[gmx-developers] Gromacs python api

Peter Kasson kasson at virginia.edu
Mon Oct 13 13:28:17 CEST 2014


We (Kasson, Shirts, Abraham, Lindahl) have been planning a broader Gromacs
API, but the spec isn't complete yet, and the project isn't fully staffed.
Speaking for myself at least, I would say that having some clean working
code now is better than having beautiful plans.  So this sounds great!  A
few comments below:

1.  Depending on how much you want to merge this into master and how much
you want the code in master 2 years from now to look like your initial
commits (i.e. future radical refactoring), please feel free to ignore the
rest of what I say :).

2.  It's probably best to get an API spec reviewed before committing full
code (or ideally before writing it).  If the code review consensus is that
the design should look different, there's a lot less work that way.

3.  IMO the Python API should look a lot like the C++ API.  For most of
Gromacs, the form of the C++ API isn't clear.  But for the analysis
framework, Teemu has done a great job with that...

4.   Again, depending on your plans for how this code should relate to the
Gromacs master, we should probably have a redmine discussion.

5.  Coding style--we use the following guidelines, and they're the ones I
would advocate:

6.  Directory structure should probably mirror the module import structure.


Peter Kasson, MD, PhD
Assistant Professor
Departments of Molecular Physiology and Biological Physics
and of Biomedical Engineering
University of Virginia
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