def get_iron_bi_1() -> stk.BuildingBlock:
return 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=(),
),
])
def get_complex_ligand() -> stk.BuildingBlock:
return 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=(),
),
])
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_bi_2() -> stk.BuildingBlock:
return 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=(),
),
]
)
def get_palladium_bi_1() -> stk.BuildingBlock:
return stk.BuildingBlock(
smiles='[H]N([H])C([H])([H])C([H])([H])N([H])[H]',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#7]~[#6]',
bonders=(0, ),
deleters=(),
),
],
)
def get_linker() -> stk.BuildingBlock:
return 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=(),
),
])
def get_mo_1() -> stk.BuildingBlock:
return stk.BuildingBlock(
smiles='c1cc2c(cn1)CCCCC2',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
def _get_bi_1() -> stk.BuildingBlock:
return stk.BuildingBlock(
smiles='NCCN',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#7]~[#6]',
bonders=(0, ),
deleters=(),
),
]
)
def _get_quad_1() -> stk.BuildingBlock:
return stk.BuildingBlock(
smiles=('Brc1ccc(C2=C3C=CC(=C(c4ccc(Br)cc4)C4=NC(=C(c5ccc(Br)cc5)'
'C5=CC=C([N]5)C(c5ccc(Br)cc5)=C5C=CC2=N5)C=C4)[N]3)cc1'),
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
def get_functional_groups(self, molecule):
generic_functional_groups = stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=self._bonders,
deleters=self._deleters).get_functional_groups(molecule)
for fg in generic_functional_groups:
atom_ids = (i.get_id() for i in fg.get_atoms())
atoms = tuple(molecule.get_atoms(atom_ids))
yield AromaticCNC(
carbon1=atoms[0],
nitrogen=atoms[1],
carbon2=atoms[2],
bonders=tuple(atoms[i] for i in self._bonders),
deleters=tuple(atoms[i] for i in self._deleters),
)
def _get_palladium_cispbi_sqpl() -> stk.BuildingBlock:
palladium_cispbi_sqpl = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.CisProtectedSquarePlanar(
metals=get_pd_atom(),
ligands=get_palladium_bi_1(),
), )
return stk.BuildingBlock.init_from_molecule(
molecule=palladium_cispbi_sqpl,
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[Pd]~[#7]',
bonders=(0, ),
deleters=(),
placers=(0, 1),
),
],
)
lambda: CaseData(
factory=stk.DibromoFactory(),
molecule=stk.BuildingBlock('CC(Br)C(Br)CC'),
functional_groups=(stk.Dibromo(
atom1=stk.C(1),
bromine1=stk.Br(2),
atom2=stk.C(3),
bromine2=stk.Br(4),
bonders=(stk.C(1), stk.C(3)),
deleters=(stk.Br(2), stk.Br(4)),
), ),
),
lambda: CaseData(
factory=stk.SmartsFunctionalGroupFactory(
smarts='[C][N]',
bonders=(0, ),
deleters=(1, ),
),
molecule=stk.BuildingBlock('NCC'),
functional_groups=(stk.GenericFunctionalGroup(
atoms=(stk.N(0), stk.C(1)),
bonders=(stk.C(1), ),
deleters=(stk.N(0), ),
), ),
),
lambda: CaseData(
factory=stk.SmartsFunctionalGroupFactory(
smarts='CBr',
bonders=(0, ),
deleters=(1, ),
placers=(1, ),
_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, ),
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(
stk.GenericReactionFactory(
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], ),
)
palladium_bi_1 = stk.BuildingBlock(
smiles='[H]N([H])C([H])([H])C([H])([H])N([H])[H]',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#7]~[#6]',
bonders=(0, ),
deleters=(),
),
])
palladium_cispbi_sqpl = stk.ConstructedMolecule(
stk.metal_complex.CisProtectedSquarePlanar(
metals={metal_atom: 0},
ligands={palladium_bi_1: 0},
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=[
def main():
bb1 = stk.BuildingBlock('NCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock('O=CCC=O', [stk.AldehydeFactory()])
polymer = stk.ConstructedMolecule(
stk.polymer.Linear(building_blocks=(bb1, bb2),
repeating_unit="AB",
orientations=(0, 0),
num_repeating_units=1))
bb2 = stk.BuildingBlock('O=CC(C=O)C=O', [stk.AldehydeFactory()])
cage = stk.ConstructedMolecule(topology_graph=stk.cage.FourPlusSix(
(bb1, bb2)), )
cage2 = stk.ConstructedMolecule(topology_graph=stk.cage.FourPlusSix(
building_blocks=(bb1, bb2),
optimizer=stk.MCHammer(),
), )
# Produce a Fe+2 atom with 6 functional groups.
iron_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]],
)
