[2023.05.2-base] DL edition

[AndreaVolkamer]

Description

TeachOpenCADD DL edition.

Comments from @dominiquesydow:

• I started listing the new talktorials and (new) DL-related dependencies.
• Please check if correct and add any missing new dependencies per talktorial (I listed tensorflow here although already part of the env since this package causes us a great deal of trouble for over a year now and tbh I'd love to get rid of it, tbd.)
• General note: Each new notebook should add as few new deps as possible (at least as long as we do not have a per-notebook env and CI).
• Extended MacOS/M1 chip instructions: Docs: Add more MacOS/M1 install instructions #301
• Check out the new contributor guide at https://projects.volkamerlab.org/teachopencadd/contribute.html once Add TeachOpenCADD contribution guide #274 is merged

Todos

• [DL Edition] T033: Molecular representations #314 (nb) @gerritgr
• [DL Edition] T034: GNN based molecular property prediction #287 (nb) @PaulaKramer
  • DL deps: torch and torch_geometric
• [DL Edition] T035: SMILES based property prediction #320 (nb) @azmtag
• [DL Edition] T036: Uncertainty estimation #286 (nb) @mbackenkoehler
  • DL deps: tensorflow -- which minimum version?
• [DL Edition] T037: E(3)-invariant graph neural networks #326 (nb) @joschka-gross
  • DL deps: torch and torch_geometric and torch_scatter??
• [DL Edition] T038: Protein Ligand Interaction Prediction #290 (nb) @Old-Shatterhand
  • DL deps: torch and torch_geometric
  • torch_geometric dependencies: torch_scatter, torch_sparse, torch_cluster, torch_spline_conv (without these, torch_geometric might not work. (Added by @Old-Shatterhand)
• T033-38: changed notebook ordering #357 change DL notebook ordering

Questions

• Question1

Status

• Ready to go

[dominiquesydow]

@AndreaVolkamer what is your current plan with this PR regarding the merge? First merging #345 and then this?

[AndreaVolkamer]

@dominiquesydow yes, we first merge the PR #345 to update the master branch, then we merge the new notebooks into it (this PR).

[mbackenkoehler]

I changed the target to dev. We can test out the environment and the merge in general before the DL_edition release.