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Adding DeepChemXAlphafold tutorial #3574

Merged
merged 20 commits into from
Nov 20, 2023
Merged

Adding DeepChemXAlphafold tutorial #3574

merged 20 commits into from
Nov 20, 2023

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soulpower007
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Description

Adding DeepChemXAlphafold.ipynb notebook tutorial and added it in readme and respective csv as well.
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  • Bug fix (non-breaking change which fixes an issue)
  • [x ] New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
    • In this case, we recommend to discuss your modification on GitHub issues before creating the PR
  • Documentations (modification for documents)

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  • My code follows the style guidelines of this project
    • [x ] Run yapf -i <modified file> and check no errors (yapf version must be 0.32.0)
    • [ x] Run mypy -p deepchem and check no errors
    • Run flake8 <modified file> --count and check no errors
    • [ x] Run python -m doctest <modified file> and check no errors
  • [ x] I have performed a self-review of my own code
  • [x ] I have commented my code, particularly in hard-to-understand areas
  • [ x] I have made corresponding changes to the documentation
  • I have added tests that prove my fix is effective or that my feature works
  • New unit tests pass locally with my changes
  • [x ] I have checked my code and corrected any misspellings

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rbharath
rbharath reviewed Sep 27, 2023
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examples/tutorials/AlphafoldXDeepChem.ipynb Outdated
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@rbharath rbharath Sep 27, 2023 •
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Line #10.

Make sure to remove extra whitespace


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@rbharath rbharath Sep 27, 2023 •
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Combine these lines into a paragraph. Make sure to use complete sentences, active voice


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examples/tutorials/AlphafoldXDeepChem.ipynb Outdated
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@rbharath rbharath Sep 27, 2023 •
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Formatting errors. Also, again use complete sentences.


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examples/tutorials/AlphafoldXDeepChem.ipynb Outdated
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@rbharath rbharath Sep 27, 2023 •
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Formatting


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examples/tutorials/AlphafoldXDeepChem.ipynb Outdated
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@rbharath rbharath Sep 27, 2023 •
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Formatting


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@rbharath rbharath Sep 27, 2023 •
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Break this down into a few cells and add description between them


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@rbharath rbharath Sep 27, 2023 •
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Too much code, let's break down into a few cells


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@rbharath rbharath Sep 27, 2023 •
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Formatting


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sure changed

rbharath
rbharath reviewed Oct 4, 2023
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@rbharath rbharath Oct 4, 2023 •
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Quick reminder to add the install code back in


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sure done

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@rbharath rbharath Oct 4, 2023 •
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Add a bit more detail on what this patch does. Add a few sentences about what mmseqs2


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done

examples/tutorials/DeepChemXAlphafold.ipynb Outdated
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@rbharath rbharath Oct 4, 2023 •
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Maybe rename as "Installation". This is currently confusing, put everything with install first then have a next section that gets input


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sure done

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@rbharath rbharath Oct 4, 2023 •
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Line #11.    query_sequence = 'PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK' #@param {type:"string"}

Put this query sequence in its own cell so users can easily try other sequences


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done

examples/tutorials/DeepChemXAlphafold.ipynb Outdated
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@rbharath rbharath Oct 4, 2023 •
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Can you explain what these different templates are?


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yeup added explanations

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@rbharath rbharath Oct 4, 2023 •
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Move all install dependencies to the top


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sure restructured the tutorial

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@rbharath rbharath Oct 4, 2023 •
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Can you add a reference link to the A3M format specification?


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yes done

examples/tutorials/DeepChemXAlphafold.ipynb Outdated
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@rbharath rbharath Oct 4, 2023 •
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Let's simplify and omit


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done, removed the other option of adding custom mmseq files as it wasn't being used in this tutorial

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@rbharath rbharath Oct 4, 2023 •
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Make this a "Save to Google Drive" section


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done

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@rbharath rbharath Oct 4, 2023 •
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Is there a tool we can use to visualize pockets?


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nglview is commonly used to visualize proteins. However, it does't work properly on google colab. googlecolab/colabtools#2853 (comment). An issue was raised on it and google colab team has triaged it. We might have to look for alternatives of protein visualization on google colab.

rbharath
rbharath approved these changes Nov 20, 2023
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LGTM

@rbharath rbharath merged commit f8c6f0d into deepchem:master Nov 20, 2023
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