# Define coordinating ligand with dummy bromine groups and
# metal coordinating functional groups.
oct_bb = stk.BuildingBlock(
smiles='C1=NC(C=NBr)=CC=C1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#35]',
bonders=(1, ),
deleters=(),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
# Build iron complex with delta stereochemistry.
iron_oct_delta = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.OctahedralDelta(
metals=iron_atom,
ligands=oct_bb,
optimizer=stk.MCHammer(),
), )
# Assign Bromo functional groups to the metal complex.
iron_oct_delta = stk.BuildingBlock.init_from_molecule(
molecule=iron_oct_delta,
functional_groups=[stk.BromoFactory()],
)
# Define spacer building block.
bb3 = stk.BuildingBlock(
smiles=('C1=CC(C2=CC=C(Br)C=C2)=C'
'C=C1Br'),
functional_groups=[stk.BromoFactory()],
)
# Build an M4L6 Tetrahedron with a spacer.
moc = stk.ConstructedMolecule(
topology_graph=stk.cage.M4L6TetrahedronSpacer(
building_blocks=(
iron_oct_delta,
bb3,
),
optimizer=stk.MCHammer(),
), )
host = stk.ConstructedMolecule(topology_graph=stk.cage.FourPlusSix(
building_blocks=(
stk.BuildingBlock(
smiles='NC1CCCCC1N',
functional_groups=[
stk.PrimaryAminoFactory(),
],
),
stk.BuildingBlock(
smiles='O=Cc1cc(C=O)cc(C=O)c1',
functional_groups=[stk.AldehydeFactory()],
),
),
optimizer=stk.MCHammer(),
), )
guest1 = stk.host_guest.Guest(
building_block=stk.BuildingBlock('BrBr'),
displacement=(0., 3., 0.),
)
guest2 = stk.host_guest.Guest(
building_block=stk.BuildingBlock('C1CCCC1'), )
hg_complex = stk.ConstructedMolecule(topology_graph=stk.host_guest.Complex(
host=stk.BuildingBlock.init_from_molecule(host),
guests=(guest1, guest2),
), )
cycle = stk.ConstructedMolecule(topology_graph=stk.macrocycle.Macrocycle(
building_blocks=(stk.BuildingBlock(
smiles='[Br]CC[Br]',
functional_groups=[stk.BromoFactory()],
), ),
repeating_unit='A',
num_repeating_units=8,
optimizer=stk.MCHammer(),
), )
axle = stk.ConstructedMolecule(topology_graph=stk.polymer.Linear(
building_blocks=(
stk.BuildingBlock('BrCCBr', [stk.BromoFactory()]),
stk.BuildingBlock('BrCNCBr', [stk.BromoFactory()]),
),
repeating_unit='AB',
num_repeating_units=3,
optimizer=stk.MCHammer(),
))
rotaxane = stk.ConstructedMolecule(topology_graph=stk.rotaxane.NRotaxane(
axle=stk.BuildingBlock.init_from_molecule(axle),
cycles=(stk.BuildingBlock.init_from_molecule(cycle), ),
repeating_unit='A',
num_repeating_units=1,
), )
examples_output = 'output_directory'
if not os.path.exists(examples_output):
os.mkdir(examples_output)
structures = [
('bb1', bb1),
('bb2', bb2),
('bb3', bb3),
('polymer', polymer),
('cage', cage),
('cage2', cage2),
('m_iron_oct_delta', iron_oct_delta),
('m_moc', moc),
('hg_complex', hg_complex),
('cycle', cycle),
('axle', axle),
('rotaxane', rotaxane),
]
# Run optimisations.
for name, struct in structures:
if 'm_' in name:
rdkit_uff_energy = 'NA'
else:
rdkit_uff_energy = stko.UFFEnergy(
ignore_inter_interactions=False).get_energy(struct)
obabel_uff_energy = (stko.OpenBabelEnergy('uff').get_energy(struct))
struct.write(os.path.join(examples_output, f'obabel_{name}_unopt.mol'))
opt = stko.OpenBabel(
forcefield='uff',
repeat_steps=10,
sd_steps=20,
cg_steps=20,
)
opt_struct = opt.optimize(struct)
opt_struct.write(
os.path.join(examples_output, f'obabel_{name}_opt.mol'))
if 'm_' in name:
new_rdkit_uff_energy = 'NA'
else:
new_rdkit_uff_energy = stko.UFFEnergy(
ignore_inter_interactions=False).get_energy(opt_struct)
new_obabel_uff_energy = (
stko.OpenBabelEnergy('uff').get_energy(opt_struct))
print(f'{name}:\n'
f'rdkit: {rdkit_uff_energy}, obabel: {obabel_uff_energy}\n'
f'opt rdkit: {new_rdkit_uff_energy}, '
f'opt obabel: {new_obabel_uff_energy}\n')