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[v2.0.0] CustomKinFragLib release #67

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merged 414 commits into from
Sep 18, 2024
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91fad4d
exploratory notebook and file for retrosynthesis
sonjaleo Nov 1, 2021
d3dc049
cleaned up notebook to run in background
sonjaleo Nov 1, 2021
d485cf7
removed subset use
sonjaleo Nov 1, 2021
ae23b31
changing file to untracked retro_tmp.txt file
sonjaleo Nov 1, 2021
a08a287
added check if file already exists, if not request all pairs
sonjaleo Nov 3, 2021
951e29d
changed file
sonjaleo Nov 3, 2021
fd84106
adding redo package to environment and code
sonjaleo Nov 4, 2021
9def9e9
retro fcts working, clean up files not needed, move retro file to data
sonjaleo Nov 4, 2021
20d5fdb
rename notebook from 1_5 to 1_4
sonjaleo Nov 4, 2021
ac02da9
fix missing imports
sonjaleo Nov 5, 2021
ffcee2f
added check if all pairs were requested; added plots
sonjaleo Nov 8, 2021
985fe61
added descriptions in notebook and xlabel in plots
sonjaleo Nov 8, 2021
cab9bf0
correction of path to Brenk file
sonjaleo Nov 8, 2021
bd50b76
added shape of fragment library after first filtering steps
sonjaleo Nov 8, 2021
32bddaa
removed duplicated code
sonjaleo Nov 8, 2021
0685d5e
added cell showing fragment library
sonjaleo Nov 8, 2021
eb18809
changed using ids instead iterating through molecules
sonjaleo Nov 8, 2021
0ff3496
added mol variable in function
sonjaleo Nov 9, 2021
a8af8b1
try to fix CI error, pytest runs locally without error
sonjaleo Nov 9, 2021
322f50a
added print(pair_df)
sonjaleo Nov 9, 2021
6aee1b6
added functions to notebook
sonjaleo Nov 9, 2021
270388e
added pair_df.shape and NBVAL comment
sonjaleo Nov 9, 2021
ab5c206
added some docstrings, output check in CI error cell
sonjaleo Nov 9, 2021
d09b8cb
check some more cell output
sonjaleo Nov 9, 2021
f6e25fa
added another check above error cell
sonjaleo Nov 9, 2021
b9ea528
added nbval checks to every filter step
sonjaleo Nov 9, 2021
862f744
look if bb filter is the problem
sonjaleo Nov 9, 2021
c6c1211
quick fixes for CI problems, push to run in background [skip ci]
sonjaleo Nov 10, 2021
ef763a1
removed using subset for testing [skip ci]
sonjaleo Nov 10, 2021
32f032e
save new askcos results to tmp file to switch branch [skip ci]
sonjaleo Nov 10, 2021
bf8f252
already requested results added [skip ci]
sonjaleo Nov 10, 2021
c37a3a7
some more already requested results [skip ci]
sonjaleo Nov 10, 2021
2f6913d
askos results, updates in retro functions and nb 1_4
sonjaleo Nov 13, 2021
d70d372
adaptions after rebasing to current custom-base
sonjaleo Nov 13, 2021
31fcc29
code adaptions and making children/fragment comparison parallel
sonjaleo Nov 14, 2021
e2331a4
added functions to save custom filtered fragment library and results
sonjaleo Nov 14, 2021
43713cb
text and style correction in notebook, small adaptions in retro.py
sonjaleo Nov 15, 2021
c39ae27
moved filter results file to custom_filtered library
sonjaleo Nov 15, 2021
8e51f53
updated retro analysis
sonjaleo Nov 15, 2021
c9c9cbc
retro.py text correction, comments until line 220
sonjaleo Nov 15, 2021
57626f8
rerun notebook with changes
sonjaleo Nov 15, 2021
6251d1a
code and text style corrections, moved plotting dunction to plot.py
sonjaleo Nov 16, 2021
