def test_sanitize(self):
for status, block in test_data:
print("*" * 44)
rxna = AllChem.ReactionFromRxnBlock(block)
rxnb = AllChem.ReactionFromRxnBlock(block)
rxna.Initialize()
res = rdChemReactions.PreprocessReaction(rxna)
print(AllChem.ReactionToRxnBlock(rxna))
if status == "good":
self.assertEquals(res, good_res)
elif status == "bad":
self.assertEquals(res, bad_res)
print(">" * 44)
rxnb.Initialize()
try:
rdChemReactions.SanitizeRxn(rxnb)
res = rdChemReactions.PreprocessReaction(rxnb)
print(AllChem.ReactionToRxnBlock(rxnb))
self.assertEquals(res, good_res)
assert not status == "fail"
except:
print("$RXN Failed")
if status == "fail":
continue
raise
def test_only_aromatize_if_possible(self):
rxn = AllChem.ReactionFromRxnBlock(kekule_rxn)
# test was for a seg fault
groups = rxn.RunReactants([Chem.MolFromSmiles("c1ccccc1")])
print(groups)
self.assertFalse(len(groups))
# check normal sanitization
rdChemReactions.SanitizeRxn(rxn)
groups = rxn.RunReactants([Chem.MolFromSmiles("c1ccccc1")])
self.assertTrue(len(groups[0]))
# now check adjustparams with ONLY aromatize if possible
rxn = AllChem.ReactionFromRxnBlock(kekule_rxn)
rdChemReactions.SanitizeRxn(rxn)
groups = rxn.RunReactants([Chem.MolFromSmiles("c1ccccc1")])
self.assertTrue(len(groups[0]))
def validate_reaction_smiles(reaction_smiles):
"""Validates reaction SMILES.
Args:
reaction_smiles: Text reaction SMILES.
Returns:
Updated reaction SMILES.
Raises:
ValueError: If the reaction contains errors.
"""
try:
reaction = rdChemReactions.ReactionFromSmarts(reaction_smiles,
useSmiles=True)
rdChemReactions.SanitizeRxn(reaction)
except ValueError as error:
raise ValueError(
f'reaction contains errors: {reaction_smiles}') from error
_, num_errors = reaction.Validate()
if num_errors:
raise ValueError(f'reaction contains errors: {reaction_smiles}')
return rdChemReactions.ReactionToSmiles(reaction)
def test_github_4162(self):
rxn = rdChemReactions.ReactionFromSmarts(
"[C:1](=[O:2])-[OD1].[N!H0:3]>>[C:1](=[O:2])[N:3]")
rxn_copy = rdChemReactions.ChemicalReaction(rxn)
rdChemReactions.SanitizeRxn(rxn)
rdChemReactions.SanitizeRxn(rxn_copy)
pkl = rxn.ToBinary()
rxn_from_pickle = rdChemReactions.ChemicalReaction(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = pickle.dumps(rxn)
rxn_from_pickle = pickle.loads(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = rxn_from_pickle.ToBinary()
rxn_from_pickle = rdChemReactions.ChemicalReaction(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = pickle.dumps(rxn_from_pickle)
rxn_from_pickle = pickle.loads(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
def test_unused_rlabel_in_product(self):
rxn = AllChem.ReactionFromRxnBlock(unused_rlabel_in_product)
# test was for a seg fault
rdChemReactions.SanitizeRxn(rxn)
def is_reaction_ok(rxn):
"""Check is the reaction is synthetically valid"""
return rdChemReactions.SanitizeRxn(
rxn) == rdChemReactions.SanitizeFlags.SANITIZE_NONE
def testRemoveInsaneReagents(self):
rxndata = "$RXN\nUntitled Document-1\n ChemDraw10291618492D\n\n 3 1\n$MOL\n\n\n\n 2 1 0 0 0 0 0 0 0 0999 V2000\n 0.4125 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0\n -0.4125 0.0000 0.0000 R2 0 0 0 0 0 0 0 0 0 2 0 0\n 1 2 1 0 0\nM END\n$MOL\n\n\n\n 2 1 0 0 0 0 0 0 0 0999 V2000\n -0.4125 0.0000 0.0000 R1 0 0 0 0 0 0 0 0 0 1 0 0\n 0.4125 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0\nM END\n$MOL\n\n\n\n 2 1 0 0 0 0 0 0 0 0999 V2000\n 0.4125 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 5 0 0\n -0.4125 0.0000 0.0000 R4 0 0 0 0 0 0 0 0 0 4 0 0\n 1 2 1 0 0\nM END\n$MOL\n\n\n\n 14 15 0 0 0 0 0 0 0 0999 V2000\n 0.5072 -0.5166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5072 0.3084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2949 -0.7616 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7817 -0.0880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2967 0.5794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5558 -1.5443 0.0000 R1 0 0 0 0 0 0 0 0 0 1 0 0\n -0.2073 0.7208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.9218 0.3083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.9217 -0.5167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.2073 -0.9292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.6362 0.7208 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0\n 1.5452 1.3661 0.0000 N 0 0 0 0 0 0 0 0 0 5 0 0\n 2.3507 1.5443 0.0000 R4 0 0 0 0 0 0 0 0 0 4 0 0\n -2.3507 0.3083 0.0000 R2 0 0 0 0 0 0 0 0 0 2 0 0\n 1 2 2 0 0\n 1 3 1 0 0\n 3 4 1 0 0\n 4 5 1 0 0\n 5 2 1 0 0\n 3 6 1 0 0\n 2 7 1 0 0\n 7 8 2 0 0\n 8 9 1 0 0\n 9 10 2 0 0\n 10 1 1 0 0\n 8 11 1 0 0\n 12 13 1 0 0\n 11 14 1 0 0\n 12 5 1 0 0\nM END\n"
rxn = AllChem.ReactionFromRxnBlock(rxndata)
bbs = []
r1 = [
Chem.MolFromSmiles("CCNCC"),
Chem.MolFromSmiles("NCC"),
]
r2 = [
Chem.MolFromSmiles("ClC1CCCC1"),
Chem.MolFromSmiles("ClC1CCCC1Cl"),
]
r3 = [
Chem.MolFromSmiles("CCNCC"),
Chem.MolFromSmiles("NCC"),
]
bbs = [r1, r2, r3]
# nothing matches!
for i, reagent in enumerate(rxn.GetReactants()):
for bb in bbs[i]:
self.assertFalse(bb.HasSubstructMatch(reagent))
# everything matches - yay sanitization!
rdChemReactions.SanitizeRxn(rxn)
for i, reagent in enumerate(rxn.GetReactants()):
for bb in bbs[i]:
self.assertTrue(bb.HasSubstructMatch(reagent))
en = rdChemReactions.EnumerateLibrary(rxn, bbs)
self.assertTrue(len(en.GetReagents()[0]) == 2)
self.assertTrue(len(en.GetReagents()[1]) == 2)
self.assertTrue(len(en.GetReagents()[2]) == 2)
#####################################################################################
# Match only at rgroups (ChemDraw style)
rxn = AllChem.ReactionFromRxnBlock(rxndata)
expected_matches = [[False, True], [True, True], [False, True]]
rdChemReactions.SanitizeRxn(
rxn, params=rdChemReactions.GetChemDrawRxnAdjustParams())
for i, (reagent, expected) in enumerate(
zip(rxn.GetReactants(), expected_matches)):
match = [bb.HasSubstructMatch(reagent) for reagent in bbs[i]]
self.assertTrue(match, expected)
# Now try EnumerateLibrary
en = rdChemReactions.EnumerateLibrary(rxn, bbs)
self.assertTrue(len(en.GetReagents()[0]) == 1)
self.assertTrue(len(en.GetReagents()[1]) == 2)
self.assertTrue(len(en.GetReagents()[2]) == 1)
#####################################################################################
# now set the removal options ot only make one product per reagent set
rxn = AllChem.ReactionFromRxnBlock(rxndata)
rdChemReactions.SanitizeRxn(rxn)
opts = rdChemReactions.EnumerationParams()
opts.reagentMaxMatchCount = 1
en = rdChemReactions.EnumerateLibrary(rxn, bbs, params=opts)
self.assertTrue(len(en.GetReagents()[0]) == 1)
self.assertTrue(len(en.GetReagents()[1]) == 1)
self.assertTrue(len(en.GetReagents()[2]) == 1)
#####################################################################################
# now set the removal options ot only make one product per reagent set
# but wt
rxn = AllChem.ReactionFromRxnBlock(rxndata)
rdChemReactions.SanitizeRxn(
rxn, params=rdChemReactions.GetChemDrawRxnAdjustParams())
opts = rdChemReactions.EnumerationParams()
opts.reagentMaxMatchCount = 1
en = rdChemReactions.EnumerateLibrary(rxn, bbs, params=opts)
self.assertTrue(len(en.GetReagents()[0]) == 1)
self.assertTrue(len(en.GetReagents()[1]) == 1)
self.assertTrue(len(en.GetReagents()[2]) == 1)
