From: Bachir Aoun (bachir.aoun_at_e-aoun.com)
Date: Thu Jul 24 2014 - 17:13:27 CDT

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> wrote:

> On Thu, Jul 24, 2014 at 5:33 PM, Bachir Aoun <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>
> > 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> 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 http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>

-- 
Bachir AOUN