tylerjereddy
commented
8 years ago The examples in the docstring for both 2D and 3D cases are pretty good. I'd suggest just reproducing those or something similar if you want to have a little demo code block for utilization, and I would just do the 2D example if you were to do that.
https://pythonhosted.org/MDAnalysis/documentation_pages/visualization/streamlines.html
orbeckst
Adds a brief description of the
MDAnalysis.visualizationstreamline modules for Issue #19 and the appropriate peer-reviewed citation. I'm not sure about reusing the image that is produced in our i.e., 2D docstring, but it is already open source so should be ok I guess (i.e., the open availability of that example result should be clear in the original paper).You can find sample input / output coordinate / trajectory data on Matthieu's website (http://sbcb.bioch.ox.ac.uk/flows/MDAnalysis.html). Note that, for historical reasons, Matthieu's examples use my old python scripts that leveraged MDAnalysis rather than the integrated MDAnalysis.visualization modules directly. Regardless, the input files (linked in the text) should work well with the code I wrote in MDAnalysis.
Other details relating to the necessary pre-processing of the data (i.e., filtering the trajectories / smoothing the data) are described by Matthieu on that website and almost certainly in the paper itself.