[gmx-developers] Gromacs python api

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Fri Jul 24 12:05:53 CEST 2015

It seems like eventually it would better to find a way to merge an API
development with the main gromacs repository and coding effort rather than
keep it a separate effort to minimized duplicated work and maximize future
usability. Just my $0.02, though!

Michael Shirts
Associate Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434) 243-1821

On 7/24/15, 1:05 AM, "Alexey Shvetsov" <alexxy at omrb.pnpi.spb.ru> wrote:

>Hi all!
>We have update for GROMACS python api bindings[1]:
>1. Its possible to implement some analisys tool in python with very
>similar api to c++ one
>2. c++ modules can be stacked, so for example its possible to extract
>angle distance and sasa information from trajectory from one trajectory
>example of tool in using py api [2][3]
>example of py script with stackable modules[4]
>PS once framework for analyzing energy files will be merged we will add
>it to pyapi
>[2] https://biod.pnpi.spb.ru/~alexxy/pygmx/planes.py
>Alexey Shvetsov писал 12-10-2014 14:06:
>> Hi all!
>> One of my students currently working on implementation of python (sip
>> based) api for gromacs analysis framework.
>> Some initial implementation lives here [1].
>> In its current state it implements trajectoryanalysis module (example
>> of usage in python [2]. Current setup can be build separately from
>> main gromacs repo, however i think that it will be good to merge it in
>> master branch in future.
>> Are there some policy or suggestions about python bindings
>> organization (code structure, in what dir py bindings should be
>> placed, may be some coding style suggestions)?
>> [1]
>> [2]
>> --
>> Best Regards,
>> Alexey 'Alexxy' Shvetsov, PhD
>> Department of Molecular and Radiation Biophysics
>> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
>> Leningrad region, Gatchina, Russia
>> mailto:alexxyum at gmail.com
>> mailto:alexxy at omrb.pnpi.spb.ru
>Best Regards,
>Alexey 'Alexxy' Shvetsov, PhD
>Department of Molecular and Radiation Biophysics
>FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
>Leningrad region, Gatchina, Russia
>mailto:alexxyum at gmail.com
>mailto:alexxy at omrb.pnpi.spb.ru
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