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update curate oxidation and reduction
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@TieuLongPhan
TieuLongPhan committed Apr 22, 2024
1 parent 6c7b08b commit 3586276
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63 changes: 63 additions & 0 deletions Test/SynChemImputer/test_curate_oxidation.py
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import unittest
from synrbl.SynChemImputer.curate_oxidation import CurationOxidation


class TestCurationOxidation(unittest.TestCase):

def setUp(self):
self.curate = CurationOxidation()
self.data = [
{"R-id": "alcohol_carbonyl", "reactions": "CCO.[O]>>CC=O"},
{"R-id": "alcohol_acid", "reactions": "CCO.[O]>>CC(=O)O"},
{"R-id": "carbonyl_acid", "reactions": "CC=O.[O]>>CC(=O)O"},
]

def test_alcohol_carbonyl(self):
result = self.curate.process_dict(
self.data[0],
"reactions",
return_all=True,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result["curated_reaction"][0],
"CCO.O=[Cr](Cl)(-[O-])=O.c1cc[nH+]cc1>>CC=O.O=[Cr](O)O.c1cc[nH+]cc1.[Cl-]",
)
self.assertEqual(result["stoichiometric"][0], [1])

def test_alcohol_acid(self):
result = self.curate.process_dict(
self.data[1],
"reactions",
return_all=True,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
print(result["curated_reaction"][0])
self.assertEqual(
result["curated_reaction"][0],
(
"CCO.[K][O][Mn](=O)(=O)=O.OS(=O)(=O)O>>"
+ "CC(=O)O.[K][O]S(=O)(=O)[O][K].[Mn]1[O]S(=O)(=O)[O]1"
),
)
self.assertEqual(result["stoichiometric"][0], [5, 4, 6, 5, 11, 2, 4])

def test_aldehyde_acid(self):
result = self.curate.process_dict(
self.data[2],
"reactions",
return_all=True,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result["curated_reaction"][0],
"CC=O.O=[Mn](=O)(=O)O[K].O>>CC(=O)O.O=[Mn]=O.O[K]",
)
self.assertEqual(result["stoichiometric"][0], [5, 4, 6, 5, 4, 1])


if __name__ == "__main__":
unittest.main()
165 changes: 165 additions & 0 deletions Test/SynChemImputer/test_curate_reduction.py
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import unittest
from synrbl.SynChemImputer.curate_reduction import CurationReduction


class TestCurationReduction(unittest.TestCase):

def setUp(self):
self.curate = CurationReduction()
self.data = [
{"R-id": "aldehyde", "reactions": "CC=O.[H].[H]>>CCO"},
{"R-id": "ketone", "reactions": "CC(=O)C.[H].[H]>>CC(O)C"},
{"R-id": "acid", "reactions": "CC(=O)O.[H].[H].[H].[H]>>CCO.O"},
{"R-id": "ester", "reactions": "CC(=O)OC.[H].[H].[H].[H]>>CCO.CO"},
]

def test_aldehyde(self):
result_ion = self.curate.process_dict(
self.data[0],
"reactions",
return_all=True,
neutralize=False,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result_ion["curated_reaction"][1], "CC=O.[BH4-].[Na+].[H+]>>CCO.[BH3].[Na+]"
)

result_neutral = self.curate.process_dict(
self.data[0],
"reactions",
return_all=True,
neutralize=True,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result_neutral["curated_reaction"][1],
"CC=O.[BH4-].[Na+].Cl>>CCO.[BH3].[Na][Cl]",
)

def test_ketone(self):
result_ion = self.curate.process_dict(
self.data[1],
"reactions",
return_all=True,
neutralize=False,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result_ion["curated_reaction"][2],
"CC(=O)C.[BH3-]C#N.[Na+].[H+]>>CC(O)C.[BH2]C#N.[Na+]",
)

result_neutral = self.curate.process_dict(
self.data[1],
"reactions",
return_all=True,
neutralize=True,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result_neutral["curated_reaction"][2],
"CC(=O)C.[BH3-]C#N.[Na+].Cl>>CC(O)C.[BH2]C#N.[Na][Cl]",
)