2cdb51f
added "total" column to dataframe, corrected saving filter results
sonjaleo Nov 16, 2021
ae18b71
updated filter results file
sonjaleo Nov 16, 2021
04378f3
Changes according to Andreas review, added function to show fragments
sonjaleo Nov 17, 2021
df76e3d
Merge pull request #9 from sonjaleo/fragment_pairs
sonjaleo Nov 17, 2021
baf789d
correct ' -> " and rerun notebooks with environment as in custom-base
sonjaleo Nov 17, 2021
814948a
create notebook for custom_filters_pipeline
sonjaleo Nov 5, 2021
cc1d76b
added headlines to pipeline
sonjaleo Nov 5, 2021
ee0737a
added missing headline
sonjaleo Nov 5, 2021
0a99d18
small changes in headlines
sonjaleo Nov 5, 2021
076468b
added parameter and descriptions for the different filters
sonjaleo Nov 5, 2021
6962fa5
started implementing pipeline function
sonjaleo Nov 5, 2021
90a0069
added first functionality to first pipeline functions
sonjaleo Nov 5, 2021
a523482
rename pipeline notebook from 1_5 to 2_1
sonjaleo Nov 12, 2021
fb579fe
applied changes from merging review-update into custom base
sonjaleo Nov 12, 2021
a42671e
added retrosynthesis to pipeline
sonjaleo Nov 17, 2021
e5421bf
add table with number of fragments used in retro filter, inspect results
sonjaleo Nov 17, 2021
947e67b
added: num filters passing, descriptions of filters, load results
sonjaleo Nov 18, 2021
e81b190
text and style corrections
sonjaleo Nov 18, 2021
985925f
add review changes, add log file
sonjaleo Nov 24, 2021
3f09811
add last review changes
sonjaleo Nov 25, 2021
97a9289
ignore pipeline notebook 2_1 in tests
sonjaleo Nov 25, 2021
400621b
remove / from ignore statement
sonjaleo Nov 26, 2021
e306ac3
Merge branch 'custom-pipeline' into custom-base
sonjaleo Nov 26, 2021
92bbbb5
add sum column to df, remove fragments not passing before saving
sonjaleo Nov 27, 2021
0d22d00
run notebook with corrections
sonjaleo Nov 27, 2021
9206ffa
Merge pull request #17 from sonjaleo/pipeline-corrections
sonjaleo Nov 27, 2021
3095076
added analysis notebook
sonjaleo Nov 9, 2021
563e96a
fct to compare original with reduced libraries; fct to plot t-sne
sonjaleo Nov 9, 2021
3b7bc86
rename analysis notebook from 2_1 to 2_2
sonjaleo Nov 12, 2021
5abd03a
added analysis functions and notebook structure
sonjaleo Nov 13, 2021
26c7830
modified tsne plots, added loading results file [skip ci]
sonjaleo Nov 16, 2021
d05e2bd
tsne plots for different filter steps [skip ci]
sonjaleo Nov 16, 2021
ec6d90f
rebasing to custom-base and adding custom fragment library
sonjaleo Nov 17, 2021
8318639
adapted frag sim fct, added fcts for conn freq+frag sim+frag props
sonjaleo Nov 18, 2021
131861c
read in results file and add it to fragment library again
sonjaleo Nov 18, 2021
f99d0f3
added barplot development number of fragments
sonjaleo Nov 18, 2021
583dcae
added connection frequency plot and properties per filter plots
sonjaleo Nov 19, 2021
70e3a4c
modified t-SNE plots, added text
sonjaleo Nov 19, 2021
30a246b
add analysis of brenk structures to 1_1
sonjaleo Nov 19, 2021
0aa3acb
moved functions from notebooks to .py files
sonjaleo Nov 19, 2021
23ddc2e
added some docstring, adapted fct to reduce code
sonjaleo Nov 19, 2021
db32ed1
Added comments and docstrings, text-corrections
sonjaleo Nov 20, 2021
a41fd5a
modified most common fragments part
sonjaleo Nov 22, 2021
1dad6c1
