Review 1_1 to 1_3 notebooks

sonjaleo commented 3 years ago

Description

Make changes according to Andreas notebook review

Todos

Notable points that this PR has either accomplished or will accomplish. Look at comments in https://app.reviewnb.com/sonjaleo/KinFragLib/pull/2/files/#comment-diff-731717230

[x] add new dataframe with fragment counts function and use it in notebooks
[x] add more descriptive names for dataframes than d in 1_1, 1_2 and 1_3
[x] add other input parameters
[x] add description above counting accepted and rejected cells
[x] check code and documentation
[x] create RADME.md for custom_kinfraglib
[x] add " Analyse accepted/rejected fragments" bullet points whats done

notebook 1_3

[x] name linking more explicit : (SYBA github repo)[https://github.com/lich-uct/syba]
[x] correct last sentence SYBA
[x] show docstring of calc_syba
[x] add description to histograms
[x] change bb comparison to only comparing molecules
[x] change syba function using molecules (SMILES optional)

Status

[x] Ready to go

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AndreaVolkamer commented 3 years ago

Updates on 1_2

small textual adaptions included (please check)
merged qed.py and ro3.py content in drug_likeness.py

Todos:

Please explain individual steps in helper functions (.py) a bit more (add inline comments)
Adapt QED description wording in nb

AndreaVolkamer commented 3 years ago

Updates 1_3

small textual adaptions included (please check)

Todos:

check description in check_building_blocksdoc string
in calc_syba parameter for new column_name given, not available for all previous functions, make consistent (easiest: delete it here)
[tbd] one could merge syba.py and building_blocks.py content in synthesizability.py

AndreaVolkamer commented 3 years ago

@sonjaleo the notebooks look/read nice and run without problems

See my comments to the individual three parts above
Please use a spellchecker to go through all 3 notebooks and especially also the xxx.py files
In most functions, in the filter xxx.py files a bit of guidance what the code does (inline comments) would be helpful

TODO (to be tackled in a new PR)

Add or update READMEs on the diverse levels to include the new custom-KinFragLib information/data

sonjaleo commented 3 years ago

Started the review.

Updates on 1_1

small textual adaptions included (please check)

merged pains.py content to unwanted_substructures.py

Question:

I get a warning when importing the libraries, please check:

<frozen importlib._bootstrap>:219: RuntimeWarning: to-Python converter for boost::shared_ptr<RDKit::FilterCatalogEntry const> already registered; second conversion method ignored.

This warning is also shown in https://projects.volkamerlab.org/teachopencadd/talktorials/T003_compound_unwanted_substructures.html so it doesn't seem to be a problem with my code.

sonjaleo commented 3 years ago

@AndreaVolkamer I think I did everything you mentioned. Do you want to have a final check or should I just merge it into custom-base?

AndreaVolkamer commented 3 years ago

@sonjaleo thanks! ready to be merged!

sonjaleo / KinFragLib