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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
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Oct 22, 2021

  1. text correction

    @sonjaleo
    sonjaleo committed Oct 22, 2021
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  2. add calculated scores in fragment_library; removed unused return dfs

    @sonjaleo
    sonjaleo committed Oct 22, 2021
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Commits on Nov 1, 2021

  1. added accepted_num_filters function; added more descriptive df names

    @sonjaleo
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  2. show docstring, corrected description text, added description texts

    @sonjaleo
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Commits on Nov 2, 2021

  1. running notebook 1_3

    @sonjaleo
    sonjaleo committed Nov 2, 2021
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  2. changed comparison of building blocks using only molecules not SMILES

    @sonjaleo
    sonjaleo committed Nov 2, 2021
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  3. syba calculation by default using molecules now

    @sonjaleo
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  4. changed qed function using directly ROMol instead using smile -> mol

    @sonjaleo
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  5. added README.md containing description for notebooks 1_1, 1_2, 1_3

    @sonjaleo
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  6. correction of docstrings, more descriptive names for variables

    @sonjaleo
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  7. remove useless conversion mol -> smiles in bb comp.; correct docstrings

    @sonjaleo
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  8. changes in syba docstring

    @sonjaleo
    sonjaleo committed Nov 2, 2021
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  9. update docstring of check.py function

    @sonjaleo
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  10. more explicit variable naming in pains.py

    @sonjaleo
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  11. added missing description to input variable in plots.py

    @sonjaleo
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Commits on Nov 3, 2021

  1. updated docstring in plots.py

    @sonjaleo
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  2. updated prefilters.py docstrings

    @sonjaleo
    sonjaleo committed Nov 3, 2021
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  3. changes in docstring, use ROMol directly instead MolFromSmiles(SMILES)

    @sonjaleo
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  4. unwanted_substr:use mol directly instead smiles to mol, change dict name

    @sonjaleo
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  5. changes in function for DataWarrior and README.md for DW

    @sonjaleo
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  6. Add bullet points to analysis

    @sonjaleo
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  7. changed link to current location of README.md file

    @sonjaleo
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Commits on Nov 5, 2021

  1. added plt.show() to ensure plots displayed diectly

    @sonjaleo
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Commits on Nov 8, 2021

  1. correction of table of contents

    @sonjaleo
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Commits on Nov 9, 2021

  1. small fixes in 1_1, move pains.py content in unwanted_substructures.py

    @AndreaVolkamer
    AndreaVolkamer committed Nov 9, 2021
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  2. small fixes in 1_2, move qed.py and ro3.py content in drug_likeness.py

    @AndreaVolkamer
    AndreaVolkamer committed Nov 9, 2021
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  3. small adaptions in 1_3

    @AndreaVolkamer
    AndreaVolkamer committed Nov 9, 2021
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Commits on Nov 10, 2021

  1. flake8 corrections in .py files and text correction in notebooks

    @sonjaleo
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Commits on Nov 11, 2021

  1. analysis.py, check.py spellcheck, comments

    @sonjaleo
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  2. building_blocks.py spellcheck, comments, use mol; nb 1_3 run again

    @sonjaleo
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  3. druglikeness.py spellchecked, comments, code style

    @sonjaleo
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  4. plots.py spellchecked, added missing input param to docstring, comments

    @sonjaleo
    sonjaleo committed Nov 11, 2021
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  5. prefilters.py spellchek and comments

    @sonjaleo
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  6. syba.py spellcheck, comments

    @sonjaleo
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  7. unwanted_substructures.py spellcheck and comments

    @sonjaleo
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  8. utils.py spellcheck, comments, renaming variables in code

    @sonjaleo
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  9. remove column_name parameter, text corrections

    @sonjaleo
    sonjaleo committed Nov 11, 2021
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Commits on Nov 12, 2021

  1. syba & bb into synthesizability.py, correction of nb texts & qed cutoff

    @sonjaleo
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  2. run nb 1_2 again, add # NBVAL_CHECK_OUTPUT to nb 1_1, 1_2 and 1_3

    @sonjaleo
    sonjaleo committed Nov 12, 2021
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  3. removed unuseful nbval comment

    @sonjaleo
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  4. flake8-nb corrections

    @sonjaleo
    sonjaleo committed Nov 12, 2021
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  5. black correction

    @sonjaleo
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  6. black nb 1_3

    @sonjaleo
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  7. Merge pull request #11 from sonjaleo/review-update 

    Review 1_1 to 1_3 notebooks
    @sonjaleo
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Commits on Nov 13, 2021

  1. create PR for finding matching fragment pairs

    @sonjaleo
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  2. added filtering steps and checked first fragments by hand

