Visualizing molecules and simulations

[chemicalfiend]

Hi, I felt as though the AtomsBase package had a lot of potential to be a great way for all Julia chemistry and materials science folks to outsource their structures (and simulation trajectories) visualization to. I wanted to get the ball rolling on this since I was working with a visualization issue on Molly.jl. Molly uses Makie pretty well to get the simulation trajectory output as an mp4 file.

I was looking into some other projects as well and found Alchemy.jl by @gustavojra for quantum mechanics (but can't seem to get it running for some reason) and this for single molecule visualization. However I think we could probably come up with a whole pure-Julia visualization suite for molecular simulation, similar to VMD or Ovito but free and open source and fast on Julia! Let me know what you think!

[jgreener64]

Great idea. I think this should be a separate package in the JuliaMolSim org but good to get the ball rolling here.

One way would be to modify the visualize function to only use the AtomsBase interface (i.e. nothing Molly specific), then to move it to its own package and test it with other implementations of the AtomsBase interface that are out there.

I would be very happy for it to move to its own package since GLMakie is quite a heavy dependency and the current Requires.jl setup is causing problems with testing.

BioMakie.jl also has some cool and relevant stuff.

[chemicalfiend]

Sure, moving it to its own package sounds great too. I'll mess around with visualize and AtomsBase and the other packages and then we can see about moving it to its own package.

[mfherbst]

Wow this sounds great! Thanks @chemicalfiend for getting started on this.

[rkurchin]

Seconded! Feel free to ping me whenever there's an associated repo/PR/whatever, happy to be involved in testing, etc.!