Feature request: molecules

[SimonEnsemble]

For chemists and chemical engineers, a great feature would be to visualize molecules.

Given a list of atoms and their coordinates that make up a molecule, a distance-based algorithm could infer bonds. Then GLVisualize.jl could draw the spheres (size and color according to atom) and bonds connecting them.

We study porous materials and my community frequently likes to visualize potential energy contours of a molecule inside of a porous material. This is a visualization I made with VisIt, which would be great to be able to do in GLVisualize.jl

I can certainly help in terms of file formats, bonding rules, color schemes used in the chemistry community.

We are currently writing a Julia package to basically output the 3D array of potential energies, so we could use this example to visualize the contours, but we'd like to be able to see the atoms of the material as well as in the above visualization. Thanks.

[SimonDanisch]

Have you seen: #190 and #227 ?
If you can give me some easily digestible data, I can see if I find time to play around with this. The molecule shapes seem pretty straight forward :)

[SimonEnsemble]

@SimonDanisch So #190 shows that GLVisualize.jl can handle slanted grants, which is imperative for our visualizations of crystals (which more often than not have slanted unit cells). And #227 shows that we can introduce transparency.

Thanks for your help, that would be awesome! I put up an example here:
https://github.com/SimonEnsemble/MoleculeViz.jl
include("reader.jl") should import arrays of all of the data you need with regard to each atom (element, position, color, radius).

.xyz files and .vtk are common formats for molecule visualizations and unit cell boxes, respectively. I'd be happy to write a function for the bonding rules and to allow the user to change the bonding rules. Let me know if there is anything I can do to help.

In the end, we want to draw potential energy contours on top of the molecule visualization.

Here is an example of OpenGL visualization of a molecule if that helps (but in C).