Fixing askcos

[kabu00002]

Description

Instead of using the outdated (and not working) Askcos API, we now use Askcos Core V2.

Todos

• Adapt the implementation
• Rerun notebook 1_3 and 2_1
• Update README

Questions

Status

• Ready to go

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PaulaKramer commented on 2024-05-13T14:46:26Z
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The ROMol is not displayed in dataframe

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PaulaKramer commented on 2024-05-13T14:46:27Z
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ROMol not displayed here

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PaulaKramer commented on 2024-05-13T14:46:27Z
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Same here (ROMol)

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PaulaKramer commented on 2024-05-13T14:46:28Z
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We've discussed this but for completeness: GA pocket missing in plot :)

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PaulaKramer commented on 2024-05-13T14:46:30Z
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Remove DataWarrior here

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PaulaKramer commented on 2024-05-13T14:46:30Z
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Paths have changed - I think it was renamed to data/filters/Enamine

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PaulaKramer commented on 2024-05-13T14:46:31Z
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GA missing (I assume it's the same function as above)

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PaulaKramer commented on 2024-05-13T14:46:33Z
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Spelling: succesfully -> successfully, installtion -> installation

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PaulaKramer commented on 2024-05-13T14:46:33Z
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spelling: installion -> installation

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PaulaKramer commented on 2024-05-13T14:46:35Z
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spelling last word (installation)

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PaulaKramer commented on 2024-05-13T14:46:35Z
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Plots missing GA

I'm also a little confused that the B2 pocket is completely empty now... This means that they removed some retrosynthetic pathways in ASKCOS? Because at least the fragments that were found in the earlier customkinfraglib version should technically still be found?

kabu00002 commented on 2024-05-27T07:16:35Z
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Not necessarily since we fixed the bug in kinfraglib which might disallow the combination of a B2 fragment with another one, where a retro route was found. Further, the methodology of askcos was changed (?)

[PaulaKramer]

Thanks for the changes! I have reviewed the notebooks and added small changes to the readme. Can you add another ASKCOS installation hint in the readme for the data (either in data/filters/ or in data/filters/retro) - I don't really have a preference here :)

[kabu00002]

Not necessarily since we fixed the bug in kinfraglib which might disallow the combination of a B2 fragment with another one, where a retro route was found. Further, the methodology of askcos was changed (?)

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[kabu00002]

Thanks for the changes! I have reviewed the notebooks and added small changes to the readme. Can you add another ASKCOS installation hint in the readme for the data (either in data/filters/ or in data/filters/retro) - I don't really have a preference here :)

Done :)