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Ga dba sucrose true #3

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9d2318c
On branch GA_DBA_Sucrose
sugaralc Apr 8, 2024
f5cf99e
On branch GA_DBA_Sucrose_true
sugaralc Apr 8, 2024
194ed13
Changes to be committed:
sugaralc Apr 8, 2024
6151046
Many file modifications
sugaralc Apr 11, 2024
47bc40f
crest function working
sugaralc Apr 11, 2024
e99a8c9
CREST function almost ready
sugaralc Apr 11, 2024
f318c99
Conformer function for debugging added
sugaralc Apr 12, 2024
7d24a91
Crest and Censo function almost complete
sugaralc Apr 12, 2024
16b1e2d
crest and censo functions almost ready
sugaralc Apr 13, 2024
2b39555
Function for average vector and distance of boronic gruops
sugaralc Apr 15, 2024
868af90
Function for calculation and return the S_conf from CREST
sugaralc Apr 15, 2024
41c347c
LogP implementation and popen.communicate checking
sugaralc Apr 17, 2024
85edcc4
LogP implementation ready
sugaralc Apr 17, 2024
e2d107f
LogP merged in CREST_CENSO file
sugaralc Apr 17, 2024
8cbc459
Unnecesary files
sugaralc Apr 24, 2024
edbf463
Addition of reaction for boronate neutralization
sugaralc Apr 24, 2024
5da99ae
Needed to neutralize the tweezer for LogP calculation
sugaralc Apr 24, 2024
0decdf1
Evaluation of the scoring function
sugaralc Apr 26, 2024
3219fc8
Function to evaluate the scalarized multi-objective function score
sugaralc Apr 26, 2024
e48bff4
Score function with scalarized ranges
sugaralc May 1, 2024
7bf7369
Names changed
sugaralc May 1, 2024
71c5ed5
Change of name file
sugaralc May 1, 2024
17a301d
Change of file name
sugaralc May 1, 2024
4d67388
Change of file name
sugaralc May 1, 2024
f7164a3
Change of file name
sugaralc May 1, 2024
6c979c8
Modification to run jupyter notebook
sugaralc May 1, 2024
8a2a68b
Init file for python package
sugaralc May 1, 2024
5280eb0
CREST, CENSO, and LogP routines ready.
sugaralc May 1, 2024
851cd8f
Pending change names of variables in constrained embeding
sugaralc May 1, 2024
24ef8e1
Change of file name
sugaralc May 1, 2024
0f4e4f4
File added for molecule neutralization needed for LogP calculations
sugaralc May 1, 2024
fe3951d
Individual class with new characteristics for DBAs
sugaralc May 1, 2024
738ab66
Change of file name
sugaralc May 1, 2024
8a0a337
Change of file name
sugaralc May 1, 2024
276994f
try and except functions added
sugaralc May 1, 2024
5cb2d39
Cleaning old and useless files
sugaralc May 17, 2024
d4bc207
Old and useless file
sugaralc May 17, 2024
d2c5aaa
Filter for unclassifiable molecules and Boron in ring fussed correct …
sugaralc May 17, 2024
7629145
Calculation of LogP_o/w with xtb
sugaralc May 17, 2024
9170965
Kekulized smile
sugaralc May 17, 2024
1cc43ba
dummy2BO2 function and tweezer classification refinement
sugaralc May 17, 2024
f33d459
try-except blocks implementation
sugaralc May 17, 2024
62b8e2e
submitit modifications
sugaralc May 17, 2024
6bc1ac4
Ring perception
sugaralc May 17, 2024
1454ced
Five rings PBAs deleted
sugaralc May 17, 2024
f99dc80
Ring perception
sugaralc May 17, 2024
a6fca9a
LogP_o/w with xtb
sugaralc May 17, 2024
33634fe
Free energy scoring function minor modifications
sugaralc May 17, 2024
fb65bd8
Directory cleaning
sugaralc May 17, 2024
dc476b3
DBA for sucrose case
sugaralc May 17, 2024
378ba9f
Comment lines
sugaralc May 17, 2024
efd2c4c
Deleting old LogP_o/w with orca
sugaralc May 17, 2024
e2df4ce
Routine to neutralize the tweezer
sugaralc Jun 7, 2024
f37df87
Boronate neutralization deleted
sugaralc Jun 7, 2024
07a8ea2
Long tail PBAs commented
sugaralc Jun 7, 2024
7e77f82
Modification of range values for DG
sugaralc Jun 7, 2024
2f4771c
Convergence criterium added
sugaralc Jun 7, 2024
cd8aaf5
New routine for tweezer neutralization
sugaralc Jun 7, 2024
c29be5c
Tweezer generation using complex as template
sugaralc Jun 7, 2024
8048b17
Tweezer free ligand using complex as template
sugaralc Jun 7, 2024
53b47ca
Development of new neutralization routine
sugaralc Jun 7, 2024
9605860
New neutralization routine development
sugaralc Jun 7, 2024
375fd14
routine copied to develop new neutralization routine
sugaralc Jun 7, 2024
151238a
LogP with gaussian transformation
sugaralc Jun 27, 2024
230de5a
Minor changes
sugaralc Jun 27, 2024
fbdc90a
try-except for conformer generation
sugaralc Jul 15, 2024
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16 changes: 16 additions & 0 deletions .vscode/launch.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
{
// Use IntelliSense to learn about possible attributes.
// Hover to view descriptions of existing attributes.
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [
{
"name": "Python Debugger: Current File with Arguments",
"type": "debugpy",
"request": "launch",
"program": "${file}",
"console": "integratedTerminal",
"args": "${command:pickArgs}"
}
]
}
399 changes: 399 additions & 0 deletions DBA_GA_utils.py

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