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sonjaleo / KinFragLib

Kinase-focused fragment library
MIT License
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added README.md file explaining how to get DataWarrior file #7

Closed sonjaleo closed 3 years ago

sonjaleo commented 3 years ago

Description

Create a README.md file to explain how to get the DataWarrior file

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Status

sonjaleo commented 3 years ago

Hi @sonjaleo,

Great README with all the details needed, well done! I suggest a few format changes but that's it.

You could link to your notebook as an example if you want.

@dominiquesydow not sure which notebook you mean? Because the steps that are now in the README should be deleted in the notebook. Or do you mean linking the notebook where the DataWarrior file is used?

dominiquesydow commented 3 years ago

@dominiquesydow not sure which notebook you mean? Because the steps that are now in the README should be deleted in the notebook. Or do you mean linking the notebook where the DataWarrior file is used?

Good point... you do have a notebook or script that you use to prepare the input fragments for DataWarrior, right? I would probably write something like

Please find the notebook used to prepare the KinFragLib fragment library for the DataWarrior input at notebooks/XXX.ipynb.

sonjaleo commented 3 years ago

@dominiquesydow not sure which notebook you mean? Because the steps that are now in the README should be deleted in the notebook. Or do you mean linking the notebook where the DataWarrior file is used?

Good point... you do have a notebook or script that you use to prepare the input fragments for DataWarrior, right? I would probably write something like

Please find the notebook used to prepare the KinFragLib fragment library for the DataWarrior input at notebooks/XXX.ipynb.

I wrote a function for the prefiltering which is done in every notebook. The only thing (which I would delete from ne notebook now that it is in the readme) is to safe the smiles without dummy atoms in a file.

I would think the only notebook I could mention is something like "The created DataWarrior file is used in notebooks/custom_kinfraglib/1_3_custom_filters_synthesizability.ipynb"

Edit: I could add a link to notebooks/kinfraglib/3_1_fragment_library_reduced.ipynb where the prefiltering is explained?

dominiquesydow commented 3 years ago

I would think the only notebook I could mention is something like "The created DataWarrior file is used in notebooks/custom_kinfraglib/1_3_custom_filters_synthesizability.ipynb"

Edit: I could add a link to notebooks/kinfraglib/3_1_fragment_library_reduced.ipynb where the prefiltering is explained?

Perfect! Yes to both; then the user can find more information on (a) the pre-filtering [before DataWarrior] and (b) what can be done with the new dataset [after DataWarrior].

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