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test_tautomers.py
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test_tautomers.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
class Test_Capping(unittest.TestCase):
def test_violuric_acid(self, use_ILP: bool = True) -> None:
with open('pdbs/violuric_acid.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='violuric_acid',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
#net_charge=0,
total_number_hydrogens=3,
enforce_octet_rule=True,
allow_radicals=False,
)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False, 'vertex_color_scheme': 'elements', 'vertex_label_template': ''},
)
assert len(tautomers) == 15, len(tautomers)
def test_warfarin(self, use_ILP: bool = True) -> None:
with open('pdbs/warfarin.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='warfarin',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=16,
enforce_octet_rule=True,
allow_radicals=False,
)
assert len(tautomers) == 43, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False, 'vertex_color_scheme': 'elements', 'vertex_label_template': ''},
)
def test_porphyrin(self, use_ILP: bool = True) -> None:
with open('pdbs/tetraphenylporphyrin.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='porphyrin',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=30,
enforce_octet_rule=True,
allow_radicals=False,
)
assert len(tautomers) == 21, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False},
)
def test_methylimidazole(self, use_ILP: bool = True) -> None:
with open('pdbs/methylimidazole.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='methylimidazole',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=6,
enforce_octet_rule=True,
allow_radicals=False,
)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
def test_benzene(self):
with open('pdbs/benzene.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='benzene',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=6,
enforce_octet_rule=True,
allow_radicals=False,
)
assert len(tautomers) == 1, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
def test_benzene_fail(self):
with open('pdbs/benzene.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='benzene_fail',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=6,
enforce_octet_rule=True,
allow_radicals=False,
disallow_triple_bond_in_small_rings=False,
disallow_allenes_in_small_rings=False,
disallow_allenes_completely=False,
lock_phenyl_rings=False,
)
assert len(tautomers) == 5, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
def test_ethanal(self):
with open('pdbs/ethanal.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='ethanal',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=4,
enforce_octet_rule=True,
allow_radicals=False,
)
assert len(tautomers) == 2, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
def test_propadiene(self):
with open('pdbs/propadiene.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='propadiene',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=4,
enforce_octet_rule=True,
allow_radicals=False,
disallow_allenes_completely=False,
)
assert len(tautomers) == 2, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
def test_cyclooctyne(self):
with open('pdbs/cyclooctyne.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='cyclooctyne',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=12,
enforce_octet_rule=True,
allow_radicals=False,
)
assert len(tautomers) == 4, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
def test_methane(self):
with open('pdbs/methane.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='methane',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=4,
enforce_octet_rule=True,
allow_radicals=False,
)
assert len(tautomers) == 1, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
def test_ammonium(self):
with open('pdbs/ammonium.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='ammonium',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
tautomers = input_molecule.get_all_tautomers(
net_charge=1,
total_number_hydrogens=4,
enforce_octet_rule=True,
allow_radicals=False,
)
assert len(tautomers) == 1, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
def test_ammonium_fail(self):
with open('pdbs/ammonium.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='ammonium',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
with self.assertRaises(Exception):
tautomers = input_molecule.get_all_tautomers(
net_charge=1,
total_number_hydrogens=4,
maximum_number_hydrogens_per_atom=2,
enforce_octet_rule=True,
allow_radicals=False,
)
with self.assertRaises(Exception):
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=4,
maximum_number_hydrogens_per_atom=3,
enforce_octet_rule=True,
allow_radicals=False,
)
def test_radicals(self):
with open('pdbs/nitric_oxide.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='nitric_oxide',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
with self.assertRaises(Exception):
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=0,
enforce_octet_rule=True,
allow_radicals=False,
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=0,
enforce_octet_rule=False,
allow_radicals=True,
)
assert len(tautomers) == 1, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
tautomer = tautomers[0]
assert list(tautomer.bond_orders.items()) == [2]
def test_lewis_octet_exceptions(self):
with open('pdbs/methylene.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='methylene',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(600, 600),
graph_kwargs={'include_atom_index': False},
)
with self.assertRaises(Exception):
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=2,
enforce_octet_rule=True,
allow_radicals=False,
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=2,
enforce_octet_rule=False,
allow_radicals=False,
)
assert len(tautomers) == 1, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(600, 600),
graph_kwargs={'include_atom_index': True},
)
def test_skeletal_rearrangement(self):
with open('pdbs/warfarin.pdb') as fh:
input_molecule = molecule_from_pdb_str(
fh.read(),
name='warfarin_extended',
)
input_molecule.remove_all_hydrogens(mark_all_uncapped=True)
input_molecule.write_graph(
'input',
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False},
)
with self.assertRaises(TypeError):
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=16,
enforce_octet_rule=True,
allow_radicals=False,
skeletal_rearrangements=[(1, 2, 3 )],
)
tautomers = input_molecule.get_all_tautomers(
net_charge=0,
total_number_hydrogens=16,
enforce_octet_rule=True,
allow_radicals=False,
skeletal_rearrangements=[(2, 10), (2, 8)], # Bonds ('C13', 'O1') and ('C13', 'O3')
)
assert len(tautomers) == 53, len(tautomers)
for (n, molecule) in enumerate(tautomers, start=1):
molecule.name = input_molecule.name
molecule.write_graph(
'_tautomer_{0}'.format(n),
output_size=(1200, 1200),
graph_kwargs={'include_atom_index': False, 'vertex_color_scheme': 'elements', 'vertex_label_template': ''},
)
if __name__ == '__main__':
print('Note: This test is very long (~15 minutes)')
unittest.main(warnings='ignore', verbosity=2)