VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 24 2014 - 17:49:26 CDT

On Thu, Jul 24, 2014 at 6:13 PM, Bachir Aoun <bachir.aoun_at_e-aoun.com> wrote:
> I didn't say there isn't, I am aware of vmdnumpy but im not able to make it
> work.

"cannot make it work" is a useless statement. without knowing what you
have tried and how and how it failed, nobody can help you.

> 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)

the documentation clearly states that you get direct and raw access to
the copy of coordinates over all frames that VMD maintains internally.
of course if you want a subset of that, you have to write a function
that makes a copy and assembles this array. you cannot have your cake
*and* eat it.

axel.

>
> 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 

-- 
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.