VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu Apr 28 2011 - 11:12:06 CDT

Hi Sara,

As Axel said, there isn't a command-line equivalent to the GUI for the
dowser plugin (sorry!!).

The easiest way to get what you want in the short term is for you to
write a modified version of the function
::Dowser::GUI::processInputFile from dowser_gui.tcl. It basically
calls a handful of functions defined in dowser.tcl sequentially. You'd
have something like:

package require dowser
proc modifed_version_processInputFile { } {
  # define variables as in resetGUI function
  # make sure there's no call to tk_messageBox
}

Please let me know how it goes and if you need further help with this.

Cheers,
Leo

On Wed, Apr 27, 2011 at 10:34 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> hi sara,
>
> On Wed, Apr 27, 2011 at 3:49 PM, Sara Nichols <sara.nichols_at_gmail.com> wrote:
>> Is there a way to run a plugin via a script?
>
> for many plugins there is.
>
>> I want to run the first part of the dowser plugin (the part that processes
>> the input structure) via the command line with out opening VMD.
>
> well, you will have to launch VMD in text mode, i.e. vmd -dispdev text
>
> scripted VMD plugins almost always make use of some VMD extension
> to the tcl interpreter.
>
> now, dowser is one of the (few?) plugins, where there is no direct
> command line equivalent of the GUI.
>
>> If not, is the source available to get a better understanding of the
>> workflow?
>
> the plugin _is_ the source. it is written in Tcl/Tk. there are two files
> dowser.tcl and dowser_gui.tcl.
>
> you may want to search the mailing list archive, because i remember
> a similar question that was asked rather recently.
>
> cheers,
>    axel.
>
>> Thanks for any help in advance,
>> Sara
>> --
>> ==
>> Sara E. Nichols, PhD
>> UCSD Pharmacology Postdoc
>> McCammon Research Group
>> ACS COMP Div. Assistant Treasurer
>> mccammon.ucsd.edu/~snichols
>> m: 619.940.6383
>>
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
> 

-- 
Leonardo Trabuco, Postdoctoral fellow (Russell group)
CellNetworks, University of Heidelberg, Germany
http://www.russelllab.org/people/leo/