[gmx-developers] Gromacs python api

[Shirts, Michael R. (mrs5pt)]

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
>-- 
>Gromacs Developers mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>or send a mail to gmx-developers-request at gromacs.org.