VMD-L Mailing List

From: Christopher MacDermaid (chris.macdermaid_at_gmail.com)
Date: Thu May 09 2013 - 10:43:20 CDT

OK, then that's the way it is then :-)

Thanks.

On Thu, May 9, 2013 at 11:41 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> **
> The GUI always returns a canonical file name. With the current setup you
> can have relative paths stored in scripting. Forcing those to be
> canonicalized inside of VMD removes that option. In scripting you always
> can adjust your script.
>
> If I remember correctly the current behavior was adopted because there
> were requests from people that were dissatisfied with the behavior you are
> asking for.
>
> 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>
> *Date: *Thu, 9 May 2013 11:32:35 -0400
> *To: *Axel Kohlmeyer<akohlmey_at_gmail.com>
> *Cc: *<vmd-l_at_ks.uiuc.edu>
> *Subject: *Re: vmd-l: molinfo top get filename, dialogue vs. "mol new"
>
> 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
>
> 

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