msmexplorer
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msmbuilder
Data visualizations for biomolecular dynamics
Is there a reason why an [undirected graph](https://github.com/msmexplorer/msmexplorer/blob/master/msmexplorer/plots/msm.py#L86) is built from the transition matrix in the `plot_msm_network` function? I've checked and the edges that are built when using an undirected...
There's a few mentions about keeping track of the "frame -> time" conversions in the msmbuilder code, but I didn't see any issue about it there or here. Seems like...
Taken from [here](http://www.cell.com/biophysj/fulltext/S0006-3495(17)30806-8), but probably in many papers. Should have the 2D free energy underneath? Pretty useful for exploratory analysis, especially when you look at a big grid of them....
Add a section to showcase papers that use this software.
Would be nice to have a utility that plots a user's workflow given a `Pipeline` object. Could use something like [daft](http://daft-pgm.org/) for this.
`ipymol` has an exposed API now, so it's easier to change settings, move camera, and get certain measurements: https://github.com/cxhernandez/ipymol/blob/master/examples/Example1.ipynb
https://github.com/arose/nglview/blob/a0814a824b13065b130044ca271ee19faad2d2aa/nglview/tests/notebooks/export_image.ipynb This is pretty sweet. And would be useful for interactive movie-making. @arose, @hainm: This might be a dumb question, but would it at all possible to render images independent...
e.g. https://github.com/msmexplorer/msmexplorer/pull/11 This could be broken up into a utilities module that exports to different file types?