def test_acid(self):
result_ion = self.curate.process_dict(
self.data[2],
"reactions",
return_all=True,
neutralize=False,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result_ion["curated_reaction"][0],
(
"CC(=O)O.[AlH4-].[Li+].[H+].[AlH4-].[Li+].[H+]>>"
+ "CCO.O.[AlH3].[Li+].[AlH3].[Li+]",
),
)

result_neutral = self.curate.process_dict(
self.data[2],
"reactions",
return_all=True,
neutralize=True,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result_neutral["curated_reaction"][0],
(
"CC(=O)O.[AlH4-].[Li+].Cl.[AlH4-].[Li+].Cl>>"
+ "CCO.O.[AlH3].[Li][Cl].[AlH3].[Li][Cl]"
),
)

def test_ester(self):
result_ion = self.curate.process_dict(
self.data[3],
"reactions",
return_all=True,
neutralize=False,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
self.assertEqual(
result_ion["curated_reaction"][0],
(
"CC(=O)OC.[BH4-].[Na+].[H+].[BH4-].[Na+].[H+]>>"
+ "CCO.CO.[BH3].[Na+].[BH3].[Na+]"
),
)

result_neutral = self.curate.process_dict(
self.data[3],
"reactions",
return_all=True,
neutralize=True,
compounds_template=self.curate.compounds_template,
reaction_templates=self.curate.reaction_templates,
)
print(result_neutral)
self.assertEqual(
result_neutral["curated_reaction"][0],
(
"CC(=O)OC.[BH4-].[Na+].Cl.[BH4-].[Na+].Cl>>"
+ "CCO.CO.[BH3].[Na][Cl].[BH3].[Na][Cl]"
),
)

def test_parallel_curate(self):
result = self.curate.parallel_curate(
self.data, n_jobs=2, verbose=2, return_all=True, neutralize=False
)

self.assertEqual(
result[0]["curated_reaction"][1], "CC=O.[BH4-].[Na+].[H+]>>CCO.[BH3].[Na+]"
)
self.assertEqual(
result[1]["curated_reaction"][2],
"CC(=O)C.[BH3-]C#N.[Na+].[H+]>>CC(O)C.[BH2]C#N.[Na+]",
)
self.assertEqual(
result[2]["curated_reaction"][0],
(
"CC(=O)O.[AlH4-].[Li+].[H+].[AlH4-].[Li+].[H+]>>"
+ "CCO.O.[AlH3].[Li+].[AlH3].[Li+]",
),
)
self.assertEqual(
result[3]["curated_reaction"][0],
(
"CC(=O)OC.[BH4-].[Na+].[H+].[BH4-].[Na+].[H+]>>"
+ "CCO.CO.[BH3].[Na+].[BH3].[Na+]",
),
)


if __name__ == "__main__":
unittest.main()
23 changes: 16 additions & 7 deletions synrbl/SynChemImputer/compounds_template.json
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@@ -1,9 +1,18 @@
{
"aldehyde": ["template_1", "template_2", "template_3", "template_4"],
"ketone": ["template_1", "template_2", "template_3", "template_4"],
"ester": ["template_2", "template_3", "template_4"],
"acyl_chloride": ["template_2", "template_3", "template_4"],
"amid": ["template_4"],
"carboxylic_acid": ["template_4"],
"other": ["template_1"]
"reduction": {
"aldehyde": ["template_1", "template_2", "template_3", "template_4"],
"ketone": ["template_1", "template_2", "template_3", "template_4"],
"ester": ["template_2", "template_3", "template_4"],
"acyl_chloride": ["template_2", "template_3", "template_4"],
"amid": ["template_4"],
"carboxylic_acid": ["template_4"],
"other": ["template_1"]
},
"oxidation": {
"primary_alcohol>>aldehyde": ["template_1"],
"secondary_alcohol>>ketone": ["template_1"],
"primary_alcohol>>carboxylic_acid": ["template_2"],
"aldehyde>>carboxylic_acid": ["template_3"],
"other": []
}
}
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