<div dir="ltr">One thing that immediately popped out at me when taking a quick look at the scripts is that <span style="color:rgb(36,41,46);font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,Courier,monospace;font-size:12px;white-space:pre">gmx.commandline_operation </span>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.</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jan 30, 2019 at 2:04 PM Peter Kasson <<a href="mailto:kasson@virginia.edu">kasson@virginia.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div dir="ltr" class="gmail-m_7067407791971571632gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Hi everyone,<div> 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!</div><div><br></div><div>Code at:</div><div><a href="https://github.com/kassonlab/gmxapi-scripts" target="_blank">https://github.com/kassonlab/gmxapi-scripts</a><br></div><div><br></div><div>Disclaimer 1: These are primarily demonstration scripts, not design docs or user docs.</div><div><br></div><div>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...</div><div><br></div><div>Best,</div><div>--Peter Kasson</div><div><br></div><div><div><div dir="ltr" class="gmail-m_7067407791971571632gmail-m_7562731658442928741gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>----------------------------------------------------------------------<br>Peter Kasson, MD, PhD<br>Associate Professor<br>Departments of Molecular Physiology and Biological Physics<br>and of Biomedical Engineering<br>University of Virginia<br></div><div>and </div><div><span style="font-size:12.8px">Department of Cell and Molecular Biology, Uppsala University</span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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