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 test_resolver(self):
reaction = reaction_pb2.Reaction()
ethylamine = reaction.inputs['ethylamine']
component = ethylamine.components.add()
component.identifiers.add(type='NAME', value='ethylamine')
component.is_limiting = True
component.moles.value = 2
component.moles.units = reaction_pb2.Moles.MILLIMOLE
reaction.outcomes.add().conversion.value = 25
dataset = dataset_pb2.Dataset(reactions=[reaction])
dataset_filename = os.path.join(self.test_subdirectory, 'test.pbtxt')
message_helpers.write_message(dataset, dataset_filename)
filenames = self._run_main()
self.assertLen(filenames, 2)
self.assertFalse(os.path.exists(dataset_filename))
filenames.pop(filenames.index(self.dataset_filename))
self.assertLen(filenames, 1)
dataset = message_helpers.load_message(filenames[0],
dataset_pb2.Dataset)
self.assertLen(dataset.reactions, 1)
identifiers = (dataset.reactions[0].inputs['ethylamine'].components[0].
identifiers)
self.assertLen(identifiers, 3)
self.assertEqual(
identifiers[1],
reaction_pb2.CompoundIdentifier(
type='SMILES', value='CCN',
details='NAME resolved by PubChem'))
self.assertEqual(identifiers[2].type,
reaction_pb2.CompoundIdentifier.RDKIT_BINARY)
def test_input_resolve(self):
roundtrip_smi = lambda smi: Chem.MolToSmiles(Chem.MolFromSmiles(smi))
string = '10 g of THF'
reaction_input = resolvers.resolve_input(string)
self.assertEqual(len(reaction_input.components), 1)
self.assertEqual(reaction_input.components[0].amount.mass,
reaction_pb2.Mass(value=10, units='GRAM'))
self.assertEqual(
reaction_input.components[0].identifiers[0],
reaction_pb2.CompoundIdentifier(type='NAME', value='THF'))
self.assertEqual(reaction_pb2.CompoundIdentifier.SMILES,
reaction_input.components[0].identifiers[1].type)
self.assertEqual(
roundtrip_smi(reaction_input.components[0].identifiers[1].value),
roundtrip_smi('C1COCC1'))
string = '100 mL of 5.0uM sodium hydroxide in water'
reaction_input = resolvers.resolve_input(string)
self.assertEqual(len(reaction_input.components), 2)
self.assertEqual(reaction_input.components[0].amount.moles,
reaction_pb2.Moles(value=500, units='NANOMOLE'))
self.assertEqual(
reaction_input.components[0].identifiers[0],
reaction_pb2.CompoundIdentifier(type='NAME',
value='sodium hydroxide'))
self.assertEqual(reaction_pb2.CompoundIdentifier.SMILES,
reaction_input.components[0].identifiers[1].type)
self.assertEqual(
roundtrip_smi(reaction_input.components[0].identifiers[1].value),
roundtrip_smi('[Na+].[OH-]'))
self.assertEqual(reaction_input.components[1].amount.volume,
reaction_pb2.Volume(value=100, units='MILLILITER'))
self.assertEqual(
reaction_input.components[1].amount.volume_includes_solutes, True)
self.assertEqual(
reaction_input.components[1].identifiers[0],
reaction_pb2.CompoundIdentifier(type='NAME', value='water'))
self.assertEqual(reaction_pb2.CompoundIdentifier.SMILES,
reaction_input.components[1].identifiers[1].type)
self.assertEqual(
roundtrip_smi(reaction_input.components[1].identifiers[1].value),
roundtrip_smi('O'))
def test_with_resolve_names(self):
reaction = reaction_pb2.Reaction()
component = reaction.inputs['ethylamine'].components.add()
component.identifiers.add(type='NAME', value='ethylamine')
updates.update_reaction(reaction)
self.assertLen(component.identifiers, 2)
self.assertEqual(
component.identifiers[1],
reaction_pb2.CompoundIdentifier(
type='SMILES', value='CCN',
details='NAME resolved by PubChem'))
def test_resolve_names(self):
message = reaction_pb2.Reaction()
message.inputs['test'].components.add().identifiers.add(
type='NAME', value='aspirin')
self.assertTrue(updates.resolve_names(message))
self.assertEqual(
message.inputs['test'].components[0].identifiers[1],
reaction_pb2.CompoundIdentifier(
type='SMILES',
value='CC(=O)OC1=CC=CC=C1C(=O)O',
details='NAME resolved by PubChem'))
def test_compound_rdkit_binary(self):
mol = Chem.MolFromSmiles('CC(=O)OC1=CC=CC=C1C(=O)O')
message = reaction_pb2.Compound()
identifier = message.identifiers.add()
identifier.type = identifier.SMILES
identifier.value = Chem.MolToSmiles(mol)
validations.validate_message(message) # Message is modified in place.
self.assertEqual(
message.identifiers[1],
reaction_pb2.CompoundIdentifier(type='RDKIT_BINARY',
bytes_value=mol.ToBinary()))
def test_add_binary_identifiers(self):
smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'
mol = Chem.MolFromSmiles(smiles)
message = reaction_pb2.Reaction()
message.inputs['test'].components.add().identifiers.add(type='SMILES',
value=smiles)
self.assertTrue(updates.add_binary_identifiers(message))
self.assertEqual(
message.inputs['test'].components[0].identifiers[1],
reaction_pb2.CompoundIdentifier(type='RDKIT_BINARY',
bytes_value=mol.ToBinary(),
details='Generated from SMILES'))
def test_compound_name_resolver(self):
message = reaction_pb2.Compound()
identifier = message.identifiers.add()
identifier.type = identifier.NAME
identifier.value = 'aspirin'
validations.validate_message(message) # Message is modified in place.
self.assertEqual(
message.identifiers[1],
reaction_pb2.CompoundIdentifier(
type='SMILES',
value='CC(=O)OC1=CC=CC=C1C(=O)O',
details='NAME resolved by PubChem'))
def test_identifier_setters(self):
compound = reaction_pb2.Compound()
identifier = message_helpers.set_compound_name(compound, 'water')
self.assertEqual(
identifier,
reaction_pb2.CompoundIdentifier(type='NAME', value='water'))
self.assertEqual(
compound.identifiers[0],
reaction_pb2.CompoundIdentifier(type='NAME', value='water'))
message_helpers.set_compound_smiles(compound, 'O')
self.assertEqual(
compound.identifiers[1],
reaction_pb2.CompoundIdentifier(type='SMILES', value='O'))
identifier = message_helpers.set_compound_name(compound, 'ice')
self.assertEqual(
identifier, reaction_pb2.CompoundIdentifier(type='NAME',
value='ice'))
self.assertEqual(
compound.identifiers[0],
reaction_pb2.CompoundIdentifier(type='NAME', value='ice'))
compound = reaction_pb2.Compound()
identifier = message_helpers.set_compound_molblock(
compound, _BENZENE_MOLBLOCK)
self.assertEqual(_BENZENE_MOLBLOCK, compound.identifiers[0].value)
def test_rdkit_binary_compound_identifier(self):
mol = Chem.MolFromSmiles('COO')
identifier = reaction_pb2.CompoundIdentifier(
type='RDKIT_BINARY', bytes_value=mol.ToBinary())
self.assertEqual(Chem.MolToSmiles(mol),
Chem.MolToSmiles(Chem.Mol(identifier.bytes_value)))