def get_pd_atom() -> stk.BuildingBlock:
return stk.BuildingBlock(
smiles='[Pd+2]',
functional_groups=(stk.SingleAtom(stk.Pd(0, charge=2))
for i in range(4)),
position_matrix=([0, 0, 0], ),
)
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]',
import pytest
import stk
from ....case_data import CaseData
metal_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], ),
)
linker = stk.BuildingBlock(
smiles=('[H]C1=NC([H])=C([H])C(C2=C([H])C([H])=C([H])C(C3=C([H])C([H]'
')=NC([H])=C3[H])=C2[H])=C1[H]'),
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
])
@pytest.fixture(
params=(CaseData(
molecule=stk.ConstructedMolecule(
stk.cage.M4L8(
building_blocks={
metal_atom: range(4),
linker: range(4, 12)
},
reaction_factory=stk.DativeReactionFactory(
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
