[gmx-developers] Gromacs python api

[Alexey Shvetsov]

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/heads/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/python/test.py;hb=431623ab5cb2ff34e7052b4bba0d84550a295c6a
[4] 
https://biod.pnpi.spb.ru/gitweb/?p=alexxy/gromacs.git;a=blob_plain;f=src/python/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/heads/pygromacs
> [2]
> http://biod.pnpi.spb.ru/gitweb/?p=alexxy/gromacs.git;a=blob;f=src/pygromacs/test.py;h=5c01936423f86ae9f99eaf3117adcfb8486eb1b2;hb=07e8a2a25ab5a62f63af77fe0dd1405cd41ee5ce
> --
> 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