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test_capping_wang.py
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test_capping_wang.py
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from sys import stderr
import unittest
from fragment_capping.helpers.types_helpers import Atom
from fragment_capping.helpers.molecule import Molecule, molecule_from_pdb_str
CAPPING_FUNCTION_NAME = 'get_best_capped_molecule_with_ILP'
class Test_Capping(unittest.TestCase):
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')
def test_example_1(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=3, capped=False, coordinates=None),
2: Atom(index=2, element='C', valence=3, capped=False, coordinates=None),
},
[
(1, 2),
],
name='example_1',
)
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) == 'C2H4', capped_molecule.formula(charge=True)
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_3(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=3, capped=False, coordinates=None),
2: Atom(index=2, element='C', valence=3, capped=False, 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='C', valence=3, capped=False, coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
(4, 5),
(5, 6),
(6, 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) == 'C6H6', capped_molecule.formula(charge=True)
def test_example_4(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=4, capped=False, coordinates=None),
},
[
],
name='example_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) == 'CH4', capped_molecule.formula(charge=True)
def test_example_5(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=2, capped=True, coordinates=None),
2: Atom(index=2, element='O', valence=1, capped=True, coordinates=None),
3: Atom(index=3, element='O', valence=1, capped=True, coordinates=None),
},
[
(1, 2),
(1, 3),
],
name='example_5',
)
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) == 'CO2', capped_molecule.formula(charge=True)
def test_example_6(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=4, capped=False, coordinates=None),
},
[
],
name='example_6',
)
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) == 'CH4', capped_molecule.formula(charge=True)
def test_example_7(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=3, capped=False, coordinates=None),
2: Atom(index=2, element='O', valence=2, capped=True, coordinates=None),
3: Atom(index=3, element='O', valence=1, capped=True, coordinates=None),
4: Atom(index=4, element='H', valence=1, capped=True, coordinates=None),
},
[
(1, 2),
(1, 3),
(2, 4),
],
name='example_7',
)
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) == 'CH2O2', capped_molecule.formula(charge=True)
def test_example_8(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='N', valence=None, capped=False, coordinates=None),
2: Atom(index=2, element='H', valence=1, capped=True, coordinates=None),
},
[
(1, 2),
],
name='example_0',
)
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) == 'H3N', capped_molecule.formula(charge=True)
def test_example_9(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='N', valence=None, capped=False, coordinates=None),
2: Atom(index=2, element='H', valence=1, capped=True, coordinates=None),
},
[
(1, 2),
],
name='example_0',
)
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) == 'H3N', capped_molecule.formula(charge=True)
# Source: https://doi.org/10.1016/j.jmgm.2005.12.005
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_wang_2(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='O', valence=1, capped=True, coordinates=None),
2: Atom(index=2, element='C', valence=2, capped=True, coordinates=None),
3: Atom(index=3, element='S', valence=3, capped=True, coordinates=None),
4: Atom(index=4, element='C', valence=4, capped=False, coordinates=None),
5: Atom(index=5, element='C', valence=4, capped=False, coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
(3, 5),
],
name='example_wang_2',
)
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) == 'C3H6OS', capped_molecule.formula(charge=True)
def test_example_wang_3(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=4, capped=False, coordinates=None),
2: Atom(index=2, element='C', valence=4, capped=False, coordinates=None),
3: Atom(index=3, element='C', valence=4, capped=False, coordinates=None),
4: Atom(index=4, element='P', valence=4, capped=True, coordinates=None),
5: Atom(index=5, element='O', valence=1, capped=True, coordinates=None),
6: Atom(index=6, element='O', valence=2, capped=True, coordinates=None),
7: Atom(index=7, element='O', valence=2, capped=True, coordinates=None),
8: Atom(index=8, element='C', valence=4, capped=False, coordinates=None),
9: Atom(index=9, element='C', valence=4, capped=False, coordinates=None),
},
[
(1, 2),
(2, 3),
(2, 4),
(4, 5),
(4, 6),
(4, 7),
(6, 8),
(7, 9),
],
name='example_wang_3',
)
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) == 'C5H13O3P', 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_wang_5(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=4, capped=False, coordinates=None),
2: Atom(index=2, element='C', valence=4, capped=False, coordinates=None),
3: Atom(index=3, element='C', valence=4, capped=False, coordinates=None),
4: Atom(index=4, element='C', valence=2, capped=True, coordinates=None),
5: Atom(index=5, element='N', valence=2, capped=True, coordinates=None),
6: Atom(index=6, element='C', valence=4, capped=False, coordinates=None),
},
[
(1, 2),
(2, 3),
(2, 4),
(4, 5),
(5, 6),
],
name='example_wang_5',
)
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) == 'C5H10N 1+', capped_molecule.formula(charge=True)
