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paddlewheel.py
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paddlewheel.py
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import pytest
import stk
from ....case_data import CaseData
_copper_atom = stk.BuildingBlock(
smiles='[Cu+2]',
functional_groups=(
stk.SingleAtom(stk.Cu(0, charge=2))
for i in range(4)
),
position_matrix=([0, 0, 0], ),
)
_palladium_atom = stk.BuildingBlock(
smiles='[Pd+2]',
functional_groups=(
stk.SingleAtom(stk.Pd(0, charge=2))
for i in range(4)
),
position_matrix=([0, 0, 0], ),
)
_bi_1 = stk.BuildingBlock(
smiles='O=C(O)c1ccc(Br)cc1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#8]~[#1]',
bonders=(1, ),
deleters=(2, ),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#8X1]',
bonders=(1, ),
deleters=(),
),
]
)
_bi_2 = stk.BuildingBlock(
smiles='Nc1ccc(C(=O)O)cc1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#8]~[#1]',
bonders=(1, ),
deleters=(2, ),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#8X1]',
bonders=(1, ),
deleters=(),
),
]
)
@pytest.fixture(
params=(
CaseData(
molecule=stk.ConstructedMolecule(
stk.metal_complex.Paddlewheel(
metals={
_copper_atom: (0, ),
_palladium_atom: (1, )
},
ligands={
_bi_1: (2, 3),
_bi_2: (0, 1),
},
reaction_factory=stk.DativeReactionFactory(
stk.GenericReactionFactory(
bond_orders={
frozenset({
stk.GenericFunctionalGroup,
stk.SingleAtom
}): 9
}
)
)
)
),
smiles=(
'[H]C1=C([H])C(C2=O->[Pd+2]34<-O=C(C5=C([H])C([H])=C('
'Br)C([H])=C5[H])O->[Cu+2](<-O2)(<-OC(C2=C([H])C([H])'
'=C(N([H])[H])C([H])=C2[H])=O->3)<-OC(C2=C([H])C([H])'
'=C(N([H])[H])C([H])=C2[H])=O->4)=C([H])C([H])=C1Br'
),
),
CaseData(
molecule=stk.ConstructedMolecule(
stk.metal_complex.Paddlewheel(
metals=_copper_atom,
ligands=_bi_1,
reaction_factory=stk.DativeReactionFactory(
stk.GenericReactionFactory(
bond_orders={
frozenset({
stk.GenericFunctionalGroup,
stk.SingleAtom
}): 9
}
)
)
)
),
smiles=(
'[H]C1=C([H])C(C2=O->[Cu+2]34<-O=C(C5=C([H])C([H])=C('
'Br)C([H])=C5[H])O->[Cu+2](<-O2)(<-OC(C2=C([H])C([H])'
'=C(Br)C([H])=C2[H])=O->3)<-OC(C2=C([H])C([H])=C(Br)C'
'([H])=C2[H])=O->4)=C([H])C([H])=C1Br'
),
),
),
)
def metal_complex_paddlewheel(request):
return request.param