def test_metabolize(self):
""" Treat it as blackbox, do not want to know how reactor is called
just that metabolisation happened
"""
se = magma.StructureEngine(self.db_session)
#molblock = Chem.MolToMolBlock(Chem.MolFromSmiles('Oc1cc(CC2OCCC2)cc(O)c1O'))
parent_molid = se.read_smiles('Oc1cc(CC2OCCC2)cc(O)c1O')
se.metabolize(1, 'phase1',endpoints=False)
self.assertGreater(self.db_session.query(Molecule).filter(Molecule.predicted==True).count(), 0)
def test_metabolize_all(self):
se = magma.StructureEngine(self.db_session)
molblock = Chem.MolToMolBlock(
Chem.MolFromSmiles('Oc1cc(CC2OCCC2)cc(O)c1O'))
parent_molid = se.add_structure(
molblock, '5-(3,4,5)-trihydroxyphenyl-g-valerolactone (F,U)', 1.0,
1)
se.metabolize = mock.Mock(return_value=set([1]))
se.metabolize_all('phase1')
se.metabolize.assert_called_with(parent_molid, 'phase1', False)
def test_metabolize_unknown_metabolite_type(self):
se = magma.StructureEngine(self.db_session)
molblock = Chem.MolToMolBlock(
Chem.MolFromSmiles('Oc1cc(CC2OCCC2)cc(O)c1O'))
parent_molid = se.add_structure(
molblock, '5-(3,4,5)-trihydroxyphenyl-g-valerolactone (F,U)', 1.0,
0, 'PARENT', 1)
se.metabolize(parent_molid, 'phase1234')
# TODO metabolize requires at least one SMIRKS query
# if none given then raise exception
self.assertEqual(self.db_session.query(Molecule).count(), 1)
def test_add_structure_2nd_ignore(self):
se = magma.StructureEngine(self.db_session)
molblock = Chem.MolToMolBlock(Chem.MolFromSmiles('CCO'))
molid = se.add_structure(molblock, 'ethanol', 2.0, 0, 'PARENT', 1)
se.add_structure(molblock, 'ethanol', 1.0, 0, 'PARENT', 1)
met = self.db_session.query(Molecule).one()
self.assertDictContainsSubset({
'molid': molid,
'refscore': 2.0
}, met.__dict__)
def test_add_structure(self):
se = magma.StructureEngine(self.db_session)
molblock = Chem.MolToMolBlock(Chem.MolFromSmiles('CCO'))
molid = se.add_structure(molblock, 'ethanol', 1.0, False)
mol = self.db_session.query(Molecule).filter(
Molecule.molid == molid).one()
self.assertDictContainsSubset(
{
'mol': molblock,
'refscore': 1.0,
'reactionsequence': {},
'inchikey14': u'LFQSCWFLJHTTHZ',
'formula': u'C2H6O',
'predicted': False,
'name': u'ethanol',
'mim': 46.0418648147,
'logp': -0.0014000000000000123
}, mol.__dict__)
def test_metabolize_bad_molid(self):
se = magma.StructureEngine(self.db_session)
parent_molid = 1
se.metabolize(parent_molid, 'phase1')
self.assertEqual(self.db_session.query(Molecule).count(), 0)
def test_construct_new_db(self):
se = magma.StructureEngine(self.db_session)
self.assertIsNone(se.call_back_engine)
