Base branch for new talktorials

[jaimergp]

Description

This is the base PR for the next round of new talktorials.
Some notebooks involve refactoring and extension of the former T11 talktorial series.
Supersedes #69 originally opened by @dominiquesydow.

TODOs

• Swap indices 012_query_pubmed/013_query_klifs > 012_query_klifs/013_query_pubmed
• Talktorial splits
  • Split former T11a into T012 and T013 @dominiquesydow
  • Split former T11c into T016 and T017 @jaimergp
• New and extended talktorials
  • T000 - Talktorial template @dominiquesydow T000 - Talktorial template #85
  • T011 - Online APIs/webservices (former T11) @jaimergp T011 - Querying online API webservices #84
  • T012 - Data acquisition from KLIFS (former T11a: only KLIFS) @dominiquesydow T012 - Data acquisition from KLIFS #79
  • T013 - Data acquisition from PubChem (former T11a: only PubChem) @yonghui-cc T013 - Data acquisition from PubChem #81
  • T014 - Binding site detection (former T11b: only binding site detection) @AndreaVolkamer T014 - Binding site detection #86
  • T015 - Protein-ligand docking (former T11b: only preparation and docking) @schallerdavid T015 - Protein-ligand docking #82
  • T016 - Protein-ligand interactions (former T11c: only protein-ligand interactions) @t-kimber T016 - Protein-ligand interactions #75
  • T017 - Advanced NGLview & widget usage (former T11c: only NGLview and widget stuff) @jaimergp T017 - Advanced NGLview usage #92
  • T018 - Pipeline (former T11a-c: full pipeline without details on individual steps but reference to T012-17) (postponed) T018 Pipeline #125
  • T019 - Molecular dynamics simulations @Mika-Le T019 - Molecular dynamics simulation #56
  • T020 - Analyzing molecular dynamics simulations @Mika-Le T020 - Analyzing molecular dynamics simulations #76
  • T021 - One-hot encoding @sakshimisra T021 - One-hot encoding #54
  • T022 - Ligand-based screening: Neural networks @sakshimisra T022 - Ligand-based screening: Neural networks #64
• Fix pypdb-related talktorials T008 and T010
• T011-T018 - Talktorial review by @AndreaVolkamer Final round of text reviews for T011-T018 #106
• T014: Can we remove TODO? Check if biopandas 0.2.8 can be installed. Latest conda-forge release 0.2.7 instead of 0.2.8? BioPandas/biopandas#86
• Make sure Binder runs Include new talktorials to binder setup #130 (postponed)
• T001: Update frozen dataset strategy: T001: Frozen bioactivity dataset is not frozen #134
• T019: Remove from Windows CI: T019: No openmmforcefields under Windows #136
• Add disclaimer to README linking back to old version of repo

Questions

• How do I start ? Check out the PR template: Talktorial template #41!

Status

• Ready to go

[dominiquesydow]

@schallerdavid could you please take a look at the CI fail for T016 concerning plip, potentially propagating from the MDAnalysis 3.0.0 update:
https://github.com/volkamerlab/teachopencadd/runs/3481452711#step:8:270

The chain IDs are apparently set to X (instead of A). Have you encountered this already in your plipify project?

[schallerdavid]

@schallerdavid could you please take a look at the CI fail for T016 concerning plip, potentially propagating from the MDAnalysis 3.0.0 update:
https://github.com/volkamerlab/teachopencadd/runs/3481452711#step:8:270

The chain IDs are apparently set to X (instead of A). Have you encountered this already in your plipify project?

You are correct, it's all about the chain name being changed to "X". We did not touch plipify for quite a while, so I am not sure how this change affects this project. Anyway, OpenCADD is retrieving the PDB entry in MMTF format. In the MDAnalysis docs they list all read attributes, chain ID, and element information are not read. I rerun the notebook and pushed the updated version. Let's hope the tests pass.

[dominiquesydow]

We have passing tests incl. Windows! Fails for Ubuntu are only connection timeouts! 🥳
I will merge this PR now :)

We can deal with conda packaging, website polishing ect. (see #137) in new and more digestible PRs.

A big THANK YOU to everyone who contributed new talktorials in this PR!
Also thanks to @schallerdavid for helping me out to fix the CI problems!