    @sonjaleo
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  3. started writing function to get valid matching fragment pairs

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  4. added functions for getting matching fragment pairs, tried recombination

    @sonjaleo
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  5. functions for find matching fragment pairs, start trying recombination

    @sonjaleo
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  6. added function for getting atom indices of connecting bond

    @sonjaleo
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  7. functions for finding pairs and creating fragment pairs

    @sonjaleo
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  8. cleaned up imports, added comments, removed unused code

    @sonjaleo
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  9. matching fragment pairs found, next: retrosynthesis

    @sonjaleo
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  10. started writing api request function

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  11. function for api call working 

    next: expansion time and parallelize for runtime
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  12. added function counting how often fragments are in pairs 

    next parallel because of computing time!
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  13. created splits according to number of cores 

    next: call function in parallel
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  14. added parallel api request call 

    reduces request time by ~50%
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  15. written: parallel api request function 

    next: save them as functions and include analysis in nb 1_5
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  16. added functions to get one step retrosynthesis 

    next: clean up code, include in nb
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  17. added function documentations and code style

    @sonjaleo
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  18. included if statement to avoid KeyError

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  19. nb run with new if statement

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  20. calling structure comparison parallel, added different children df

    @sonjaleo
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  21. changes because of errors. need to test if running now

    @sonjaleo
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  22. output change

    @sonjaleo
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  23. exploratory notebook and file for retrosynthesis

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  24. cleaned up notebook to run in background

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  25. removed subset use

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  26. changing file to untracked retro_tmp.txt file

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  27. added check if file already exists, if not request all pairs

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  28. changed file

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  29. adding redo package to environment and code

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  30. retro fcts working, clean up files not needed, move retro file to data

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  31. rename notebook from 1_5 to 1_4

    @sonjaleo
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  32. fix missing imports

    @sonjaleo
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  33. added check if all pairs were requested; added plots

    @sonjaleo
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  34. added descriptions in notebook and xlabel in plots

    @sonjaleo
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  35. correction of path to Brenk file

    @sonjaleo
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  36. added shape of fragment library after first filtering steps

    @sonjaleo
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  37. removed duplicated code

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  38. added cell showing fragment library

    @sonjaleo
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  39. changed using ids instead iterating through molecules

    @sonjaleo
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  40. added mol variable in function

    @sonjaleo
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  41. try to fix CI error, pytest runs locally without error

    @sonjaleo
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  42. added print(pair_df)

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  43. added functions to notebook

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  44. added pair_df.shape and NBVAL comment

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  45. added some docstrings, output check in CI error cell

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  46. check some more cell output

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  47. added another check above error cell

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  48. added nbval checks to every filter step

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  49. look if bb filter is the problem

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  50. quick fixes for CI problems, push to run in background [skip ci]

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  51. removed using subset for testing [skip ci]

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  52. save new askcos results to tmp file to switch branch [skip ci]

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  53. already requested results added [skip ci]

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  54. some more already requested results [skip ci]

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  55. askos results, updates in retro functions and nb 1_4

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  56. adaptions after rebasing to current custom-base

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Commits on Nov 14, 2021

  1. code adaptions and making children/fragment comparison parallel

    @sonjaleo
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  2. added functions to save custom filtered fragment library and results

    @sonjaleo
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Commits on Nov 15, 2021

  1. text and style correction in notebook, small adaptions in retro.py

    @sonjaleo
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  2. moved filter results file to custom_filtered library

    @sonjaleo
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  3. updated retro analysis

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  4. retro.py text correction, comments until line 220

    @sonjaleo
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  5. rerun notebook with changes

    @sonjaleo
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Commits on Nov 16, 2021

  1. code and text style corrections, moved plotting dunction to plot.py

    @sonjaleo
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  2. added "total" column to dataframe, corrected saving filter results

    @sonjaleo
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  3. updated filter results file

    @sonjaleo
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Commits on Nov 17, 2021

  1. Changes according to Andreas review, added function to show fragments

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  2. Merge pull request #9 from sonjaleo/fragment_pairs 

    Find matching fragment pairs
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  3. correct ' -> " and rerun notebooks with environment as in custom-base

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  4. create notebook for custom_filters_pipeline

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  5. added headlines to pipeline

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  6. added missing headline

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  7. small changes in headlines

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  8. added parameter and descriptions for the different filters

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  9. started implementing pipeline function

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  10. added first functionality to first pipeline functions

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  11. rename pipeline notebook from 1_5 to 2_1

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  12. applied changes from merging review-update into custom base

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  13. added retrosynthesis to pipeline

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  14. add table with number of fragments used in retro filter, inspect results

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Commits on Nov 18, 2021

  1. added: num filters passing, descriptions of filters, load results

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  2. text and style corrections

