VMD-L Mailing List

From: Sara Nichols (sara.nichols_at_gmail.com)
Date: Thu Apr 28 2011 - 11:28:43 CDT

Thanks, I found that, and it worked.
Sara

On Thu, Apr 28, 2011 at 9:12 AM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>wrote:

> 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/
> 

-- 
==
Sara E. Nichols, PhD
UCSD Pharmacology Postdoc
McCammon Research Group
ACS COMP Div. Assistant Treasurer
mccammon.ucsd.edu/~snichols
m: 619.940.6383