def test_example_2(self) -> None:
uncapped_molecule = Molecule(
{
1:
Atom(index=1,
element='C',
valence=3,
capped=False,
coordinates=None),
2:
Atom(index=2,
element='O',
valence=1,
capped=False,
coordinates=None),
},
[
(1, 2),
],
name='example_2',
)
uncapped_molecule.write_graph('uncapped_molecule')
for use_ILP in (True, ):
capped_molecule = getattr(uncapped_molecule,
CAPPING_FUNCTION_NAME)(debug=None)
capped_molecule.write_graph('capped_molecule_with_{0}'.format(
'ILP' if use_ILP else 'bruteforce'))
assert capped_molecule.formula(
charge=True) == 'CH2O', capped_molecule.formula(charge=True)
def test_example_wang_4(self) -> None:
uncapped_molecule = Molecule(
{
1:
Atom(index=1,
element='O',
valence=1,
capped=True,
coordinates=None),
2:
Atom(index=2,
element='C',
valence=3,
capped=True,
coordinates=None),
3:
Atom(index=3,
element='C',
valence=3,
capped=False,
coordinates=None),
4:
Atom(index=4,
element='C',
valence=3,
capped=False,
coordinates=None),
5:
Atom(index=5,
element='C',
valence=3,
capped=False,
coordinates=None),
6:
Atom(index=6,
element='N',
valence=2,
capped=True,
coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
(4, 5),
(5, 6),
(6, 2),
],
name='example_wang_4',
)
uncapped_molecule.write_graph('uncapped_molecule')
for use_ILP in (True, False):
capped_molecule = getattr(uncapped_molecule,
CAPPING_FUNCTION_NAME)(debug=None)
capped_molecule.write_graph('capped_molecule_with_{0}'.format(
'ILP' if use_ILP else 'bruteforce'))
assert capped_molecule.formula(
charge=True) == 'C4H3NO', capped_molecule.formula(charge=True)
def test_example_0(self) -> None:
molecule = Molecule(
[
Atom(index=1,
element='C',
valence=3,
capped=True,
coordinates=None),
Atom(index=2,
element='O',
valence=1,
capped=True,
coordinates=None),
Atom(index=3,
element='O',
valence=2,
capped=True,
coordinates=None),
Atom(index=4,
element='H',
valence=1,
capped=True,
coordinates=None),
Atom(index=5,
element='H',
valence=1,
capped=True,
coordinates=None),
],
[
(1, 2),
(1, 3),
(3, 4),
(1, 5),
],
name='methoanoic acid',
)
molecule.write_graph('raw_molecule')
molecule.assign_bond_orders_and_charges_with_ILP()
molecule.write_graph('molecule_with_electrons')
molecule.get_all_tautomers(
**OPTIONS[molecule_name] if molecule_name in
OPTIONS else {}))
else:
print(
molecule.assign_bond_orders_and_charges_with_ILP(
enforce_octet_rule=True))
print(
molecule.write_graph(molecule_name,
output_size=(int(2100 / 1.5),
int(2970 / 1.5))))
if molecule_name == 'warfarin':
print(molecule)
print()
molecule = Molecule([
Atom(index=1, element='C', valence=3, capped=True, coordinates=None),
Atom(index=2, element='C', valence=3, capped=True, coordinates=None)
], [(1, 2)])
print(molecule.get_all_tautomers())
print(molecule.write_graph('ethene', output_size=(200, 200)))
molecule = Molecule([
Atom(index=1, element='H', valence=1, capped=True, coordinates=None),
Atom(index=2, element='O', valence=1, capped=True, coordinates=None)
], [(1, 2)],
netcharge=0,
name='hydroxyl_radical')
print(molecule.assign_bond_orders_and_charges_with_ILP())
print(molecule.write_graph('', output_size=(200, 200)))
def test_example_wang_1(self) -> None:
uncapped_molecule = Molecule(
{
1:
Atom(index=1,
element='C',
valence=3,
capped=True,
coordinates=None),
2:
Atom(index=2,
element='C',
valence=3,
capped=True,
coordinates=None),
3:
Atom(index=3,
element='C',
valence=3,
capped=True,
coordinates=None),
4:
Atom(index=4,
element='C',
valence=3,
capped=True,
coordinates=None),
5:
Atom(index=5,
element='C',
valence=3,
capped=True,
coordinates=None),
6:
Atom(index=6,
element='C',
valence=3,
capped=True,
coordinates=None),
7:
Atom(index=7,
element='H',
valence=1,
capped=True,
coordinates=None),
8:
Atom(index=8,
element='H',
valence=1,
capped=True,
coordinates=None),
9:
Atom(index=9,
element='H',
valence=1,
capped=True,
coordinates=None),
10:
Atom(index=10,
element='H',
valence=1,
capped=True,
coordinates=None),
11:
Atom(index=11,
element='H',
valence=1,
capped=True,
coordinates=None),
12:
Atom(index=12,
element='O',
valence=1,
capped=True,
coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