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Commits on Nov 24, 2021

  1. add review changes, add log file

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Commits on Nov 25, 2021

  1. add last review changes

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  2. ignore pipeline notebook 2_1 in tests

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Commits on Nov 26, 2021

  1. remove / from ignore statement

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  2. Merge branch 'custom-pipeline' into custom-base

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Commits on Nov 27, 2021

  1. add sum column to df, remove fragments not passing before saving

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  2. run notebook with corrections

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  3. Merge pull request #17 from sonjaleo/pipeline-corrections 

    Pipeline corrections
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  4. added analysis notebook

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  5. fct to compare original with reduced libraries; fct to plot t-sne

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  6. rename analysis notebook from 2_1 to 2_2

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  7. added analysis functions and notebook structure

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  8. modified tsne plots, added loading results file [skip ci]

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  9. tsne plots for different filter steps [skip ci]

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  10. rebasing to custom-base and adding custom fragment library

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  11. adapted frag sim fct, added fcts for conn freq+frag sim+frag props

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  12. read in results file and add it to fragment library again

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  13. added barplot development number of fragments

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  14. added connection frequency plot and properties per filter plots

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  15. modified t-SNE plots, added text

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  16. add analysis of brenk structures to 1_1

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  17. moved functions from notebooks to .py files

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  18. added some docstring, adapted fct to reduce code

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  19. Added comments and docstrings, text-corrections

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  20. modified most common fragments part

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  21. run notbook with new most common fragments

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  22. added subpocket information to most common fragments

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  23. added some notes

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  24. correction of clustering most common molecules

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  25. added titles, modified dataframes

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  26. added prints, added subset df

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  27. looking for most common fragments in most specific frags

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  28. change python version in CI test

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  29. added legends to analysis most common & specific; change title in barplt

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  30. legends to tsne, modec pipeline_analysis.py to analysis.py and plots.py

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  31. changes in text and t-sne plots

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  32. run notebook with correct custom fragment library

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  33. changes in notebook readme

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  34. added README.md to notebooks folder

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  35. modified README.md in data folder

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  36. Added filters and Brenk readme

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  37. modified Brenk readme

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  38. added retrosynthesizability readme

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  39. added readme to fragment_library_custom_filtered

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  40. added readme to custom filtered library

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  41. Added description for custom_filter_results.csv

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  42. adapted paths to notebooks in readmes

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  43. correct enumeration

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  44. small changes in README texts

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  45. small changes in plots

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Commits on Nov 28, 2021

  1. review parameter names and text changes

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  2. changed ylimits on boxplots to be equal

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  3. adaptions on plots

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Commits on Nov 29, 2021

  1. implement review feedback

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  2. Moved function to plots.py; added text, changed order of plots

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Commits on Nov 30, 2021

  1. Update README.md 

    Co-authored-by: AndreaVolkamer <[email protected]>
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  2. Update README.md 

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  3. Update data/README.md 

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  4. Update data/README.md 

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  5. Update data/fragment_library_custom_filtered/README.md 

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  6. Update data/fragment_library_custom_filtered/README.md 

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  7. Update data/fragment_library_custom_filtered/README.md 

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  8. Update data/fragment_library_custom_filtered/README.md 

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  9. Update data/filters/Brenk/README.md 

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  10. Update data/filters/README.md 

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  11. Update data/filters/README.md 

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  12. Update notebooks/README.md 

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  13. Update notebooks/custom_kinfraglib/README.md 

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  14. Update notebooks/custom_kinfraglib/README.md 

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  15. Update data/fragment_library_custom_filtered/README.md 

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  16. Update data/fragment_library_custom_filtered/README.md 

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  17. updates on readme

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  18. final updates on readme's

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  19. change title 3.5

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  20. Merge pull request #14 from sonjaleo/add-readmes 

    Add README.md's
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  21. Merge pull request #13 from sonjaleo/analysis 

    PR for analysis
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Commits on Dec 10, 2021

  1. small changes in images and print number of building blocks

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  2. correct ro3 docstring

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  3. rerun synthesizability notebook

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  4. Merge pull request #18 from sonjaleo/corrections 

    correct small errors
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  5. run without output, correct markdown

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  6. run notebook with outputs and corrected markdown cells

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  7. Merge pull request #19 from sonjaleo/correct-pipeline 

    correct pipeline markdown
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Commits on Oct 17, 2022

  1. Create empty base branch

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  2. Merge pull request #2 from sonjaleo/custom-base 

    Custom-KinFragLib
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  3. Sync CI with KinFragLib's repo (master branch)

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Commits on May 11, 2023

  1. solve merge conflict with custom-kinfraglib

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  2. solve merge conflict with custom-kinfraglib

