[gmx-developers] Gromacs python api

[Alexey Shvetsov]

Hi!

I updated relevant change on gerrit 
https://gerrit.gromacs.org/#/c/4269/12

Alexey Shvetsov писал 24-07-2015 13:27:
> 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

-- 
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