(4, 5),
(5, 6),
(6, 1),
(7, 1),
(8, 2),
(9, 3),
(10, 4),
(11, 5),
(12, 6),
],
name='example_wang_1',
)
uncapped_molecule.write_graph('uncapped_molecule')
for use_ILP in (True, False):
capped_molecule = getattr(uncapped_molecule,
CAPPING_FUNCTION_NAME)(debug=None)
capped_molecule.write_graph('capped_molecule_with_{0}'.format(
'ILP' if use_ILP else 'bruteforce'))
assert capped_molecule.formula(
charge=True) == 'C6H5O 1-', capped_molecule.formula(charge=True)
def test_example_taxol_core(self) -> None:
uncapped_molecule = Molecule(
{
5:
Atom(index=5,
element="C",
valence=3,
capped=False,
coordinates=(0.746, 3.138, 0.794)),
7:
Atom(index=7,
element="O",
valence=2,
capped=True,
coordinates=(1.175, 1.853, 0.61)),
8:
Atom(index=8,
element="C",
valence=4,
capped=True,
coordinates=(1.672, 1.0, 1.641)),
9:
Atom(index=9,
element="C",
valence=4,
capped=True,
coordinates=(2.696, 1.617, 2.644)),
10:
Atom(index=10,
element="H",
valence=1,
capped=True,
coordinates=(2.871, 2.705, 2.545)),
11:
Atom(index=11,
element="H",
valence=1,
capped=True,
coordinates=(3.667, 1.113, 2.766)),
12:
Atom(index=12,
element="O",
valence=2,
capped=True,
coordinates=(1.805, 1.347, 3.756)),
13:
Atom(index=13,
element="C",
valence=4,
capped=True,
coordinates=(0.741, 0.845, 2.897)),
14:
Atom(index=14,
element="H",
valence=1,
capped=True,
coordinates=(-0.111, 1.567, 2.942)),
15:
Atom(index=15,
element="C",
valence=4,
capped=False,
coordinates=(0.262, -0.558, 3.171)),
18:
Atom(index=18,
element="C",
valence=4,
capped=False,
coordinates=(1.353, -1.632, 3.131)),
20:
Atom(index=20,
element="O",
valence=2,
capped=True,
coordinates=(1.998, -1.605, 4.383)),
21:
Atom(index=21,
element="H",
valence=1,
capped=True,
coordinates=(2.798, -2.116, 4.304)),
22:
Atom(index=22,
element="C",
valence=4,
capped=False,
coordinates=(2.315, -1.541, 1.879)),
29:
Atom(index=29,
element="C",
valence=4,
capped=True,
coordinates=(1.951, -0.352, 0.936)),
30:
Atom(index=30,
element="H",
valence=1,
capped=True,
coordinates=(0.931, -0.608, 0.548)),
31:
Atom(index=31,
element="C",
valence=4,
capped=True,
coordinates=(2.911, -0.285, -0.293)),
32:
Atom(index=32,
element="H",
valence=1,
capped=True,
coordinates=(3.702, -1.082, -0.163)),
33:
Atom(index=33,
element="O",
valence=2,
capped=False,
coordinates=(3.52, 1.006, -0.367)),
101:
Atom(index=101,
element="C",
valence=4,
capped=False,
coordinates=(0.908, -3.278, 0.308)),
47:
Atom(index=47,
element="C",
valence=4,
capped=True,
coordinates=(2.191, -0.548, -1.701)),
48:
Atom(index=48,
element="O",
valence=2,
capped=True,
coordinates=(3.132, -0.275, -2.729)),
49:
Atom(index=49,
element="H",
valence=1,
capped=True,
coordinates=(3.241, 0.668, -2.768)),
50:
Atom(index=50,
element="C",
valence=4,
capped=False,
coordinates=(0.937, 0.345, -1.879)),
53:
Atom(index=53,
element="C",
valence=4,
capped=False,
coordinates=(1.845, -2.08, -1.847)),
54:
Atom(index=54,
element="C",
valence=3,
capped=True,
coordinates=(0.733, -2.32, -0.843)),
59:
Atom(index=59,
element="C",
valence=3,
capped=False,
coordinates=(-0.388, -1.56, -0.899))
},
{
frozenset({5, 7}),
frozenset({13, 15}),
frozenset({18, 20}),
frozenset({18, 15}),
frozenset({50, 47}),
frozenset({18, 22}),
frozenset({8, 29}),
frozenset({8, 9}),
frozenset({32, 31}),
frozenset({48, 47}),
frozenset({9, 10}),
frozenset({29, 30}),
frozenset({29, 31}),
frozenset({9, 11}),
frozenset({53, 54}),
frozenset({9, 12}),
frozenset({20, 21}),
frozenset({48, 49}),
frozenset({29, 22}),
frozenset({33, 31}),
frozenset({31, 47}),
frozenset({12, 13}),
frozenset({13, 14}),
frozenset({59, 54}),
frozenset({8, 7}),
frozenset({53, 47}),
frozenset({101, 54}),
frozenset({8, 13})
},
name='example_taxol_core',
)
uncapped_molecule.write_graph('uncapped_molecule',
output_size=(1200, 1200))
for use_ILP in (True, ):
capped_molecule = getattr(uncapped_molecule,
CAPPING_FUNCTION_NAME)(debug=None)
capped_molecule.write_graph('capped_molecule_with_{0}'.format(
'ILP' if use_ILP else 'bruteforce'),
output_size=(1200, 1200))
assert capped_molecule.formula(
charge=True) == 'C16H26O5', capped_molecule.formula(charge=True)