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Add Buchwald Hartwig dataset #81

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Add Buchwald Hartwig dataset #81

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pschwllr
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@pschwllr pschwllr commented Mar 8, 2023

Adding meta.yaml , transform.py and example_processing_and_templates.ipynb for Buchwald-Hartwig dataset from https://www.science.org/doi/10.1126/science.aar5169.

Related to #80

@kjappelbaum kjappelbaum linked an issue Mar 9, 2023 that may be closed by this pull request
New Task: Buchwald-Hartwig yield prediction data #80
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@phalem phalem mentioned this pull request Mar 9, 2023
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kjappelbaum
kjappelbaum reviewed Mar 28, 2023
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data/buchwald_hartwig/meta.yaml
name: buchwald_hartwig_doyle
description: High-throughput experimentation palladium-catalyzed Buchwald Hardwig
data set with yields.
targets:
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we have now also RXN-SMILES identifiers that might be useful to add

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can also look into that

kjappelbaum
kjappelbaum reviewed Mar 28, 2023
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data/buchwald_hartwig/meta.yaml Outdated
- id: reaction_SMILES
type: SMILES
description: SMILES
license: MIT license
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Suggested change
license: MIT license
license: MIT

kjappelbaum
kjappelbaum requested changes Mar 28, 2023
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Thanks for this addition, we should add the rxn-smiles. Should I take care of that?

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pschwllr commented May 6, 2023

How would you add the rxn-smiles?

Currently, the data_clean.csv looks like:

ligand,additive,base,aryl_halide,reaction_SMILES,yield
CC(C)C(C=C(C(C)C)C=C1C(C)C)=C1C2=C(P([C@@]3(C[C@@H]4C5)C[C@H](C4)C[C@H]5C3)[C@]6(C7)C[C@@H](C[C@@H]7C8)C[C@@H]8C6)C(OC)=CC=C2OC,CC1=CC(C)=NO1,CN(C)P(N(C)C)(N(C)C)=NP(N(C)C)(N(C)C)=NCC,ClC1=NC=CC=C1,CCN=P(N=P(N(C)C)(N(C)C)N(C)C)(N(C)C)N(C)C.COc1ccc(OC)c(P([C@]23C[C@H]4C[C@H](C[C@H](C4)C2)C3)[C@]23C[C@H]4C[C@H](C[C@H](C4)C2)C3)c1-c1c(C(C)C)cc(C(C)C)cc1C(C)C.Cc1cc(C)on1.Cc1ccc(N)cc1.Clc1ccccn1.O=S(=O)(O[Pd]1c2ccccc2-c2ccccc2[NH2]1)C(F)(F)F>>Cc1ccc(Nc2ccccn2)cc1,70.41045785
CC(C)C(C=C(C(C)C)C=C1C(C)C)=C1C2=C(P([C@@]3(C[C@@H]4C5)C[C@H](C4)C[C@H]5C3)[C@]6(C7)C[C@@H](C[C@@H]7C8)C[C@@H]8C6)C(OC)=CC=C2OC,O=C(OC)C1=CC=NO1,CN(C)P(N(C)C)(N(C)C)=NP(N(C)C)(N(C)C)=NCC,BrC1=NC=CC=C1,Brc1ccccn1.CCN=P(N=P(N(C)C)(N(C)C)N(C)C)(N(C)C)N(C)C.COC(=O)c1ccno1.COc1ccc(OC)c(P([C@]23C[C@H]4C[C@H](C[C@H](C4)C2)C3)[C@]23C[C@H]4C[C@H](C[C@H](C4)C2)C3)c1-c1c(C(C)C)cc(C(C)C)cc1C(C)C.Cc1ccc(N)cc1.O=S(=O)(O[Pd]1c2ccccc2-c2ccccc2[NH2]1)C(F)(F)F>>Cc1ccc(Nc2ccccn2)cc1,11.06445724

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New Task: Buchwald-Hartwig yield prediction data
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