Visualization Tools and Options

[umesh-timalsina]

At this point, I think we can incorporate some form of visualization for a topology. I am opening this issue to discuss options for visualization, libraries we want to use as well as a proper techniques.

[vyasr]

AFAIK nglview is sort of the default option in this space, assuming you're talking about visualizing in a Jupyter notebook or something similar. I assume that once the topology has been put into some trajectory format you'd fall back to standard tools like VMD or PyMol.

[mattwthompson]

I don't think much has changed in "3D" world within Jupyter; NGLview is still the best if it works.

If you can get into "2D" world, RDKit and some similar tools work really nicely for i.e. visualizing individual molecules. That probably won't work for an entire (multi-molecule) topology.