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Custom kinfraglib #56

Merged
merged 348 commits into from
Apr 16, 2024
Merged

Custom kinfraglib #56

merged 348 commits into from
Apr 16, 2024

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AndreaVolkamer
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@AndreaVolkamer AndreaVolkamer commented Jun 2, 2023 •
edited by kabu00002
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Description

Add custom-kinfraglib notebooks

Todos

Questions

  • Question1

Status

  • Ready to go

sonjaleo and others added 30 commits October 22, 2021 15:40
@sonjaleo
text correction
7201343
@sonjaleo
add calculated scores in fragment_library; removed unused return dfs
dfcce4a
@sonjaleo
added accepted_num_filters function; added more descriptive df names
b211403
@sonjaleo
show docstring, corrected description text, added description texts
637dd3f
@sonjaleo
running notebook 1_3
b60a884
@sonjaleo
changed comparison of building blocks using only molecules not SMILES
49ee3e7
@sonjaleo
syba calculation by default using molecules now
ad8d24a
@sonjaleo
changed qed function using directly ROMol instead using smile -> mol
307be34
@sonjaleo
added README.md containing description for notebooks 1_1, 1_2, 1_3
323329a
@sonjaleo
correction of docstrings, more descriptive names for variables
4a3e9bf
@sonjaleo
remove useless conversion mol -> smiles in bb comp.; correct docstrings
1a6397e
@sonjaleo
changes in syba docstring
dde3fe1
@sonjaleo
update docstring of check.py function
d3328e8
@sonjaleo
more explicit variable naming in pains.py
4e35ae8
@sonjaleo
added missing description to input variable in plots.py
82c536c
@sonjaleo
updated docstring in plots.py
fae6bc9
@sonjaleo
updated prefilters.py docstrings
8981717
@sonjaleo
changes in docstring, use ROMol directly instead MolFromSmiles(SMILES)
6269761
@sonjaleo
unwanted_substr:use mol directly instead smiles to mol, change dict name
26676b4
@sonjaleo
changes in function for DataWarrior and README.md for DW
071554f
@sonjaleo
Add bullet points to analysis
98004ea
@sonjaleo
changed link to current location of README.md file
c5c9c1b
@sonjaleo
added plt.show() to ensure plots displayed diectly
c743c40
@sonjaleo
correction of table of contents
f6f379a
@AndreaVolkamer
small fixes in 1_1, move pains.py content in unwanted_substructures.py
8bcd72c
@AndreaVolkamer
small fixes in 1_2, move qed.py and ro3.py content in drug_likeness.py
9578830
@AndreaVolkamer
small adaptions in 1_3
243fa5f
@sonjaleo
flake8 corrections in .py files and text correction in notebooks
470f679
@sonjaleo
analysis.py, check.py spellcheck, comments
ee85f7a
@sonjaleo
building_blocks.py spellcheck, comments, use mol; nb 1_3 run again
66b8571
kabu00002 and others added 22 commits December 12, 2023 12:27
@kabu00002
WIP: TODO fixed custom_filter_results.csv
f32f579
@kabu00002
resolved all warnings for custom notebook 2_2
e0dcd81
@kabu00002
correct custom_filters file
d714427
@kabu00002
remove temp files
29b94e9
@PaulaKramer
added enamine substructure search
0dfc357
@PaulaKramer
figures and code for custom paper plots
9d85dab
@PaulaKramer
add average tanimoto sim
f4ee83c
@PaulaKramer
tsne plot for each filter
ba5f81e
@PaulaKramer
fix non-deterministic t-sne
1594d56
@PaulaKramer
clean code, adapt fragment statistics plot
d7c7666
@PaulaKramer
adapted code for enamine building blocks, removed datawarrior
fee69f8
@kabu00002
added sse calculations + tanimoto similarity per subpocket
6ec4203
@PaulaKramer
kinfraglib old vs new plot
c098dd0
@PaulaKramer
adapted readmes
608b78d
@PaulaKramer
adapted readmes
40af753
@PaulaKramer
Merge pull request #60 from volkamerlab/fixing_issue_59
7eaa3b8 
Fixed issue #59
@PaulaKramer
enamine substructure parameters adapted for ring matching
fbb9c98
@kabu00002
added command line arguments to enamine search
b0a7b5a
@PaulaKramer
small path fix
ca3c181
@kabu00002
renamed input files
65a95ca
@kabu00002
Merge pull request #63 from volkamerlab/enamine_search
cea1cf6 
Enamine building blocks comparison
@kabu00002
Merge pull request #64 from volkamerlab/paper_plots
edc6c2d 
CustomKinFragLib plots used in paper
@AndreaVolkamer AndreaVolkamer changed the base branch from master to dev April 10, 2024 13:28
@PaulaKramer PaulaKramer merged commit 2bd3540 into dev Apr 16, 2024
0 of 2 checks passed
@PaulaKramer PaulaKramer deleted the custom-kinfraglib branch April 16, 2024 10:29
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6 participants
@AndreaVolkamer @PaulaKramer @sonjaleo @dominiquesydow @bp-kelley @kabu00002