[gmx-developers] Gromacs python api

[Alexey Shvetsov]

Hi!

Its implemented as part of GROMACS source tree. In current state its 
usable for writing simple python tools or for batch processing 
trajectoryes with c++ analysis modules.


Shirts, Michael R. (mrs5pt) писал 24-07-2015 13:05:
> 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!
> 
> Best
> ~~~~~~~~~~~~
> 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
>> read
>> 
>> 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
>> 
>> [1]
>> http://biod.pnpi.spb.ru/gitweb/?p=alexxy/gromacs.git;a=shortlog;h=refs/hea
>> ds/pygromacs
>> [2] https://biod.pnpi.spb.ru/~alexxy/pygmx/planes.py
>> [3]
>> https://biod.pnpi.spb.ru/gitweb/?p=alexxy/gromacs.git;a=blob_plain;f=src/p
>> ython/test.py;hb=431623ab5cb2ff34e7052b4bba0d84550a295c6a
>> [4]
>> https://biod.pnpi.spb.ru/gitweb/?p=alexxy/gromacs.git;a=blob_plain;f=src/p
>> ython/pipeline_test.py;hb=431623ab5cb2ff34e7052b4bba0d84550a295c6a
>> 
>> 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]
>>> 
>>> http://biod.pnpi.spb.ru/gitweb/?p=alexxy/gromacs.git;a=shortlog;h=refs/he
>>> ads/pygromacs
>>> [2]
>>> 
>>> http://biod.pnpi.spb.ru/gitweb/?p=alexxy/gromacs.git;a=blob;f=src/pygroma
>>> cs/test.py;h=5c01936423f86ae9f99eaf3117adcfb8486eb1b2;hb=07e8a2a25ab5a62f
>>> 63af77fe0dd1405cd41ee5ce
>>> --
>>> 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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-- 
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