run notbook with new most common fragments
sonjaleo Nov 22, 2021
eff28e2
added subpocket information to most common fragments
sonjaleo Nov 22, 2021
55fcbb2
added some notes
sonjaleo Nov 24, 2021
4dd9bbb
correction of clustering most common molecules
sonjaleo Nov 25, 2021
7215b6f
added titles, modified dataframes
sonjaleo Nov 25, 2021
7a9828f
added prints, added subset df
sonjaleo Nov 25, 2021
379626c
looking for most common fragments in most specific frags
sonjaleo Nov 25, 2021
e5bf28c
change python version in CI test
sonjaleo Nov 26, 2021
27308e5
added legends to analysis most common & specific; change title in barplt
sonjaleo Nov 26, 2021
5634f88
legends to tsne, modec pipeline_analysis.py to analysis.py and plots.py
sonjaleo Nov 26, 2021
5c37844
changes in text and t-sne plots
sonjaleo Nov 27, 2021
28768ee
run notebook with correct custom fragment library
sonjaleo Nov 27, 2021
5dbe1d0
changes in notebook readme
sonjaleo Nov 22, 2021
d500a61
added README.md to notebooks folder
sonjaleo Nov 22, 2021
a552b06
modified README.md in data folder
sonjaleo Nov 22, 2021
8ade9d1
Added filters and Brenk readme
sonjaleo Nov 22, 2021
3587dde
modified Brenk readme
sonjaleo Nov 22, 2021
814bccb
added retrosynthesizability readme
sonjaleo Nov 22, 2021
c7f1a77
added readme to fragment_library_custom_filtered
sonjaleo Nov 22, 2021
47b66cb
added readme to custom filtered library
sonjaleo Nov 22, 2021
09879bc
Added description for custom_filter_results.csv
sonjaleo Nov 22, 2021
0404108
adapted paths to notebooks in readmes
sonjaleo Nov 24, 2021
1a45214
correct enumeration
sonjaleo Nov 24, 2021
4036164
small changes in README texts
sonjaleo Nov 27, 2021
76bc474
small changes in plots
sonjaleo Nov 27, 2021
bd28f0a
review parameter names and text changes
sonjaleo Nov 28, 2021
8455205
changed ylimits on boxplots to be equal
sonjaleo Nov 28, 2021
b98db8c
adaptions on plots
sonjaleo Nov 28, 2021
8851113
implement review feedback
sonjaleo Nov 29, 2021
f722aa1
Moved function to plots.py; added text, changed order of plots
sonjaleo Nov 29, 2021
4740902
Update README.md
sonjaleo Nov 30, 2021
a781c24
Update README.md
sonjaleo Nov 30, 2021
fa673f7
Update data/README.md
sonjaleo Nov 30, 2021
3bc50e1
Update data/README.md
sonjaleo Nov 30, 2021
72aa61e
Update data/fragment_library_custom_filtered/README.md
sonjaleo Nov 30, 2021
81dd2c3
Update data/fragment_library_custom_filtered/README.md
sonjaleo Nov 30, 2021
afef354
Update data/fragment_library_custom_filtered/README.md
sonjaleo Nov 30, 2021
6a1320c
Update data/fragment_library_custom_filtered/README.md
sonjaleo Nov 30, 2021
b6297e2
Update data/filters/Brenk/README.md
sonjaleo Nov 30, 2021
75daea8
Update data/filters/README.md
sonjaleo Nov 30, 2021
0863cbb
Update data/filters/README.md
sonjaleo Nov 30, 2021
cd3aecb
Update notebooks/README.md
sonjaleo Nov 30, 2021
e03b615
Update notebooks/custom_kinfraglib/README.md
sonjaleo Nov 30, 2021
133e608
Update notebooks/custom_kinfraglib/README.md
sonjaleo Nov 30, 2021
89d45fd
Update data/fragment_library_custom_filtered/README.md
sonjaleo Nov 30, 2021
e122a84
Update data/fragment_library_custom_filtered/README.md
sonjaleo Nov 30, 2021
0224250
updates on readme
sonjaleo Nov 30, 2021
f120ea5
final updates on readme's
sonjaleo Nov 30, 2021
3133373
change title 3.5
sonjaleo Nov 30, 2021
6ac1235
