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mosdef-hub / gmso

Flexible storage of chemical topology for molecular simulation
https://gmso.mosdef.org
MIT License
52 stars 33 forks source link

Visualization Tools and Options #394

Open umesh-timalsina opened 4 years ago

umesh-timalsina commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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.