def get_palladium_cispbi_sqpl() -> stk.BuildingBlock:
molecule = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.CisProtectedSquarePlanar(
metals={get_pd_atom(): 0},
ligands={get_palladium_bi_1(): 0},
reaction_factory=stk.DativeReactionFactory(
reaction_factory=stk.GenericReactionFactory(bond_orders={
frozenset({
stk.GenericFunctionalGroup,
stk.SingleAtom,
}):
9,
}, ), ),
), )
return stk.BuildingBlock.init_from_molecule(
molecule=molecule,
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[Pd]~[#7]',
bonders=(0, ),
deleters=(),
placers=(0, 1),
),
],
)
def get_iron_complex() -> stk.BuildingBlock:
iron_complex = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.OctahedralDelta(
metals={get_fe_atom(): 0},
ligands={get_complex_ligand(): (0, 1, 2)},
reaction_factory=stk.DativeReactionFactory(
reaction_factory=stk.GenericReactionFactory(bond_orders={
frozenset({
stk.GenericFunctionalGroup,
stk.SingleAtom,
}):
9,
}))))
return stk.BuildingBlock.init_from_molecule(
molecule=iron_complex, functional_groups=[stk.BromoFactory()])
def dative_reaction(
functional_group1,
functional_group1_2,
periodicity,
bond_order,
):
bond_order_key = frozenset({
type(functional_group1),
type(functional_group1_2),
})
edge = MockEdge(0, periodicity)
return CaseData(
factory=stk.DativeReactionFactory(
stk.GenericReactionFactory(
bond_orders={
bond_order_key: bond_order,
},
)
),
construction_state=MockConstructionState(
edges=(edge, ),
edge_functional_groups={
0: (
functional_group1,
functional_group1_2,
)
}
),
edge_group=stk.EdgeGroup(
edges=(edge, )
),
reaction_result=ReactionResult(
new_atoms=(),
new_bonds=get_new_bonds(
functional_group1=functional_group1,
functional_group2=functional_group1_2,
order=bond_order,
periodicity=periodicity,
),
deleted_atoms=it.chain(
functional_group1.get_deleters(),
functional_group1_2.get_deleters(),
),
deleted_bonds=(),
),
)
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(
],
)
@pytest.fixture(
scope='session',
params=(
lambda name: CaseData(
molecule=stk.ConstructedMolecule(
stk.cage.M4L4Square(corners=_get_palladium_cispbi_sqpl(),
linkers=get_other_linker(),
reaction_factory=stk.DativeReactionFactory(
stk.GenericReactionFactory(
bond_orders={
frozenset({
stk.GenericFunctionalGroup,
stk.GenericFunctionalGroup,
}):
9,
})))),
smiles=('[H]C1=C2C([H])=C([H])N(->[Pd+2]3(<-N4=C([H])C([H])=C'
'(C([H])=C4[H])C4=C([H])C([H])=N(->[Pd+2]5(<-N6=C([H]'
')C([H])=C(C([H])=C6[H])C6=C([H])C([H])=N(->[Pd+2]7(<'
'-N8=C([H])C([H])=C(C([H])=C8[H])C8=C([H])C([H])=N(->'
'[Pd+2]9(<-N%10=C([H])C([H])=C2C([H])=C%10[H])<-N([H]'
')([H])C([H])([H])C([H])([H])N->9([H])[H])C([H])=C8[H'
'])<-N([H])([H])C([H])([H])C([H])([H])N->7([H])[H])C('
'[H])=C6[H])<-N([H])([H])C([H])([H])C([H])([H])N->5(['
'H])[H])C([H])=C4[H])<-N([H])([H])C([H])([H])C([H])(['
'H])N->3([H])[H])=C1[H]'),
name=name,
def build_cage_isomers(name, ligand):
"""
Build all four cage isomers.
Parameters
----------
name : :class:`str`
Cage identifier.
ligand : :class:`stk.BuildingBlock`
Ligand building block.
Returns
-------
cage_isomers : :class:`dict` of :class:`stk.ConstructedMolecule`
Constructed cage isomers.
"""
cage_isomers = {}
v_alignments = {
'A': {
2: 0,
3: 0,
4: 0,
5: 0
},
'B': {
2: 1,
3: 0,
4: 0,
5: 0
},
'C': {
2: 1,
3: 1,
4: 0,
5: 0
},
'D': {
2: 1,
3: 0,
4: 1,
5: 0
},
}
complex = stk.BuildingBlock(
smiles='[Pd+2]',
functional_groups=(stk.SingleAtom(stk.Pd(0, charge=2))
for i in range(4)),
position_matrix=np.array([[0, 0, 0]]),
)
for v_a in v_alignments:
v_align = v_alignments[v_a]
name_ = f'{name}_{v_a}'
opt_file = f'{name_}_optc.mol'
# Build cage.
cage = stk.ConstructedMolecule(
stk.cage.M2L4Lantern(
building_blocks={
complex: (0, 1),
ligand: (2, 3, 4, 5)
},
vertex_alignments=v_align,
reaction_factory=stk.DativeReactionFactory(
stk.GenericReactionFactory(
bond_orders={
frozenset({AromaticCNC, stk.SingleAtom}): 9,
frozenset({AromaticCNN, stk.SingleAtom}): 9,
}))))
if exists(opt_file):
cage = cage.with_structure_from_file(opt_file)
else:
print(f'optimizing {name_}')
cage.write(f'{name_}_unopt.mol')
cage = optimize_cage(cage, name_)
cage_isomers[v_a] = cage
return cage_isomers
