VMD-L Mailing List

From: Christopher MacDermaid (chris.macdermaid_at_gmail.com)
Date: Thu May 09 2013 - 10:32:35 CDT

Hi Axel,

On Thu, May 9, 2013 at 10:21 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> **
> Why not simply canonicalize the file name yourself before calling mol new?
>

Of course, which is the workaround. However, this doesn't change that fact
that molinfo returns different things depending on how the mol was loaded.
I think it's pretty clear that the expectation should be that the absolute
path is always returned. What's the advantage the way it currently is?

> Axel
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> ------------------------------
> *From: * Christopher MacDermaid <chris.macdermaid_at_gmail.com>
> *Sender: * owner-vmd-l_at_ks.uiuc.edu
> *Date: *Thu, 9 May 2013 09:30:13 -0400
> *To: *<vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: molinfo top get filename, dialogue vs. "mol new"
>
> Hello,
>
> When calling "molinfo top get filename", the filename returned is
> different depending on the method in which I choose to load the molecule.
>
> If I use the file browser dialogue, molinfo returns the absolute path,
> however if I use the console with "mol new" it returns the relative path:
>
> vmd> mol new ../../../../test/test.pdb
>
> vmd > molinfo top get filename
> ../../../../test/test.pdb
>
> detrimental in the event that I want to reload the molecule like so and if
> I've changed working directories...
>
> proc reload { mol } {
> lassign {*}[molinfo $mol get filename] psf dcd
> mol delete $mol
> mol new $psf type psf waitfor all
> mol addfile $dcd waitfor all
> }
>
> Can this be fixed such that "mol new" will set the correct file name to
> one that is the absolute path of the loaded files. I realize this may
> present complications since mol new can be used to create an empty
> molecule, but the behavior regarding the file names is rather unexpected.
>
> Thanks!
>
> Dr. Chris MacDermaid, Postdoctoral Fellow
> Institute for Computational Molecular Science
> Temple University, Philadelphia, PA
>
> 

-- 
--
C
Dr. Chris MacDermaid, Postdoctoral Fellow
Institute for Computational Molecular Science
Temple University, Philadelphia, PA