Wishlist / Project Ideas for Google Summer of Code 2022

We will once again apply to be a part of Google Summer of Code 2022.

Last year, Marc added both ribbon / cartoon rendering and the layer system.

I’ve posted a few ideas to the Open Chemistry wiki:

  • Python scripting (i.e., both a terminal and running scripts, e.g., rendering a movie from rotating a molecule)
  • Integration with RDKit (e.g., for coordinate generation using ETKDG, optimizing with UFF / MMFF94, etc.)
  • Fast, efficient molecular surfaces / orbitals
  • Interactive molecular dynamics - improving on the “auto-optimize” in Avogadro v1, it would be great to apply a temperature and watch a system evolve … even if you pull/push on an atom or molecule
  • Generating “systems” like packed membranes, MOF or COF frameworks, etc.

Other ideas or suggestions?

This is a great list, @ghutchis! I can add some ideas:

  • Fragments to insert, and it will be good if we can point to the exact atom where to put them
  • Rendering styles as in VMD
  • Labels for atoms/amino acid residues
  • Generation of high-resolution images. Also, vector images would be highly appreciated, since I never saw an application that can generate them correctly.
  • Geometry optimization and MD with periodic boundaries. Building them from scratch is a huge pain!
  • Surfaces! Not only orbitals, but ESP with coloring, .cube data…
  • Vibrations and IR spectra
  • Non-covalent interactions, from quantum chemistry output or based on protein-ligand complex
    Sadly, many functions in v.1.90 are not working properly for me, so it would be great to fix them, too.
1 Like

Can you describe this a bit more?

A few other comments:

  • Fragments to insert, and it will be good if we can point to the exact atom where to put them

This is coming. I have a new fragment builder tool. You’d be able to point to one atom (or more, e.g. bidentate ligands)

  • Labels for atoms/amino acid residues

This was part of last year’s GSoC. There’s even a new label tool to add custom labels to atoms.

  • Generation of high-resolution images. Also, vector images would be highly appreciated, since I never saw an application that can generate them correctly.

Marc added a simple SVG export, but we can definitely build on that.

  • Surfaces! Not only orbitals, but ESP with coloring, .cube data…

Cube data should already work, but yes, the project for surfaces would include mapping properties, ESP, etc.

  • Vibrations and IR spectra

You can animate vibrations now, but plotting spectra is important. Actually, I should go add that to the project list.