def test_is_limiting(self):
self.assertTrue(
message_helpers.build_compound(is_limiting=True).is_limiting)
self.assertFalse(
message_helpers.build_compound(is_limiting=False).is_limiting)
self.assertFalse(
message_helpers.build_compound().HasField('is_limiting'))
def test_set_solute_moles(self):
solute = message_helpers.build_compound(name='Solute')
solvent2 = message_helpers.build_compound(name='Solvent',
amount='100 mL')
message_helpers.set_solute_moles(solute, [solvent2], '1 molar')
self.assertEqual(solute.amount.moles,
reaction_pb2.Moles(units='MILLIMOLE', value=100))
solvent3 = message_helpers.build_compound(name='Solvent',
amount='75 uL')
message_helpers.set_solute_moles(solute, [solvent3],
'3 mM',
overwrite=True)
self.assertEqual(solute.amount.moles,
reaction_pb2.Moles(units='NANOMOLE', value=225))
solvent4 = message_helpers.build_compound(name='Solvent',
amount='0.2 uL')
message_helpers.set_solute_moles(solute, [solvent4],
'30 mM',
overwrite=True)
self.assertEqual(solute.amount.moles,
reaction_pb2.Moles(units='NANOMOLE', value=6))
solvent5 = message_helpers.build_compound(name='Solvent',
amount='0.8 uL')
message_helpers.set_solute_moles(solute, [solvent4, solvent5],
'30 mM',
overwrite=True)
self.assertEqual(solute.amount.moles,
reaction_pb2.Moles(units='NANOMOLE', value=30))
def test_set_solute_moles_should_fail(self):
solute = message_helpers.build_compound(name='Solute')
solvent = message_helpers.build_compound(name='Solvent')
with self.assertRaisesRegex(ValueError, 'defined volume'):
message_helpers.set_solute_moles(solute, [solvent], '10 mM')
solute = message_helpers.build_compound(name='Solute', amount='1 mol')
solvent = message_helpers.build_compound(name='Solvent', amount='1 L')
with self.assertRaisesRegex(ValueError, 'overwrite'):
message_helpers.set_solute_moles(solute, [solvent], '10 mM')
def test_is_limiting(self):
self.assertTrue(
message_helpers.unconvert_boolean(
message_helpers.build_compound(is_limiting=True).is_limiting))
self.assertFalse(
message_helpers.unconvert_boolean(
message_helpers.build_compound(is_limiting=False).is_limiting))
self.assertEqual(
message_helpers.unconvert_boolean(
message_helpers.build_compound().is_limiting), None)
def test_smiles_and_name(self):
compound = message_helpers.build_compound(smiles='c1ccccc1',
name='benzene')
expected = reaction_pb2.Compound(identifiers=[
reaction_pb2.CompoundIdentifier(value='c1ccccc1', type='SMILES'),
reaction_pb2.CompoundIdentifier(value='benzene', type='NAME')
])
self.assertEqual(compound, expected)
def resolve_input(input_string):
"""Resolve a text-based description of an input in one of the following
formats:
(1) [AMOUNT] of [NAME]
(2) [AMOUNT] of [CONCENTRATION] [SOLUTE] in [SOLVENT]
Args:
input_string: String describing the input.
Returns:
ReactionInput message.
Raises:
ValueError: if the string cannot be parsed properly.
"""
reaction_input = reaction_pb2.ReactionInput()
if ' of ' not in input_string:
raise ValueError('String does not match template!')
amount_string, description = input_string.split(' of ')
if ' in ' not in description:
component_name = description
component = reaction_input.components.add()
component.CopyFrom(
message_helpers.build_compound(name=component_name.strip(),
amount=amount_string))
resolve_names(reaction_input)
return reaction_input
pattern = re.compile(r'(\d+.?\d*)\s?(\w+)\s(.+)\sin\s(.+)')
match = pattern.fullmatch(description.strip())
if not match:
raise ValueError('String did not match template!')
conc_value, conc_units, solute_name, solvent_name = match.groups()
solute = reaction_input.components.add()
solvent = reaction_input.components.add()
solute.CopyFrom(message_helpers.build_compound(name=solute_name.strip()))
solvent.CopyFrom(
message_helpers.build_compound(name=solvent_name.strip(),
amount=amount_string))
if solvent.amount.WhichOneof('kind') != 'volume':
raise ValueError('Total amount of solution must be a volume!')
