Support MDAnalysis.Universe as the frame parameter

[GardevoirX]

Closes #358

This PR allows passing a Universe object to the frame parameter of chemiscope.show. It can be checked by running

import chemiscope
import MDAnalysis as mda

u = mda.Universe("./python/examples/data/trajectory.xyz")
chemiscope.show(frames=u, mode="structure")

As mda is usually used in analyzing biosystem-related trajectories, I also tried it on a pdb file containing two peptides, but I found the current representation schemes cannot display the protein well (see below), maybe we can later consider supporting the ribbon diagram representation?

[Luthaf]

Thanks a lot, this is very nice!

From the screenshot, it looks like the structure is using the wrong unit. Chemiscope/3Dmol.js assumes Angstroms, but I think MDA is using nm. I think there should be at least some automatically guessed bonds in this structure.

As a related point, does MDA add back the implicit H atoms that are often missing in bioinformatics file formats?

maybe we can later consider supporting the ribbon diagram representation?

This is #127, PR welcome! The biggest issue there will be that we will need to add another field to chemiscope's JSON containing information about alpha carbons / some level of pre-computed secondary structure information.

[GardevoirX]

From the screenshot, it looks like the structure is using the wrong unit. Chemiscope/3Dmol.js assumes Angstroms, but I think MDA is using nm. I think there should be at least some automatically guessed bonds in this structure.

In this screenshot, I turned off the bond display, otherwise it would be totally a mess 👇 But I agree that there might be a unit issue. I will look at it later.

As a related point, does MDA add back the implicit H atoms that are often missing in bioinformatics file formats?

No, it doesn't.

[GardevoirX]

Regarding the unit issue, I think mda read the coordinate in the structure file as-is. The real difference comes from the units that are used by different formats (like Å for xyz and nm for pdb, generally speaking). And it might be hard to tell which unit is being using from chemiscope side.

[Luthaf]

https://userguide.mdanalysis.org/stable/units.html Looks like everything should be in A. I'm not sure what's happening in the initial screenshot though. Which file did you use for it?

[GardevoirX]

Ahh yes, thanks! I used this file. And in the initial screenshot, I toggled off the bond. Perhaps you can take the latter one for your reference.