WIP (no active development) - New talktorial: T029: GPCR data acquisition from GPCRdb

[dominiquesydow]

Details - new talktorial

• Talktorial ID: T029
• Title: GPCR data acquisition from GPCRdb
• Original authors: @dominiquesydow

Content TODOs

• GPCR background
• GPCRdb background
• Show case programmatic access
• Add use case: Interaction profile for query target
• Show interacting residues in 3D (NGLviewer)
• Show interacting residues in snake plot or helix box plot (can be requested from https://gpcrdb.org/services/)
• Add user structures (not in GPCRdb) to dataset

Content checklist

• Potential labels or categories (e.g. machine learning, small molecules, online APIs): XXXXXXXX
• One line summary: XXXXXXXXXX
• I have used the talktorial template and followed the formatting suggested there
• The table of contents reflects the talktorial story-line; order of #, ##, ### headers is correct
• URLs are linked with meaningful words, instead of pasting the URL directly or linking words like here.
• I have spell-checked the notebook
• Images have enough resolution to be rendered with quality, without being too heavy.
• All figures have a description
• Markdown cell content is still in-line with code cell output (whenever results are discussed)
• I have checked that cell outputs are not incredibly long (this applies also to DataFrames)
• Formatting looks correctly on the Sphinx render (bold, italics, figure placing)

Code checklist

• Time it took to execute (approx.):
• Variable and function names follow snake case rules (e.g. a_variable_name vs aVariableName)
• Spacing follows PEP8 (run Black on the code cells if needed)
• Code line are under 99 characters each (run black -l 99)
• Comments are useful and well placed
• There are no unpythonic idioms like for i in range(len(list)) (see slides)
• All 3rd party dependencies are listed at the top of the notebook
• I have marked all code cell with output referenced in markdown cells with the label # NBVAL_CHECK_OUTPUT
• I have identified potential candidates for a code refactor / useful functions
• All import ... lines are at the top (practice part) cell, ordered by standard library / 3rd party packages / our own (teachopencadd.*)
• I have update the relative paths to absolute paths.

  HERE = Path(_dh[-1])
  DATA = HERE / "data"

• List here unfamiliar libraries you find in the imports and their intended use:

Before merging

• Revert the changes in the CI: bc8aa2e

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