dialog, the method close_gui is available, as in
dlg$close_gui(). (The proto methods for an object dlg are shown in a web page by
calling dlg$show_help().)

--John

..snipped..