Merge pull request #14 from sonjaleo/add-readmes
sonjaleo Nov 30, 2021
4148494
Merge pull request #13 from sonjaleo/analysis
sonjaleo Nov 30, 2021
eda41ec
small changes in images and print number of building blocks
sonjaleo Dec 10, 2021
29672f6
correct ro3 docstring
sonjaleo Dec 10, 2021
037280e
rerun synthesizability notebook
sonjaleo Dec 10, 2021
f6d579e
Merge pull request #18 from sonjaleo/corrections
sonjaleo Dec 10, 2021
18eb528
run without output, correct markdown
sonjaleo Dec 10, 2021
97edbb9
run notebook with outputs and corrected markdown cells
sonjaleo Dec 10, 2021
f1426b0
Merge pull request #19 from sonjaleo/correct-pipeline
sonjaleo Dec 10, 2021
cdf171a
Create empty base branch
dominiquesydow Oct 17, 2022
b022bf1
Merge pull request #2 from sonjaleo/custom-base
dominiquesydow Oct 17, 2022
df429be
Sync CI with KinFragLib's repo (master branch)
dominiquesydow Oct 17, 2022
735bc59
solve merge conflict with custom-kinfraglib
dominiquesydow Sep 10, 2021
5284deb
solve merge conflict with custom-kinfraglib
dominiquesydow Sep 10, 2021
f983984
Fix missing find_packages import
bp-kelley Oct 19, 2021
0da8e2b
Trigger CI with empty commit
dominiquesydow May 15, 2022
154554e
Create empty base branch
dominiquesydow Oct 17, 2022
88da7d9
merge custom-kinfraglib
PaulaKramer May 11, 2023
4bc7153
Fixed issue #59
kabu00002 Dec 6, 2023
4825c51
update notebook1
kabu00002 Dec 6, 2023
ae9d5a3
notebook1_2
kabu00002 Dec 6, 2023
d34ce23
notebook 1_§
kabu00002 Dec 6, 2023
7a1246b
working stage
kabu00002 Dec 6, 2023
f32f579
WIP: TODO fixed custom_filter_results.csv
kabu00002 Dec 12, 2023
e0dcd81
resolved all warnings for custom notebook 2_2
kabu00002 Dec 13, 2023
d714427
correct custom_filters file
kabu00002 Dec 13, 2023
29b94e9
remove temp files
kabu00002 Dec 13, 2023
0dfc357
added enamine substructure search
PaulaKramer Mar 6, 2024
9d85dab
figures and code for custom paper plots
PaulaKramer Mar 6, 2024
f4ee83c
add average tanimoto sim
PaulaKramer Mar 12, 2024
ba5f81e
tsne plot for each filter
PaulaKramer Mar 14, 2024
1594d56
fix non-deterministic t-sne
PaulaKramer Mar 18, 2024
d7c7666
clean code, adapt fragment statistics plot
PaulaKramer Mar 18, 2024
fee69f8
adapted code for enamine building blocks, removed datawarrior
PaulaKramer Mar 19, 2024
6ec4203
added sse calculations + tanimoto similarity per subpocket
kabu00002 Mar 19, 2024
c098dd0
kinfraglib old vs new plot
PaulaKramer Mar 26, 2024
608b78d
adapted readmes
PaulaKramer Mar 26, 2024
40af753
adapted readmes
PaulaKramer Mar 26, 2024
7eaa3b8
Merge pull request #60 from volkamerlab/fixing_issue_59
PaulaKramer Mar 26, 2024
fbb9c98
enamine substructure parameters adapted for ring matching
PaulaKramer Mar 27, 2024
b0a7b5a
added command line arguments to enamine search
kabu00002 Apr 10, 2024
ca3c181
small path fix
PaulaKramer Apr 10, 2024
65a95ca
renamed input files
kabu00002 Apr 10, 2024
cea1cf6
Merge pull request #63 from volkamerlab/enamine_search
kabu00002 Apr 10, 2024
edc6c2d
Merge pull request #64 from volkamerlab/paper_plots
kabu00002 Apr 10, 2024
acf15ba
resolved issues
kabu00002 Apr 15, 2024
5eb2738
Merge pull request #61 from volkamerlab/re_runcustom
kabu00002 Apr 15, 2024
b3582af
merge
kabu00002 Apr 16, 2024
4506a7b
Merge branch 'custom-kinfraglib' of github.com:volkamerlab/KinFragLib…
kabu00002 Apr 16, 2024
e056e57
