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d3d3c7a
inital code dump
Allend95 Jan 24, 2021
66a8be2
data for modules and tests
Allend95 Jan 24, 2021
711dd9d
imported tests
Allend95 Jan 24, 2021
650860e
changed python formatter to black
Allend95 Jan 24, 2021
f334d12
fixed init.py path
Allend95 Feb 7, 2021
09c6078
path adjustment
Allend95 Feb 7, 2021
491ad7c
moved files
Allend95 Feb 7, 2021
158d9b0
changed back to relative imports
Allend95 Feb 10, 2021
0885a18
first draft of Notebook
Allend95 Feb 10, 2021
67bb603
PocketViewer: Show pocket residues only
dominiquesydow Feb 16, 2021
8a03435
Merge pull request #72 from volkamerlab/extend-viewer
dominiquesydow Feb 16, 2021
ca11703
detailed explanation based on Fourches 2010
Allend95 Mar 8, 2021
08d52f0
Pseudocode for removal of mixtures added
Allend95 Mar 16, 2021
6a9430b
first 2 rudimental standardization steps coded
Allend95 Mar 31, 2021
a76827c
added a test data file
Allend95 Apr 6, 2021
e0d9c38
clean up, scoring, more explanational text
Allend95 Apr 6, 2021
7008594
changed test entries to showcase functionality
Allend95 Apr 7, 2021
c2b1996
testing different approaches to handling entries
Allend95 Apr 7, 2021
225b4cb
going back to what worked
Allend95 Apr 7, 2021
aa03e05
adjusted subsets and steps
Allend95 Apr 8, 2021
a7319de
step 2 working
Allend95 Apr 8, 2021
63ed4eb
added data to evaluate functionality
Allend95 Apr 8, 2021
d09c4ae
Salt Remover fails -> RDKit ERROR: Empty structure
Allend95 Apr 8, 2021
44a02c6
more entries to test
Allend95 Apr 9, 2021
bfef147
remove duplicates, generate canonical tautomer
Allend95 Apr 9, 2021
d1606ce
status after meeting
Allend95 Apr 9, 2021
18238b1
Fixed salt removal part, added TODOs
Allend95 Apr 11, 2021
e40f855
Merge remote-tracking branch 'allen/master' into standardizer
jaimergp Apr 13, 2021
12fda36
JRG: Initial cleaning
jaimergp Apr 13, 2021
cf131b4
replace failTask helper with nicer lambda
jaimergp Apr 13, 2021
a4e31d6
added a new function detect_carbon
Allend95 May 5, 2021
8afe84c
search single Carbon atom, instead of substruct
Allend95 May 5, 2021
b9a81a5
modified the test datat for empty smiles cases
Allend95 May 5, 2021
5d98ec0
added selenium
Allend95 May 5, 2021
a26ec10
inorganic_elements array now can be customized
Allend95 May 5, 2021
23a6e9b
deleted comment
Allend95 May 5, 2021
a6addc1
new function created
Allend95 May 5, 2021
7711e09
Updated the notebook to Step 2 Task 4
Allend95 May 5, 2021
d8434d7
runned black-nb
Allend95 May 5, 2021
512203f
new function detect_metals
Allend95 May 6, 2021
246e17a
corrected notes in docstring
Allend95 May 6, 2021
bd1c756
adjusted task 5 (metal detection)
Allend95 May 6, 2021
a6ee7d3
checked docstring
Allend95 May 9, 2021
aa9385e
new function detect salts
Allend95 May 9, 2021
34803e1
prior changes broke the function, fixed now
Allend95 May 9, 2021
7cce5ae
more test entries added
Allend95 May 9, 2021
42eae99
reviewed to task 7...not finished
Allend95 May 9, 2021
4cdfcfd
added info to notes
Allend95 May 11, 2021
9599f5c
added test structure
Allend95 May 11, 2021
20c405c
finished notebook
Allend95 May 11, 2021
f7aacb0
added a remark about the test dataset
Allend95 May 14, 2021
4f40a55
fixed typo
Allend95 May 19, 2021
2c66331
info about max tautomeric enumerations added
Allend95 May 20, 2021
9a67937
JRG rev
jaimergp May 20, 2021
9192ca7
minor text fixes
Allend95 May 23, 2021
5a44757
text adjustment
Allend95 May 24, 2021
1fde238
Adjusted notebook and updated test data
Allend95 May 24, 2021
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2 changes: 2 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ A Python library for structural cheminformatics.

> This library is still in early stages of development.

- `compounds.standardization`: standardize chemical records.
- `databases.klifs`: utilities to query the KLIFS database, offline or online.
- `io`: read and write molecules from/to files.
- `structure.pocket`: identification and analysis of protein (sub)pockets.
Expand All @@ -34,6 +35,7 @@ The Documentation will be available soon.
- Jaime Rodríguez-Guerra, PhD
- Dominique Sydow
- Dennis Köser, Annie Pham, Enes Kurnaz, Julian Pipart (structural superposition, 2020)
- Allen Dumler (standardizer, 2021)

# Acknowledgements

Expand Down
961 changes: 961 additions & 0 deletions docs/tutorials/data/standardization_test_data.csv

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