How to use the stk.SmartsFunctionalGroupFactory function in stk
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lukasturcani / stk / tests / molecular / molecules / molecule / fixtures / cage / metal_topologies / m8l6_cube.py View on Github 
smiles=(
'[H]C1=C([H])C(C(C2=C([H])C([H])=C(Br)C([H])=C2[H])C(C2=C([H])'
'C([H])=C(Br)C([H])=C2[H])C2=C([H])C([H])=C(Br)C([H])=C2[H])=C'
'([H])C([H])=C1Br'
),
functional_groups=[stk.BromoFactory()]
)
complex_ligand = stk.BuildingBlock(
smiles='[H]C1=NC(C([H])=NBr)=C([H])C([H])=C1[H]',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#35]',
bonders=(1, ),
deleters=(),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
]
)
iron_complex = stk.ConstructedMolecule(
stk.metal_complex.OctahedralDelta(
metals={metal_atom: 0},
ligands={complex_ligand: (0, 1, 2)},
reaction_factory=stk.DativeReactionFactory(
stk.GenericReactionFactory(
bond_orders={
frozenset({
stk.GenericFunctionalGroup,
stk.SingleAtommolecule=palladium_cispbi_sqpl,
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[Pd]~[#7]',
bonders=(0, ),
deleters=(),
placers=(0, 1),
),
]
)
linker = stk.BuildingBlock(
smiles=(
'[H]C1=NC([H])=C([H])C(C2=C([H])C([H])=NC([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.M4L4Square(
corners=palladium_cispbi_sqpl,
linkers=linker,
reaction_factory=stk.DativeReactionFactory(from ....case_data import CaseData
_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], ),
)
_mo_1 = stk.BuildingBlock(
smiles='c1cc2c(cn1)CCCCC2',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
]
)
@pytest.fixture(
params=(
CaseData(
molecule=stk.ConstructedMolecule(
stk.metal_complex.SquarePlanar(
metals={_palladium_atom: 0},
ligands={_mo_1: (0, 1, 2, 3)},
)from ....case_data import CaseData
_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='NCCN',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#7]~[#6]',
bonders=(0, ),
deleters=(),
),
]
)
@pytest.fixture(
params=(
CaseData(
molecule=stk.ConstructedMolecule(
stk.metal_complex.CisProtectedSquarePlanar(
metals={_palladium_atom: 0},
ligands={_bi_1: 0},
reaction_factory=stk.DativeReactionFactory(reaction_factory=stk.DativeReactionFactory(
stk.GenericReactionFactory(
bond_orders={
frozenset({
stk.GenericFunctionalGroup,
stk.SingleAtom
}): 9
}
)
)
)
)
palladium_cispbi_sqpl = stk.BuildingBlock.init_from_molecule(
molecule=palladium_cispbi_sqpl,
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[Pd]~[#7]',
bonders=(0, ),
deleters=(),
placers=(0, 1),
),
]
)
linker = stk.BuildingBlock(
smiles=(
'[H]C1=NC([H])=C([H])C(C2=C([H])C([H])=NC([H])=C2[H])=C1[H]'
),
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),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.M24L48(
building_blocks={
metal_atom: range(24),
linker: range(24, 72)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.M2L4Lantern(
building_blocks={
metal_atom: range(2),
linker: range(2, 6)metal_atom = stk.BuildingBlock(
smiles='[Fe+2]',
functional_groups=(
stk.SingleAtom(stk.Fe(0, charge=2))
for i in range(6)
),
position_matrix=([0, 0, 0], ),
)
complex_ligand = stk.BuildingBlock(
smiles=(
'[H]C1=NC(C([H])=NC2=C([H])C([H])=C(Br)C([H])=C2[H])=C([H])C'
'([H])=C1[H]'
),
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#35]',
bonders=(1, ),
deleters=(),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
]
)
iron_complex = stk.ConstructedMolecule(
stk.metal_complex.OctahedralDelta(
metals={metal_atom: 0},
ligands={complex_ligand: (0, 1, 2)},
reaction_factory=stk.DativeReactionFactory(_iron_atom = stk.BuildingBlock.init_from_rdkit_mol(atom)
atom_0, = _iron_atom.get_atoms(0)
_iron_atom = _iron_atom.with_functional_groups(
(stk.SingleAtom(atom_0) for i in range(6))
)
_iron_bi_1 = stk.BuildingBlock(
smiles='BrN=Cc1ccccn1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#35]',
bonders=(1, ),
deleters=(),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
]
)
@pytest.fixture(
params=(
CaseData(
molecule=stk.ConstructedMolecule(
stk.metal_complex.OctahedralLambda(
metals={_iron_atom: 0},
ligands={_iron_bi_1: (0, 1, 2)},
reaction_factory=stk.DativeReactionFactory(
Popular stk functions
- stk.AboveAverage
- stk.BuildingBlock
- stk.BuildingBlock.init_from_file
- stk.cage
- stk.cage.FourPlusSix
- stk.ConstructedMolecule
- stk.DativeReactionFactory
- stk.GenericFunctionalGroup
- stk.GenericReactionFactory
- stk.MacroModelMD
- stk.normalize_vector
- stk.NullOptimizer
- stk.Pd
- stk.polymer
- stk.polymer.Linear
- stk.Population
- stk.Roulette
- stk.SingleAtom
- stk.SmartsFunctionalGroupFactory
- stk.utilities.FunctionData