modified README to suit after merge
kabu00002 Apr 16, 2024
2bd3540
Merge pull request #56 from volkamerlab/custom-kinfraglib
PaulaKramer Apr 16, 2024
6b77b49
Tiny change in README
kabu00002 Apr 16, 2024
1f56872
custom/1_1 completed
kabu00002 Apr 16, 2024
8fa0ee2
custom/1_2 completed
kabu00002 Apr 16, 2024
61048be
custom/1_3 completed
kabu00002 Apr 16, 2024
5704c37
modified use of askcos api
kabu00002 Apr 23, 2024
b6b5166
bug fixed
kabu00002 Apr 30, 2024
ccd65cd
running 1_4
kabu00002 Apr 30, 2024
90e55d1
updated README
kabu00002 May 6, 2024
011843e
Title
kabu00002 May 6, 2024
15a6f8b
add custom in main readme
PaulaKramer May 6, 2024
2a57c3f
Merge pull request #68 from volkamerlab/update_READMEs
kabu00002 May 6, 2024
676f7dc
rerun 1_4 + fix plots retro
kabu00002 May 13, 2024
412ac55
removed redundant code for writin to sdf
kabu00002 May 13, 2024
a588b6c
updated custom kinfraglib
kabu00002 May 13, 2024
4ef05c8
updated sutsom kinfraglib
kabu00002 May 13, 2024
344576f
added comments
kabu00002 May 13, 2024
96545d6
rerun 1_4
kabu00002 May 13, 2024
3e3a7c5
added note to notebook
kabu00002 May 13, 2024
74c2459
Merge branch 'fixing_askcos' of github.com:volkamerlab/KinFragLib int…
kabu00002 May 13, 2024
ece5741
updated readme
kabu00002 May 13, 2024
550b66c
updated readme
kabu00002 May 13, 2024
6670107
fixed bug in plots
kabu00002 May 13, 2024
53cde35
rerun syba
kabu00002 May 13, 2024
fb2029f
fixed bug in plots
kabu00002 May 13, 2024
7849e83
rerun syba
kabu00002 May 13, 2024
da4475f
fixed another bug (showing decimals for mean)
kabu00002 May 13, 2024
c004530
Merge branch 'update_custom_kinfraglib' of github.com:volkamerlab/Kin…
kabu00002 May 13, 2024
b77e35f
changed path
kabu00002 May 13, 2024
a9f207a
Merge branch 'fixing_askcos' of github.com:volkamerlab/KinFragLib int…
kabu00002 May 13, 2024
74d3009
rerun 2_2
kabu00002 May 13, 2024
debbada
spelling and small rephrasing
PaulaKramer May 13, 2024
012be92
wip
kabu00002 May 27, 2024
ff36cf2
wip
kabu00002 May 27, 2024
6ce9426
review
kabu00002 May 27, 2024
e0bca1d
Merge branch 'fixing_askcos' of github.com:volkamerlab/KinFragLib int…
kabu00002 May 27, 2024
0c66eeb
added installation hint to README
kabu00002 May 27, 2024
ad138e8
Merge pull request #69 from volkamerlab/fixing_askcos
kabu00002 May 27, 2024
03592a7
wip update
kabu00002 May 27, 2024
a633d4c
running notebook
kabu00002 May 27, 2024
17c7950
finalized
kabu00002 May 27, 2024
3c10589
added missing HTML
kabu00002 May 27, 2024
cc98cdd
solving merge conflict
kabu00002 May 27, 2024
0125ee6
fixed HTML
kabu00002 May 27, 2024
04786e1
auto reload
kabu00002 May 27, 2024
ec4c3ae
Merge pull request #71 from volkamerlab/update_custom_kinfraglib
kabu00002 May 27, 2024
14c42b3
rerun notebook
PaulaKramer Jun 6, 2024
07a4ab2
increase time out, ignore custom notebook 2_3
PaulaKramer Jun 7, 2024
65b2b9c
change CI build status to master
PaulaKramer Jun 7, 2024
5de064d
format readme
PaulaKramer Jun 7, 2024
e1d354b
github action badge fix
PaulaKramer Jun 7, 2024
a700a00
ci timeout
PaulaKramer Jun 7, 2024
2fd280f
change paths in 4_4
PaulaKramer Jun 7, 2024
100b07c
more path changes 4_4
PaulaKramer Jun 7, 2024
7763beb
remove files before writing lib (custom kinfraglib)
kabu00002 Jun 10, 2024
c22109a
Merge pull request #73 from volkamerlab/custom_ci
PaulaKramer Jun 10, 2024
920d725
rerunning affected notebooks
