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(
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, ),
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')
carbon=stk.C(0),
oxygen=stk.O(1),
sulfur=stk.S(2),
hydrogen=stk.H(3),
atom=stk.C(4),
bonders=(stk.C(0), ),
deleters=(stk.S(2), stk.H(3)),
),
lambda: stk.Thiol(
sulfur=stk.S(0),
hydrogen=stk.H(1),
atom=stk.C(2),
bonders=(stk.C(2), ),
deleters=(stk.S(0), stk.H(1)),
),
lambda: stk.SingleAtom(atom=stk.Fe(0)),
),
)
def functional_group1(request) -> stk.GenericFunctionalGroup:
"""
A :class:`.GenericFunctionalGroup` with 1 bonder atom.
"""
return request.param()
@pytest.fixture
def functional_group1_2(functional_group1):
"""
A :class:`.GenericFunctionalGroup` with 1 bonder atom.
import pytest
import stk
from ....case_data import CaseData
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], ),
)
ditopic_linker = stk.BuildingBlock(
smiles=(
'[H]C1=C([H])C(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]',
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
functional_groups=[stk.BromoFactory()],
),
stk.BuildingBlock(
smiles='BrCNCCBr',
functional_groups=[stk.BromoFactory()],
),
),
repeating_unit='AB',
num_repeating_units=2,
), )
_square_planar = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.SquarePlanar(
metals=stk.BuildingBlock(
smiles='[Pd+2]',
functional_groups=(stk.SingleAtom(stk.Fe(0, charge=2))
for i in range(4)),
position_matrix=[[0, 0, 0]],
),
ligands=stk.BuildingBlock(
smiles='NBr',
functional_groups=(stk.PrimaryAminoFactory(), ),
),
optimizer=stk.MCHammer(),
))
uff = stko.OpenBabel('uff')
_square_planar_uff = uff.optimize(_square_planar)
_octahedral = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.Octahedral(
metals=stk.BuildingBlock(
smiles='[Fe+2]',
carbon=stk.C(0),
oxygen=stk.O(1),
sulfur=stk.S(2),
hydrogen=stk.H(3),
atom=stk.C(4),
bonders=(stk.C(0), ),
deleters=(stk.S(2), stk.H(3)),
),
stk.Thiol(
sulfur=stk.S(0),
hydrogen=stk.H(1),
atom=stk.C(2),
bonders=(stk.C(2), ),
deleters=(stk.S(0), stk.H(1)),
),
stk.SingleAtom(atom=stk.Fe(0)),
), )
def functional_group1(request):
"""
A :class:`.GenericFunctionalGroup` with 1 bonder atom.
"""
return request.param.clone()
@pytest.fixture
def functional_group1_2(functional_group1):
"""
A :class:`.GenericFunctionalGroup` with 1 bonder atom.
import pytest
import stk
from rdkit.Chem import AllChem as rdkit
from ....case_data import CaseData
atom = rdkit.MolFromSmiles('[Fe+2]')
atom.AddConformer(rdkit.Conformer(atom.GetNumAtoms()))
_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=(