    @dominiquesydow @PaulaKramer
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  3. Fix missing find_packages import

    @bp-kelley @PaulaKramer
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  4. Trigger CI with empty commit

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  5. Create empty base branch

    @dominiquesydow @PaulaKramer
    dominiquesydow authored and PaulaKramer committed May 11, 2023
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  6. merge custom-kinfraglib

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    PaulaKramer committed May 11, 2023
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Commits on Dec 6, 2023

  1. Fixed issue #59

    @kabu00002
    kabu00002 committed Dec 6, 2023
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  2. update notebook1

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    kabu00002 committed Dec 6, 2023
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  3. notebook1_2

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    kabu00002 committed Dec 6, 2023
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  4. notebook 1_§

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    kabu00002 committed Dec 6, 2023
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  5. working stage

    @kabu00002
    kabu00002 committed Dec 6, 2023
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Commits on Dec 12, 2023

  1. WIP: TODO fixed custom_filter_results.csv

    @kabu00002
    kabu00002 committed Dec 12, 2023
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Commits on Dec 13, 2023

  1. resolved all warnings for custom notebook 2_2

    @kabu00002
    kabu00002 committed Dec 13, 2023
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  2. correct custom_filters file

    @kabu00002
    kabu00002 committed Dec 13, 2023
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  3. remove temp files

    @kabu00002
    kabu00002 committed Dec 13, 2023
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Commits on Mar 6, 2024

  1. added enamine substructure search

    @PaulaKramer
    PaulaKramer committed Mar 6, 2024
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  2. figures and code for custom paper plots

    @PaulaKramer
    PaulaKramer committed Mar 6, 2024
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Commits on Mar 12, 2024

  1. add average tanimoto sim

    @PaulaKramer
    PaulaKramer committed Mar 12, 2024
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Commits on Mar 14, 2024

  1. tsne plot for each filter

    @PaulaKramer
    PaulaKramer committed Mar 14, 2024
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Commits on Mar 18, 2024

  1. fix non-deterministic t-sne

    @PaulaKramer
    PaulaKramer committed Mar 18, 2024
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  2. clean code, adapt fragment statistics plot

    @PaulaKramer
    PaulaKramer committed Mar 18, 2024
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Commits on Mar 19, 2024

  1. adapted code for enamine building blocks, removed datawarrior

    @PaulaKramer
    PaulaKramer committed Mar 19, 2024
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  2. added sse calculations + tanimoto similarity per subpocket

    @kabu00002
    kabu00002 committed Mar 19, 2024
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Commits on Mar 26, 2024

  1. kinfraglib old vs new plot

    @PaulaKramer
    PaulaKramer committed Mar 26, 2024
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  2. adapted readmes

    @PaulaKramer
    PaulaKramer committed Mar 26, 2024
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  3. adapted readmes

    @PaulaKramer
    PaulaKramer committed Mar 26, 2024
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  4. Merge pull request #60 from volkamerlab/fixing_issue_59 

    Fixed issue #59
    @PaulaKramer
    PaulaKramer authored Mar 26, 2024
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Commits on Mar 27, 2024

  1. enamine substructure parameters adapted for ring matching

    @PaulaKramer
    PaulaKramer committed Mar 27, 2024
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Commits on Apr 10, 2024

  1. added command line arguments to enamine search

    @kabu00002
    kabu00002 committed Apr 10, 2024
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  2. small path fix

    @PaulaKramer
    PaulaKramer committed Apr 10, 2024
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  3. renamed input files

    @kabu00002
    kabu00002 committed Apr 10, 2024
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  4. Merge pull request #63 from volkamerlab/enamine_search 

    Enamine building blocks comparison
    @kabu00002
    kabu00002 authored Apr 10, 2024
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  5. Merge pull request #64 from volkamerlab/paper_plots 

    CustomKinFragLib plots used in paper
    @kabu00002
    kabu00002 authored Apr 10, 2024
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Commits on Apr 15, 2024

  1. resolved issues

    @kabu00002
    kabu00002 committed Apr 15, 2024
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  2. Merge pull request #61 from volkamerlab/re_runcustom 

    Update custom kinfraglib
    @kabu00002
    kabu00002 authored Apr 15, 2024
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Commits on Apr 16, 2024

  1. merge

    @kabu00002
    kabu00002 committed Apr 16, 2024
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  2. Merge branch 'custom-kinfraglib' of github.com:volkamerlab/KinFragLib… 

    … into custom-kinfraglib
    @kabu00002
    kabu00002 committed Apr 16, 2024
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  3. modified README to suit after merge

    @kabu00002
    kabu00002 committed Apr 16, 2024
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