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 setUp(self):
super().setUp()
self._resolver = units.UnitResolver()
def build_compound(smiles=None,
name=None,
amount=None,
role=None,
is_limiting=None,
prep=None,
prep_details=None,
vendor=None):
"""Builds a Compound message with the most common fields.
Args:
smiles: Text compound SMILES.
name: Text compound name.
amount: Text amount string, e.g. '1.25 g'.
role: Text reaction role. Must match a value in ReactionRoleType.
is_limiting: Boolean whether this compound is limiting for the reaction.
prep: Text compound preparation type. Must match a value in
PreparationType.
prep_details: Text compound preparation details. If provided, `prep` is
required.
vendor: Text compound vendor/supplier.
Returns:
Compound message.
Raises:
KeyError: if `role` or `prep` does not match a supported enum value.
TypeError: if `amount` units are not supported.
ValueError: if `prep_details` is provided and `prep` is None.
"""
compound = reaction_pb2.Compound()
if smiles:
compound.identifiers.add(value=smiles, type='SMILES')
if name:
compound.identifiers.add(value=name, type='NAME')
if amount:
resolver = units.UnitResolver()
amount_pb = resolver.resolve(amount)
if isinstance(amount_pb, reaction_pb2.Mass):
compound.amount.mass.CopyFrom(amount_pb)
elif isinstance(amount_pb, reaction_pb2.Moles):
compound.amount.moles.CopyFrom(amount_pb)
elif isinstance(amount_pb, reaction_pb2.Volume):
compound.amount.volume.CopyFrom(amount_pb)
else:
raise TypeError(f'unsupported units for amount: {amount_pb}')
if role:
field = reaction_pb2.Compound.DESCRIPTOR.fields_by_name[
'reaction_role']
values_dict = field.enum_type.values_by_name
try:
compound.reaction_role = values_dict[role.upper()].number
except KeyError as error:
raise KeyError(
f'{role} is not a supported type: {values_dict.keys()}'
) from error
if is_limiting is not None:
if not (is_limiting is True or is_limiting is False):
raise TypeError(
f'is_limiting must be a boolean value: {is_limiting}')
compound.is_limiting = is_limiting
if prep:
field = reaction_pb2.CompoundPreparation.DESCRIPTOR.fields_by_name[
'type']
values_dict = field.enum_type.values_by_name
try:
compound.preparations.add().type = values_dict[prep.upper()].number
except KeyError as error:
raise KeyError(
f'{prep} is not a supported type: {values_dict.keys()}'
) from error
if (compound.preparations[0].type
== reaction_pb2.CompoundPreparation.CUSTOM
and not prep_details):
raise ValueError(
'prep_details must be provided when CUSTOM prep is used')
if prep_details:
if not prep:
raise ValueError('prep must be provided when prep_details is used')
compound.preparations[0].details = prep_details
if vendor:
compound.source.vendor = vendor
return compound
def set_solute_moles(solute, solvents, concentration, overwrite=False):
"""Helps define components for stock solution inputs with a single solute
and a one or more solvent compounds.
Args:
solute: Compound with identifiers, roles, etc.; this argument is
modified in place to define an amount in moles.
solvents: list of Compounds each with defined volume.
concentration: string defining solute concentration.
overwrite: whether to overwrite an existing solute amount if defined.
Defaults to False
Raises:
ValueError: if any solvent does not have a defined volume.
ValueError: if the solute has an existing amount field and overwrite
is set to False.
Returns:
List of Compounds to assign to a repeated components field.
"""
# Check solute definition
if solute.amount.WhichOneof('kind') and not overwrite:
raise ValueError('solute has defined amount and overwrite is False')
# Get total solvent volume in liters.
volume_liter = 0
for solvent in solvents:
amount = solvent.amount
if not amount.HasField('volume') or not amount.volume.value:
raise ValueError('solvent must have defined volume')
if amount.volume.units == amount.volume.LITER:
volume_liter += amount.volume.value
elif amount.volume.units == amount.volume.MILLILITER:
volume_liter += amount.volume.value * 1e-3
elif amount.volume.units == amount.volume.MICROLITER:
volume_liter += amount.volume.value * 1e-6
elif amount.volume.units == amount.volume.NANOLITER:
volume_liter += amount.volume.value * 1e-9
else:
raise ValueError(
'solvent units not recognized by set_solute_moles')
# Get solute concentration in molar.
resolver = units.UnitResolver(
unit_synonyms=units.CONCENTRATION_UNIT_SYNONYMS, forbidden_units={})
concentration_pb = resolver.resolve(concentration)
if concentration_pb.units == concentration_pb.MOLAR:
concentration_molar = concentration_pb.value
elif concentration_pb.units == concentration_pb.MILLIMOLAR:
concentration_molar = concentration_pb.value * 1e-3
elif concentration_pb.units == concentration_pb.MICROMOLAR:
concentration_molar = concentration_pb.value * 1e-6
else:
raise ValueError(f'unsupported units: {concentration_pb.units}')
# Assign moles amount and return.
moles = volume_liter * concentration_molar
if moles < 1e-6:
value = moles * 1e9
unit = reaction_pb2.Moles.NANOMOLE
elif moles < 1e-3:
value = moles * 1e6
unit = reaction_pb2.Moles.MICROMOLE
elif moles < 1:
value = moles * 1e3
unit = reaction_pb2.Moles.MILLIMOLE
else:
value = moles
unit = reaction_pb2.Moles.MOLE
solute.amount.moles.value = value
solute.amount.moles.units = unit
return [solute] + solvents
