[gmx-developers] Gromacs API development and example scripts

Joe Jordan e.jjordan12 at gmail.com
Wed Jan 30 15:29:52 CET 2019

One thing that immediately popped out at me when taking a quick look at the
scripts is that gmx.commandline_operation takes a complicated series of
arguments that maps directly onto the flags you would pass on the command
line. This is rather unpythonic (that dreaded word!) and caused me to
wonder how it is implemented under the hood. A quick grep of the gmxapi
branches from github did not turn up anything. Is this feature in some
unreleased version? Further, and more to the point, is the ultimate plan to
convert this to take *args and **kwargs? I guess my question here boils do
to, what are the plans surrounding wrapping (or otherwise) of gromacs calls
in python and is there a place where that discussion is taking place? Since
many users will be quite excited to be able to run gromacs from python, I
think this is a key feature that merits some discussion.

On Wed, Jan 30, 2019 at 2:04 PM Peter Kasson <kasson at virginia.edu> wrote:

> Hi everyone,
>   We are working on the next round of features for gmxapi, the high-level
> Gromacs API with Python bindings.  We have written a set of python scripts
> that demonstrate our planned functionality.  There are a few syntax issues
> being ironed out, but we thought this would be a good time to share them
> with the community.  If there are a) things that are obviously stupid, b)
> missing functionality that would be particularly important for a big
> fraction of the community, or c) things we're planning that you're super
> excited about, please let us know!
> Code at:
> https://github.com/kassonlab/gmxapi-scripts
> Disclaimer 1: These are primarily demonstration scripts, not design docs
> or user docs.
> Disclaimer 2:  We are taking an incremental approach to API
> functionality.  We're trying to do a few things well and then expand the
> scope of things we do.  But we want those few things to cover as many use
> cases as we can...
> Best,
> --Peter Kasson
> ----------------------------------------------------------------------
> Peter Kasson, MD, PhD
> Associate Professor
> Departments of Molecular Physiology and Biological Physics
> and of Biomedical Engineering
> University of Virginia
> and
> Department of Cell and Molecular Biology, Uppsala University
> --
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Joe Jordan
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