def main():
bb1 = stk.BuildingBlock('NCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock(
smiles='O=CC(C=O)C=O',
functional_groups=[stk.AldehydeFactory()],
)
cage1 = stk.ConstructedMolecule(topology_graph=stk.cage.FourPlusSix(
(bb1, bb2)), )
broken_bonds_by_id = []
disconnectors = []
for bi in cage1.get_bond_infos():
if bi.get_building_block() is None:
a1id = bi.get_bond().get_atom1().get_id()
a2id = bi.get_bond().get_atom2().get_id()
broken_bonds_by_id.append(sorted((a1id, a2id)))
disconnectors.extend((a1id, a2id))
print(broken_bonds_by_id)
print(disconnectors)
print('--')
new_topology_graph = stko.TopologyExtractor()
tg_info = new_topology_graph.extract_topology(
molecule=cage1,
broken_bonds_by_id=broken_bonds_by_id,
disconnectors=set(disconnectors),
)
print(tg_info.get_vertex_positions())
print(tg_info.get_connectivities())
print(tg_info.get_edge_pairs())
cage1.write(os.path.join('output_directory', 'tg_cage.mol'))
tg_info.write(os.path.join('output_directory', 'tg_info.pdb'))
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))
# Run calculations for bb.
bb1.write('output_directory/tors_test_bb1.mol')
tors_calculator = stko.TorsionCalculator()
tors_results = tors_calculator.get_results(bb1)
print(tors_results.get_molecule())
for t, ang in tors_results.get_torsion_angles():
print(t, ang, t.get_atom_ids())
# Run calculations for constructed molecule.
polymer.write('output_directory/tors_test_polymer.mol')
tors_calculator = stko.ConstructedMoleculeTorsionCalculator()
tors_results = tors_calculator.get_results(polymer)
print(tors_results.get_molecule())
for t, ang in tors_results.get_torsion_angles():
print(t, ang, t.get_atom_ids())
for t in tors_results.get_torsion_infos():
print(
'c',
t.get_torsion(),
t.get_building_block(),
t.get_building_block_id(),
t.get_building_block_torsion(),
)
print(tors_results.get_torsion_infos_by_building_block())
for t in tors_results.get_torsion_infos():
print(get_torsion_info_angles(polymer, t))
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 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 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 not os.path.exists(examples_output):
os.mkdir(examples_output)
print(stko.ZMatrix().get_zmatrix(bb1))
bb1.write(os.path.join(examples_output, 'bb1.mol'))
print(stko.ZMatrix().get_zmatrix(bb2))
bb2.write(os.path.join(examples_output, 'bb2.mol'))
print(stko.ZMatrix().get_zmatrix(polymer))
polymer.write(os.path.join(examples_output, 'polymer.mol'))
def test_torsion_matching():
"""
Confirm torsions are appropriately mapped.
Check corresponding torsion angles between building blocks and
constructed molecules to confirm that the angle is the same in
both.
"""
bb1 = stk.BuildingBlock('NCCNCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock('O=CCCC=O', [stk.AldehydeFactory()])
assert _polymer_angles_match(bb1, bb2)
# Test case designed such that default rdkit torsion for
# constructed molecule spans over both building blocks, requiring
# stko to correctly clean this up.
bonders3 = (stk.C(1), )
deleters3 = (stk.H(7), )
functional_group3 = stk.GenericFunctionalGroup(atoms=bonders3 + deleters3,
bonders=bonders3,
deleters=deleters3)
bb3 = stk.BuildingBlock('CCCC', [functional_group3])
bonders4 = (stk.C(0), )
deleters4 = (stk.H(1), )
functional_group4 = stk.GenericFunctionalGroup(atoms=bonders4 + deleters4,
bonders=bonders4,
deleters=deleters4)
bb4 = stk.BuildingBlock('C', [functional_group4])
assert _polymer_angles_match(bb3, bb4)
# Test case for an exterior atom of a building block torsion being
# deleted in construction.
bonders5 = (stk.C(1), )
deleters5 = (stk.C(0), stk.H(4), stk.H(5), stk.H(6))
functional_group5 = stk.GenericFunctionalGroup(atoms=bonders5 + deleters5,
bonders=bonders5,
deleters=deleters5)
bb5 = stk.BuildingBlock('CCCC', [functional_group5])
bb6 = bb4
assert not _polymer_angles_match(bb5, bb6)
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))