def test_example_wang_6(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=3, capped=False, coordinates=None),
2: Atom(index=2, element='C', valence=3, capped=False, 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=True, coordinates=None),
6: Atom(index=6, element='C', valence=3, capped=False, coordinates=None),
7: Atom(index=7, element='C', valence=3, capped=False, coordinates=None),
8: Atom(index=8, element='C', valence=3, capped=False, coordinates=None),
9: Atom(index=9, element='C', valence=3, capped=False, coordinates=None),
10: Atom(index=10, element='C', valence=3, capped=True, coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
(4, 5),
(5, 6),
(6, 7),
(7, 8),
(8, 9),
(9, 10),
(10, 1),
(10, 5),
],
name='example_wang_6',
)
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) == 'C10H8', capped_molecule.formula(charge=True)
def test_example_wang_7(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=4, capped=False, coordinates=None),
2: Atom(index=2, element='C', valence=2, capped=True, coordinates=None),
3: Atom(index=3, element='N', valence=2, capped=True, coordinates=None),
4: Atom(index=4, element='S', valence=1, capped=True, coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
],
name='example_wang_7',
)
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) == 'C2H3NS', capped_molecule.formula(charge=True)
def test_example_wang_8(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='N', valence=1, capped=True, coordinates=None),
2: Atom(index=2, element='N', valence=2, 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=False, coordinates=None),
5: Atom(index=5, element='P', valence=2, capped=True, coordinates=None),
6: Atom(index=6, element='N', valence=2, capped=True, coordinates=None),
7: Atom(index=7, element='C', valence=3, capped=False, coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
(4, 5),
(5, 6),
(6, 7),
(7, 3),
],
name='example_wang_8',
)
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) == 'C3H2N3P', capped_molecule.formula(charge=True)
def test_example_wang_9(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='H', valence=1, capped=True, coordinates=None),
2: Atom(index=2, element='N', valence=2, 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=True, coordinates=None),
5: Atom(index=5, element='C', valence=3, capped=False, coordinates=None),
6: Atom(index=6, element='P', valence=2, capped=True, coordinates=None),
7: Atom(index=7, element='H', valence=1, capped=True, coordinates=None),
8: Atom(index=8, element='N', valence=2, capped=True, coordinates=None),
9: Atom(index=9, element='N', valence=1, capped=True, coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
(4, 5),
(5, 6),
(6, 7),
(4, 8),
(8, 9),
],
name='example_wang_9',
)
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) == 'C3H4N3P', capped_molecule.formula(charge=True)
def test_example_wang_10(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='O', 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='O', valence=1, capped=True, coordinates=None),
11: Atom(index=11, element='H', valence=1, capped=True, coordinates=None),
12: Atom(index=12, element='H', 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_10',
)
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) == 'C6H4O2', capped_molecule.formula(charge=True)
def test_example_wang_11(self) -> None:
uncapped_molecule = Molecule(
{
1: Atom(index=1, element='C', valence=3, capped=False, coordinates=None),
2: Atom(index=2, element='N', valence=3, capped=True, coordinates=None),
3: Atom(index=3, element='H', valence=1, 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=False, coordinates=None),
6: Atom(index=6, element='N', valence=2, capped=True, coordinates=None),
7: Atom(index=7, element='S', valence=2, capped=True, coordinates=None),
8: Atom(index=8, element='C', valence=3, capped=True, coordinates=None),
9: Atom(index=9, element='N', valence=3, capped=True, coordinates=None),
10: Atom(index=10, element='H', valence=1, capped=True, coordinates=None),
},
[
(1, 2),
(2, 3),
(2, 4),
(4, 5),
(5, 6),
(6, 7),
(7, 8),
(8, 9),
(9, 10),
(9, 1),
(4, 8),
],
name='example_wang_11',
)
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) == 'C4H4N3S 1+', capped_molecule.formula(charge=True)
def test_example_wang_12(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=False, 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='P', valence=4, capped=True, coordinates=None),
7: Atom(index=7, element='O', valence=2, capped=True, coordinates=None),
8: Atom(index=8, element='H', valence=1, capped=True, coordinates=None),
9: Atom(index=9, element='O', valence=2, capped=True, coordinates=None),
10: Atom(index=10, element='H', valence=1, capped=True, coordinates=None),
11: Atom(index=11, element='O', valence=1, capped=True, coordinates=None),
},
[
(1, 2),
(2, 3),
(3, 4),
(4, 5),
(5, 1),
(1, 6),
(6, 7),
(7, 8),
(6, 9),
(9, 10),
(6, 11),
],
name='example_wang_12',
)
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) == 'C5H6O3P 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)
def test_example_porphyrin(self, use_ILP: bool = True) -> None:
with open('pdbs/tetraphenylporphyrin.pdb') as fh:
uncapped_molecule = molecule_from_pdb_str(
fh.read(),
name='porphyrin',
)
_, _, pos = uncapped_molecule.write_graph(
'input',
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False},
)
capped_molecule = getattr(uncapped_molecule, CAPPING_FUNCTION_NAME)(debug=None)
capped_molecule.write_graph(
'output',
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False},
pos=None,
)
if __name__ == '__main__':
unittest.main()