[R] GUI commands to call for a protein from protein data bank

[j verzani]

Amitoj S. Chopra <amitojc <at> gmail.com> writes:

> 
> 
> 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!
> 

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


> 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()