def test_ReadMolFromMolFile(self):
"""Test reading the sample MOL file."""
molecule = PyChem2D()
molecule.ReadMolFromMolFile(MOL_FILE)
self.assertEqual(molecule.mol.GetNumHeavyAtoms(), self.num_heavy_atoms)
self.assertEqual(Chem.rdMolDescriptors.CalcMolFormula(molecule.mol),
self.formula)
self.molecules.append(molecule)
def test_ReadMolFromSmiles(self):
"""Test reading from sample SMILES."""
molecule = PyChem2D()
molecule.ReadMolFromSmile(
'CC1=C2[C@H](C(=O)[C@@]3([C@H](C[C@@H]4'
'[C@]([C@H]3[C@@H]([C@@](C2(C)C)(C[C@@H]1OC(=O)[C@@H]([C@H]'
'(C5=CC=CC=C5)NC(=O)OC(C)(C)C)O)O)OC(=O)C6=CC=CC=C6)(CO4)OC(=O)C)O)C)O'
)
self.assertEqual(molecule.mol.GetNumHeavyAtoms(), self.num_heavy_atoms)
self.assertEqual(Chem.rdMolDescriptors.CalcMolFormula(molecule.mol),
self.formula)
self.molecules.append(molecule)
def test_ReadMolFromInchi(self):
"""Test reading from sample InChI."""
molecule = PyChem2D()
molecule.ReadMolFromInchi(
'InChI=1S/C43H53NO14/c1-22-26'
'(55-37(51)32(48)30(24-15-11-9-12-16-24)44-38(52)58-39(3,4)5)'
'20-43(53)35(56-36(50)25-17-13-10-14-18-25)33-41(8,34(49)31(47)'
'29(22)40(43,6)7)27(46)19-28-42(33,21-54-28)57-23(2)45/h9-18,'
'26-28,30-33,35,46-48,53H,19-21H2,1-8H3,(H,44,52)/t26-,27-,28+,'
'30-,31+,32+,33-,35-,41+,42-,43+/m0/s1')
self.assertEqual(molecule.mol.GetNumHeavyAtoms(), self.num_heavy_atoms)
self.assertEqual(Chem.rdMolDescriptors.CalcMolFormula(molecule.mol),
self.formula)
self.molecules.append(molecule)
def test_ChEMBL_GetMolFromEBI(self):
"""Test reading from sample ChEMBL ID."""
molecule = PyChem2D()
# Ensure TimeoutError is consistent
passed, tryouts = False, 0
while not passed and tryouts < 5:
try:
molecule.GetMolFromNCBI('CHEMBL92')
passed = True
except TimeoutError:
tryouts += 1
self.assertLess(
tryouts, 5,
'Too many Timeout exceptions. Verify your internet connection.')
self.assertEqual(molecule.mol.GetNumHeavyAtoms(), self.num_heavy_atoms)
self.assertEqual(Chem.rdMolDescriptors.CalcMolFormula(molecule.mol),
self.formula)
self.molecules.append(molecule)