VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jul 24 2014 - 17:54:39 CDT

Unfortunately its as simple as recompiling VMD with python support,
since the default binaries distributed don't include it (which is why
you can't get it to work in all likelihood). Not many people use the
python interface to VMD (<1% of the VMD install base) since it means you
need to compile VMD yourself to accommodate your system version of
python. If you've ever compiled VMD before, its trivial to add it, and
the docs are all there online on how to use it. If not, I'd encourage
you to learn, as it took me a weekend to get it all figured out the
first time I compiled VMD from source. Since then, its probably
increased my productivity by an order of magnitude, since I can do math
on results without going through expr.
-Josh
On 7/24/14, 6:13 PM, Bachir Aoun wrote:
> I didn't say there isn't, I am aware of vmdnumpy but im not able to
> make it work.
> if you have any example that you can share that would be very helpful.
> any example that would lets say export a numpy array of a selection of
> atoms over a number of configurations (frames)
> something like that: export(atomsIndexes, framesIndexes, outputFileName)
>
> thanks
>
>
> On Thu, Jul 24, 2014 at 5:04 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> <mailto:akohlmey_at_gmail.com>> wrote:
>
> On Thu, Jul 24, 2014 at 5:33 PM, Bachir Aoun
> <bachir.aoun_at_e-aoun.com <mailto:bachir.aoun_at_e-aoun.com>> wrote:
> > thank you guys,
> > I already know about MDanalysis, it's a package itself and uses
> c libraries
> > to parse dcd files. Since vmd support python I was hoping there
> is a simple
> > solution within vmd itself.
>
> what makes you think there isn't?
>
> >
> > thanks
> >
> >
> > On Thu, Jul 24, 2014 at 2:59 PM, Ajasja Ljubetič
> <ajasja.ljubetic_at_gmail.com <mailto:ajasja.ljubetic_at_gmail.com>>
> > wrote:
> >>
> >> Just save the frames into a DCD and load that directly into
> python using
> >> https://code.google.com/p/mdanalysis/.
> >>
> >>
> >> On 24 July 2014 20:58, Bachir Aoun <bachir.aoun_at_e-aoun.com
> <mailto:bachir.aoun_at_e-aoun.com>> wrote:
> >>>
> >>> Hi
> >>>
> >>> I am having hard time extracting atoms coordinates from vmd to
> do some
> >>> data analysis using python scripts.
> >>> the way i am doing it right now is to export all trajectory
> frames in pdb
> >>> files, read all the pdbf iles with a python script and parse
> the coordinates
> >>> into a numpy array.
> >>>
> >>> is there any way to directly export an array of atoms
> coordinates along
> >>> all trajectory configurations from vmd to a python environment
> (usually
> >>> numpy).
> >>>
> >>> thanks
> >>
> >>
> >
> >
> >
> > --
> > Bachir AOUN
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia
> PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
> --
> Bachir AOUN