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add cofactor example as a cookbook #284

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add cofactor example as a cookbook #284

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a128629
Add eg5 cofactors files
IAlibay Jun 1, 2023
07574c8
Update for cofactors & user charges
IAlibay Dec 11, 2023
252283f
Merge branch 'main' into cofactors
IAlibay Dec 11, 2023
fcc20dd
a few tweaks to eg5 notebook
richardjgowers Jan 31, 2024
ce90abf
Merge branch 'main' into cofactors
atravitz Dec 4, 2025
7484c5a
Merge branch 'main' into cofactors
atravitz Jan 16, 2026
4e26dba
add cookbook
atravitz Jan 16, 2026
a608742
adding cli instructions
atravitz Jan 16, 2026
703f8f4
add cofactors notebook as cookbook
atravitz Jan 16, 2026
51bf4e0
fix path typo
atravitz Jan 20, 2026
4af5abc
Merge branch 'main' into cofactors_cookbook
atravitz Jan 20, 2026
a6dfa57
pre-charge molecules
atravitz Jan 20, 2026
0c9ead2
pre-charge molecules
atravitz Jan 20, 2026
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98 changes: 98 additions & 0 deletions cookbook/assets/cofactors/eg5_cofactor_charged.sdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,98 @@
3L9H
RDKit 3D

39 41 0 0 0 0 0 0 0 0999 V2000
17.7103 1.3810 16.7258 P 0 0 0 0 0 5 0 0 0 0 0 0
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22.8150 1.3580 21.9342 C 0 0 1 0 0 0 0 0 0 0 0 0
24.0771 1.7580 22.4399 O 0 0 0 0 0 0 0 0 0 0 0 0
22.4830 -0.0283 22.4899 C 0 0 2 0 0 0 0 0 0 0 0 0
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24.3615 2.5656 21.9940 H 0 0 0 0 0 0 0 0 0 0 0 0
22.8770 -0.1608 23.5002 H 0 0 0 0 0 0 0 0 0 0 0 0
21.5746 -1.2447 20.0891 H 0 0 0 0 0 0 0 0 0 0 0 0
26.3917 -5.1389 19.8129 H 0 0 0 0 0 0 0 0 0 0 0 0
24.9075 -4.6313 19.0027 H 0 0 0 0 0 0 0 0 0 0 0 0
26.7890 -2.6030 23.5264 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
1 3 1 0
1 4 1 0
1 8 1 0
5 6 2 0
5 7 1 1
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10 28 1 0
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M CHG 3 3 -1 4 -1 7 -1
M END

> <ofe-name>
3L9H

> <atom.dprop.PartialCharge>
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0.35724874358974357 0.35724874358974357 0.0010487435897435762

$$$$
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