kabu00002 Jun 12, 2024
6b741aa
removed B2
kabu00002 Jul 8, 2024
99870d9
Merge pull request #74 from volkamerlab/cleanup_library_before_writing
kabu00002 Jul 8, 2024
7317791
Merge branch 'dev' into paper_notebook_fixes
PaulaKramer Aug 1, 2024
efe373d
update paper plots
PaulaKramer Jul 24, 2024
f91c084
Merge pull request #72 from volkamerlab/paper_notebook_fixes
PaulaKramer Aug 1, 2024
cc51094
add fragment statistics to notebook 2_3
PaulaKramer Aug 5, 2024
ba2b845
checking readmes
PaulaKramer Aug 5, 2024
1d606b6
Merge pull request #76 from volkamerlab/readme_changes
PaulaKramer Aug 5, 2024
fd62244
Merge branch 'master' into dev
PaulaKramer Sep 18, 2024
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added functions to notebook
  • Loading branch information
sonjaleo committed Nov 13, 2021
commit 6aee1b6c0148f40924959fad35a38e16bcbaf88d
Original file line number Diff line number Diff line change
Expand Up @@ -1580,66 +1580,46 @@
{
"cell_type": "code",
"execution_count": 31,
"id": "1117a8b8-b194-4c0f-b351-759de62cb7d5",
"id": "6cd2bfd5-4a6d-4239-ae17-8ae89aeb18b9",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of fragments: 487\n",
" fragment ids fragment 1 \\\n",
"0 [AP_0, SE_0] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"1 [AP_0, SE_2] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"2 [AP_0, SE_3] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"3 [AP_0, SE_4] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"4 [AP_0, SE_5] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"... ... ... \n",
"31913 [B2_15, GA_5] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31914 [B2_15, GA_6] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31915 [B2_15, GA_52] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31916 [B2_15, GA_56] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31917 [B2_15, GA_79] <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"\n",
" fragment 2 \\\n",
"0 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"1 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"2 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"3 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"4 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"... ... \n",
"31913 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31914 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31915 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31916 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31917 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"\n",
" pair \n",
"0 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"1 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"2 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"3 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"4 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"... ... \n",
"31913 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31914 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31915 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31916 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"31917 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"\n",
"[31918 rows x 4 columns]\n",
"Number of unique pairs: 14943\n"
]
}
],
"source": [
"valid_fragment_pairs, unique_pairs = filters.retro.get_valid_fragment_pairs(fragment_library)\n",
