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_UFF_opt(case_uff_molecule):
energy = (stko.UFFEnergy().get_energy(case_uff_molecule.molecule))
optimizer = stko.UFF()
opt_res = optimizer.optimize(case_uff_molecule.molecule)
is_equivalent_molecule(opt_res, case_uff_molecule.molecule)
inequivalent_position_matrices(opt_res, case_uff_molecule.molecule)
opt_energy = (stko.UFFEnergy().get_energy(opt_res))
assert np.isclose(energy, case_uff_molecule.unoptimised_energy, atol=1E-3)
assert opt_energy < case_uff_molecule.unoptimised_energy
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 main():
examples_output = 'aligner_directory'
if not os.path.exists(examples_output):
os.mkdir(examples_output)
bb1 = stk.BuildingBlock('NCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock(
smiles='O=CC(C=O)C=O',
functional_groups=[stk.AldehydeFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.FourPlusSix(
(bb1, bb2), optimizer=stk.MCHammer(num_steps=2000),
),
)
mol_list = [
(stk.BuildingBlock('NCCNCCN'), (('N', 'N'), ), True),
(
stk.BuildingBlock('CN1C=NC2=C1C(=O)N(C(=O)N2C)C'),
(('N', 'N'), ('O', 'O'), ),
True,
),
(stk.BuildingBlock('C1=CN=CN=C1'), (('N', 'N'), ), True),
(stk.BuildingBlock('c1ccccc1'), (('C', 'C'), ), True),
(stk.BuildingBlock('C1CCCCC1'), (('C', 'C'), ), True),
(cage, (('N', 'N'), ), True),
]
_opt = stko.UFF()
for i, (mol, pairs, uff_opt) in enumerate(mol_list):
initial = mol.with_rotation_about_axis(
1.34, np.array((0, 0, 1)), np.array((0, 0, 0)),
)
mol.write(os.path.join(examples_output, f'unaligned_{i}.mol'))
initial.write(os.path.join(examples_output, f'init_{i}.mol'))
aligner = stko.Aligner(
initial_molecule=initial,
matching_pairs=pairs,
)
if uff_opt:
mol = aligner.optimize(_opt.optimize(mol))
else:
mol = aligner.optimize(mol)
mol.write(os.path.join(examples_output, f'aligned_{i}.mol'))
rmsd_calculator = stko.RmsdMappedCalculator(initial)
rmsd = rmsd_calculator.get_results(mol).get_rmsd()
print(f'molecule {i} RMSD: {rmsd}')
def test_UFF_opt(unoptimized_mol):
optimizer = stko.UFF()
opt_res = optimizer.optimize(unoptimized_mol)
is_equivalent_molecule(opt_res, unoptimized_mol)
inequivalent_position_matrices(opt_res, unoptimized_mol)
rmsd:
The RMSD of the pair of molecules.
"""
position_matrix: np.ndarray
def __init__(self, mol1, mol2, rmsd):
self.mol1 = mol1
self.mol2 = mol2
self.rmsd = rmsd
_optimizer = stko.UFF()
_polymer = stk.ConstructedMolecule(topology_graph=stk.polymer.Linear(
building_blocks=(
stk.BuildingBlock(
smiles='BrCCBr',
functional_groups=[stk.BromoFactory()],
),
stk.BuildingBlock(
smiles='BrCNCCBr',
functional_groups=[stk.BromoFactory()],
),
),
repeating_unit='AB',
num_repeating_units=2,
optimizer=stk.MCHammer(),
), )