# Zipping calculations together.
mols = [
# Perfect linear short.
stk.BuildingBlock('C#C'),
# Kind of linear long.
stk.BuildingBlock('C#CC#C'),
stk.BuildingBlock('CCCC'),
# Flat.
stk.BuildingBlock('C1=CC=CC=C1'),
# Less flat.
stk.BuildingBlock('C1CCCCC1'),
# Sphere - CH4.
stk.BuildingBlock('C'),
# Sphere - adamantane.
stk.BuildingBlock('C1C3CC2CC(CC1C2)C3'),
# Constructed Molecule.
polymer,
]
shape_calc = stko.ShapeCalculator()
for mol in mols:
print(
mol,
stko.ShapeResults(
shape_calc.calculate(mol)).get_spherocity_index(),
stko.ShapeResults(shape_calc.calculate(mol)).get_eccentricity(),
)
atom2=stk.C(2),
bonders=(stk.N(1), ),
deleters=(stk.H(10), ),
),
stk.SecondaryAmino(
nitrogen=stk.N(4),
hydrogen=stk.H(15),
atom1=stk.C(3),
atom2=stk.C(5),
bonders=(stk.N(4), ),
deleters=(stk.H(15), ),
),
),
),
lambda: CaseData(
factory=stk.AldehydeFactory(),
molecule=stk.BuildingBlock('O=CCC=O'),
functional_groups=(
stk.Aldehyde(
carbon=stk.C(1),
oxygen=stk.O(0),
hydrogen=stk.H(5),
atom=stk.C(2),
bonders=(stk.C(1), ),
deleters=(stk.O(0), ),
),
stk.Aldehyde(
carbon=stk.C(3),
oxygen=stk.O(4),
hydrogen=stk.H(8),
atom=stk.C(2),
and su_id != su
]
for su_id, bb_id in has_same_bb_id:
for i in subunits[su_id]:
compound_subunit.add(i)
taken_subunits.add(su_id)
new_subunits[su] = compound_subunit
return new_subunits
# Building a cage from the examples on the stk docs.
bb1 = stk.BuildingBlock(
smiles='O=CC(C=O)C=O',
functional_groups=[stk.AldehydeFactory()],
)
bb2 = stk.BuildingBlock(
smiles='O=CC(Cl)(C=O)C=O',
functional_groups=[stk.AldehydeFactory()],
)
bb3 = stk.BuildingBlock('NCCN', [stk.PrimaryAminoFactory()])
bb4 = stk.BuildingBlock.init_from_file(
'some_complex.mol',
functional_groups=[stk.PrimaryAminoFactory()],
)
bb5 = stk.BuildingBlock('NCCCCN', [stk.PrimaryAminoFactory()])
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.FourPlusSix(
# building_blocks is now a dict, which maps building
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')
def main():
username = input('Username: '******'mongodb+srv://{username}:{password}@stk-vis-example.x4bkl.'
'mongodb.net/stk?retryWrites=true&w=majority')
database = 'stk'
client.drop_database(database)
constructed_db = stk.ConstructedMoleculeMongoDb(client, database)
atoms_db = stk.ValueMongoDb(client, 'Num Atoms')
bonds_db = stk.ValueMongoDb(client, 'Num Bonds')
energy_db = stk.ValueMongoDb(client, 'UFF Energy')
macrocycle = uff(
stk.ConstructedMolecule(topology_graph=stk.macrocycle.Macrocycle(
building_blocks=(
stk.BuildingBlock(
smiles='BrCCBr',
functional_groups=[stk.BromoFactory()],
),
stk.BuildingBlock(
smiles='BrNNBr',
functional_groups=[stk.BromoFactory()],
),
stk.BuildingBlock(
smiles='BrOOBr',
functional_groups=[stk.BromoFactory()],
),
),
repeating_unit='ABC',
num_repeating_units=2,
), ))
atoms_db.put(macrocycle, macrocycle.get_num_atoms())
bonds_db.put(macrocycle, macrocycle.get_num_bonds())
energy_db.put(macrocycle, uff_energy(macrocycle))
constructed_db.put(macrocycle)
polymer = uff(
stk.ConstructedMolecule(topology_graph=stk.polymer.Linear(
building_blocks=(
stk.BuildingBlock(
smiles='BrCCBr',
functional_groups=[stk.BromoFactory()],
),
stk.BuildingBlock(
smiles='BrNNBr',
functional_groups=[stk.BromoFactory()],
),
),
repeating_unit='AB',
num_repeating_units=4,
), ))
atoms_db.put(polymer, polymer.get_num_atoms())
bonds_db.put(polymer, polymer.get_num_bonds())
energy_db.put(polymer, uff_energy(polymer))
constructed_db.put(polymer)
rotaxane = uff(
stk.ConstructedMolecule(topology_graph=stk.rotaxane.NRotaxane(
axle=stk.BuildingBlock.init_from_molecule(polymer),
cycles=(stk.BuildingBlock(
smiles=('C1=CC2=CC3=CC=C(N3)C=C4C=CC(=N4)'
'C=C5C=CC(=N5)C=C1N2'), ), ),
repeating_unit='A',
num_repeating_units=1,
), ))
atoms_db.put(rotaxane, rotaxane.get_num_atoms())
bonds_db.put(rotaxane, rotaxane.get_num_bonds())
energy_db.put(rotaxane, uff_energy(rotaxane))
constructed_db.put(rotaxane)
kagome = uff(
stk.ConstructedMolecule(topology_graph=stk.cof.Honeycomb(
building_blocks=(
stk.BuildingBlock('BrC=CBr', [stk.BromoFactory()]),
stk.BuildingBlock(
smiles='Brc1cc(Br)cc(Br)c1',
functional_groups=[stk.BromoFactory()],
),
),
lattice_size=(2, 2, 1)), ))
atoms_db.put(kagome, kagome.get_num_atoms())
bonds_db.put(kagome, kagome.get_num_bonds())
energy_db.put(kagome, uff_energy(kagome))
constructed_db.put(kagome)
cc3 = 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()],
),
), ), )
cc3 = uff(cc3)
atoms_db.put(cc3, cc3.get_num_atoms())
bonds_db.put(cc3, cc3.get_num_bonds())
energy_db.put(cc3, uff_energy(cc3))
constructed_db.put(cc3)