"# NBVAL_CHECK_OUTPUT"
"res = filters.retro.get_valid_pairs(fragment_library)\n",
"valids = filters.retro.checkvalid(res, fragment_library)\n",
"bonds = filters.retro.get_bonds(valids, res, fragment_library)\n",
"pair_df = filters.retro.get_pairs(valids, bonds, fragment_library)\n",
"pair_smiles = []\n",
"for pair in pair_df['pair']:\n",
" pair_mol = Chem.MolToSmiles(mol=pair)\n",
" pair_smiles.append(pair_mol)\n",
"unique_smiles = pd.DataFrame({'pair': pair_smiles})['pair'].unique()\n",
"print(\"Number of unique pairs: %s\" % len(unique_smiles))\n",
"valid_fragment_pairs = pair_df\n",
"unique_pairs = unique_smiles"
]
},
{
"cell_type": "code",
"execution_count": 32,
"id": "1117a8b8-b194-4c0f-b351-759de62cb7d5",
"metadata": {},
"outputs": [],
"source": [
"# valid_fragment_pairs, unique_pairs = filters.retro.get_valid_fragment_pairs(fragment_library)"
]
},
{
"cell_type": "code",
"execution_count": 33,
"id": "616a69ab-3eaf-4d5b-a203-8c7f3ca84755",
"metadata": {},
"outputs": [
Expand All @@ -1649,7 +1629,7 @@
"31918"
]
},
"execution_count": 32,
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -1677,7 +1657,7 @@
},
{
"cell_type": "code",
"execution_count": 33,
"execution_count": 34,
"id": "0703f93a-9daf-46ab-ab6f-55f9aa4fb95e",
"metadata": {},
"outputs": [],
Expand All @@ -1698,7 +1678,7 @@
},
{
"cell_type": "code",
"execution_count": 34,
"execution_count": 35,
"id": "b95e14ee-d016-44ed-b2ed-63a0cb01bab7",
"metadata": {},
"outputs": [
Expand All @@ -1712,8 +1692,8 @@
"Checking if all fragment pairs were requested..\n",
"All fragments were requested.\n",
"Done.\n",
"CPU times: user 3min 46s, sys: 2.31 s, total: 3min 49s\n",
"Wall time: 3min 49s\n"
"CPU times: user 3min 33s, sys: 2.38 s, total: 3min 35s\n",
"Wall time: 3min 35s\n"
]
}
],
Expand All @@ -1733,7 +1713,7 @@
},
{
"cell_type": "code",
"execution_count": 35,
"execution_count": 36,
"id": "27ec3820-7d31-491c-953a-a8680a3b5d17",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -2133,7 +2113,7 @@
"[128 rows x 27 columns]"
]
},
"execution_count": 35,
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -2144,7 +2124,7 @@
},
{
"cell_type": "code",
"execution_count": 36,
"execution_count": 37,
"id": "3faadcb8-2f14-4682-a483-7ba4deee749b",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -2270,7 +2250,7 @@
"4 None 0.000000 "
]
},
"execution_count": 36,
"execution_count": 37,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -2281,7 +2261,7 @@
},
{
"cell_type": "code",
"execution_count": 37,
"execution_count": 38,
"id": "2623b6c3-9471-4e1d-93f9-1488a285cf10",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -2407,7 +2387,7 @@
"4 <img data-content=\"rdkit/molecule\" src=\"data:i... 0.982270 "
]
},
"execution_count": 37,
"execution_count": 38,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -2437,7 +2417,7 @@
},
{
"cell_type": "code",
"execution_count": 38,
"execution_count": 39,
"id": "1de5d54c-aab5-4441-9b36-4e3df55ffb4e",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -2542,7 +2522,7 @@
"Total 70 "
]
},
"execution_count": 38,
"execution_count": 39,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -2572,7 +2552,7 @@
},
{
"cell_type": "code",
"execution_count": 39,
"execution_count": 40,
"id": "6a4c85ee-142d-4037-8cd0-42b775d4dd54",
"metadata": {
"tags": []
Expand Down