solvent.amount.volume_includes_solutes = True
message_helpers.set_solute_moles(solute, [solvent],
f'{conc_value} {conc_units}')
resolve_names(reaction_input)
return reaction_input
def test_get_compound_mol(self):
mol = Chem.MolFromSmiles('c1ccccc1')
compound = message_helpers.build_compound(smiles='c1ccccc1',
name='benzene')
identifier = compound.identifiers.add()
identifier.type = identifier.RDKIT_BINARY
identifier.bytes_value = mol.ToBinary()
self.assertEqual(
Chem.MolToSmiles(mol),
Chem.MolToSmiles(message_helpers.get_compound_mol(compound)))
def reaction() -> reaction_pb2.Reaction:
resolver = units.UnitResolver()
reaction = reaction_pb2.Reaction()
reaction.setup.is_automated = True
reaction.inputs["dummy_input"].components.add().CopyFrom(
message_helpers.build_compound(
name="n-hexane",
smiles="CCCCCC",
role="reactant",
amount="1 milliliters",
)
)
reaction.inputs["dummy_input"].components.add().CopyFrom(
message_helpers.build_compound(
name="THF",
smiles="C1OCCC1",
role="solvent",
amount="40 liters",
)
)
reaction.inputs["dummy_input2"].components.add().CopyFrom(
message_helpers.build_compound(
name="Pd",
smiles="[Pd]",
role="catalyst",
amount="catalytic",
)
)
reaction.conditions.pressure.atmosphere.type = reaction_pb2.PressureConditions.Atmosphere.OXYGEN
reaction.conditions.stirring.rate.rpm = 100
reaction.conditions.temperature.control.type = reaction_pb2.TemperatureConditions.TemperatureControl.OIL_BATH
reaction.conditions.temperature.setpoint.CopyFrom(
reaction_pb2.Temperature(value=100, units=reaction_pb2.Temperature.CELSIUS)
)
outcome = reaction.outcomes.add()
outcome.reaction_time.CopyFrom(resolver.resolve("40 minutes"))
outcome.products.add().identifiers.extend(
message_helpers.build_compound(name="hexanone", smiles="CCCCC(=O)C").identifiers
)
yield reaction
def setUp(self):
super().setUp()
self.test_subdirectory = tempfile.mkdtemp(dir=flags.FLAGS.test_tmpdir)
self._resolver = units.UnitResolver()
reaction = reaction_pb2.Reaction()
reaction.setup.is_automated = True
reaction.inputs['dummy_input'].components.add().CopyFrom(
message_helpers.build_compound(
name='n-hexane',
smiles='CCCCCC',
role='reactant',
amount='1 milliliters',
))
reaction.inputs['dummy_input'].components.add().CopyFrom(
message_helpers.build_compound(
name='THF',
smiles='C1OCCC1',
role='solvent',
amount='40 liters',
))
reaction.conditions.pressure.atmosphere.type = (
reaction_pb2.PressureConditions.Atmosphere.OXYGEN)
reaction.conditions.stirring.rate.rpm = 100
reaction.conditions.temperature.control.type = (
reaction_pb2.TemperatureConditions.TemperatureControl.OIL_BATH)
reaction.conditions.temperature.setpoint.CopyFrom(
reaction_pb2.Temperature(value=100,
units=reaction_pb2.Temperature.CELSIUS))
outcome = reaction.outcomes.add()
outcome.reaction_time.CopyFrom(self._resolver.resolve('40 minutes'))
outcome.products.add().identifiers.extend(
message_helpers.build_compound(
name='hexanone',
smiles='CCCCC(=O)C',
).identifiers)
reaction.reaction_id = 'dummy_reaction_id'
self._reaction = reaction
self._input = os.path.join(self.test_subdirectory, 'reaction.pbtxt')
message_helpers.write_message(self._reaction, self._input)
def setUp(self):
super().setUp()
self._resolver = units.UnitResolver()
reaction = reaction_pb2.Reaction()
reaction.setup.is_automated = reaction_pb2.Boolean.TRUE
reaction.inputs['dummy_input'].components.add().CopyFrom(
message_helpers.build_compound(
name='n-hexane',
smiles='CCCCCC',
role='reactant',
amount='1 milliliters',
))
reaction.inputs['dummy_input'].components.add().CopyFrom(
message_helpers.build_compound(
name='C1OCCC1',
smiles='THF',
role='solvent',
amount='40 liters',
))
reaction.conditions.pressure.atmosphere.type = (
reaction_pb2.PressureConditions.Atmosphere.OXYGEN)
reaction.conditions.stirring.rate.rpm = 100
reaction.conditions.temperature.control.type = (
reaction_pb2.TemperatureConditions.TemperatureControl.OIL_BATH)
reaction.conditions.temperature.setpoint.CopyFrom(
reaction_pb2.Temperature(value=100,
units=reaction_pb2.Temperature.CELSIUS))
outcome = reaction.outcomes.add()
outcome.reaction_time.CopyFrom(self._resolver.resolve('40 minutes'))
outcome.products.add().compound.CopyFrom(
message_helpers.build_compound(
name='hexanone',
smiles='CCCCC(=O)C',
role='product',
))
reaction.reaction_id = 'dummy_reaction_id'
self._reaction = reaction
def test_bad_role(self):
with self.assertRaisesRegex(KeyError, 'not a supported type'):
message_helpers.build_compound(role='flavorant')
def test_get_compound_smiles(self):
compound = message_helpers.build_compound(smiles='c1ccccc1',
name='benzene')
self.assertEqual(message_helpers.get_compound_smiles(compound),
'c1ccccc1')
def test_vendor(self):
self.assertEqual(
message_helpers.build_compound(vendor='Sally').source.vendor,
'Sally')
def test_custom_prep_without_details(self):
with self.assertRaisesRegex(ValueError,
'prep_details must be provided'):
message_helpers.build_compound(prep='custom')
def test_prep_details_without_prep(self):
with self.assertRaisesRegex(ValueError, 'prep must be provided'):
message_helpers.build_compound(prep_details='rinsed gently')
def test_bad_prep(self):
with self.assertRaisesRegex(KeyError, 'not a supported type'):
message_helpers.build_compound(prep='shaken')
def test_prep(self, prep, details, expected):
compound = message_helpers.build_compound(prep=prep,
prep_details=details)
self.assertEqual(compound.preparations[0], expected)
def test_amount(self, amount, expected):
compound = message_helpers.build_compound(amount=amount)
self.assertEqual(
getattr(compound.amount, compound.amount.WhichOneof('kind')),
expected)
def test_role(self):
compound = message_helpers.build_compound(role='solvent')
self.assertEqual(compound.reaction_role,
reaction_pb2.ReactionRole.SOLVENT)
def test_bad_amount(self, amount):
with self.assertRaises((KeyError, ValueError)):
message_helpers.build_compound(amount=amount)