def test_ETKDG_opt(unoptimized_mol):
optimizer = stko.ETKDG()
opt_res = optimizer.optimize(unoptimized_mol)
is_equivalent_molecule(opt_res, unoptimized_mol)
inequivalent_position_matrices(opt_res, unoptimized_mol)
optimizer = stko.ETKDG(random_seed=2584)
opt_res = optimizer.optimize(unoptimized_mol)
is_equivalent_molecule(opt_res, unoptimized_mol)
inequivalent_position_matrices(opt_res, unoptimized_mol)
def test_ETKDG_opt(case_etkdg_molecule):
optimizer = stko.ETKDG()
opt_res = optimizer.optimize(case_etkdg_molecule)
is_equivalent_molecule(opt_res, case_etkdg_molecule)
inequivalent_position_matrices(opt_res, case_etkdg_molecule)
optimizer = stko.ETKDG(random_seed=2584)
opt_res = optimizer.optimize(case_etkdg_molecule)
is_equivalent_molecule(opt_res, case_etkdg_molecule)
inequivalent_position_matrices(opt_res, case_etkdg_molecule)
def main():
bb1 = stk.BuildingBlock('NCCNCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock('O=CCCC=O', [stk.AldehydeFactory()])
polymer = stk.ConstructedMolecule(
stk.polymer.Linear(building_blocks=(bb1, bb2),
repeating_unit="AB",
orientations=[0, 0],
num_repeating_units=1))
examples_output = 'output_directory'
if os.path.exists(examples_output):
shutil.rmtree(examples_output)
os.mkdir(examples_output)
# Run optimisations.
uff = stko.UFF()
polymer = uff.optimize(polymer)
polymer.write(f'{examples_output}/poly_uff.mol')
mmff = stko.MMFF()
polymer = mmff.optimize(polymer)
polymer.write(f'{examples_output}/poly_mmff.mol')
etkdg = stko.ETKDG()
polymer = etkdg.optimize(polymer)
polymer.write(f'{examples_output}/poly_etkdg.mol')
def test_fake_opt(benzene_build):
# Perform optimisation.
optimizer = stko.ETKDG()
opt_benzene = optimizer.optimize(benzene_build)
compare_benzenes(
initial_molecule=benzene_build,
optimized_molecule=opt_benzene,
)
def main():
if len(sys.argv) > 1:
orca_path = sys.argv[1]
else:
print('usage: orca_example.py orca_path')
sys.exit()
bb1 = stk.BuildingBlock('NCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock('O=CC=O', [stk.AldehydeFactory()])
polymer = stk.ConstructedMolecule(
stk.polymer.Linear(building_blocks=(bb1, bb2),
repeating_unit="AB",
orientations=(0, 0),
num_repeating_units=1))
examples_output = 'orca_output_directory'
if not os.path.exists(examples_output):
os.mkdir(examples_output)
# Run optimisations.
etkdg = stko.ETKDG()
polymer = etkdg.optimize(polymer)
orca_ey_1 = stko.OrcaEnergy(
orca_path=orca_path,
topline='! SP B97-3c',
basename='example1',
output_dir=f'{examples_output}/orca_e1_dir',
)
print(orca_ey_1.get_energy(polymer))
uff = stko.UFF()
polymer = uff.optimize(polymer)
orca_ey_2 = stko.OrcaEnergy(
orca_path=orca_path,
topline='! SP B97-3c',
basename='example2',
output_dir=f'{examples_output}/orca_e2_dir',
)
print(orca_ey_2.get_energy(polymer))
orca_ey_3 = stko.OrcaEnergy(
orca_path=orca_path,
topline='! SP B97-3c',
basename='example3',
output_dir=f'{examples_output}/orca_e3_dir',
write_input_only=True,
)
orca_ey_3.get_results(polymer)
def build_guests():
guest_smiles = {
'oF': 'C1=CC=C(C(=C1)C=O)F',
'oB': 'C1=CC=C(C(=C1)C=O)Br',
'oC': 'C1=CC=C(C(=C1)C=O)Cl',
'pF': 'C1=CC(=CC=C1C=O)F',
'pB': 'C1=CC(=CC=C1C=O)Br',
'pC': 'C1=CC(=CC=C1C=O)Cl',
'mF': 'C1=CC(=CC(=C1)F)C=O',
'mB': 'C1=CC(=CC(=C1)Br)C=O',
'mC': 'C1=CC(=CC(=C1)Cl)C=O',
}
guests = {}
for guest in guest_smiles:
opt_file = f'{guest}_unopt.mol'
if exists(opt_file):
guests[guest] = stk.BuildingBlock.init_from_file(opt_file)
else:
print(f'>> optimising {guest}')
# Build BuildingBlocks.
molecule = stk.BuildingBlock(guest_smiles[guest])
# Optimise with ETKDG.
etkdg = stko.ETKDG()
molecule = etkdg.optimize(molecule)
# Save file.
molecule.write(opt_file)
# Initialise as building block.
guests[guest] = stk.BuildingBlock.init_from_molecule(
molecule=molecule, )
return guests
def build_linker(lig1_smiles, lig2_smiles, linker_smiles, name):
"""
Build a linker from 3 components.
Parameters
----------
lig1_smiles : :class:`str`
SMILES string representing ligand component.
lig2_smiles : :class:`str`
SMILES string representing ligand component.
linker_smiles : :class:`str`
SMILES string representing linker component.
name : :class:`str`
Identifier for ligand.
Returns
-------
:class:`stk.BuildingBlock`
Building block constructed from ligand components with
functional groups assigned.
"""
opt_file = f'{name}_opt.mol'
# Build polymer if not already done.
if exists(opt_file):
molecule = stk.BuildingBlock.init_from_file(
path=opt_file,
functional_groups=[AromaticCNCFactory(),
AromaticCNNFactory()],
)
else:
print(f'>> building {name}')
# Build BuildingBlocks.
lig1 = stk.BuildingBlock(lig1_smiles, [stk.BromoFactory()])
lig2 = stk.BuildingBlock(lig2_smiles, [stk.BromoFactory()])
link = stk.BuildingBlock(linker_smiles, [stk.BromoFactory()])
# Build polymer.
molecule = stk.ConstructedMolecule(
topology_graph=stk.polymer.Linear(building_blocks=(lig1, link,
lig2),
repeating_unit='ABC',
num_repeating_units=1,
orientations=(0, 0, 0),
num_processes=1))
# Optimise with ETKDG.
etkdg = stko.ETKDG()
molecule = etkdg.optimize(molecule)
# Initialise as building block.
molecule = stk.BuildingBlock.init_from_molecule(
molecule=molecule,
functional_groups=[
AromaticCNCFactory(),
AromaticCNNFactory(),
],
)
# Save file.
molecule.write(opt_file)
return molecule