def testHelium(self):
"""
adjlist: Test that the adjlist reading and writing works with Helium.
"""
smiles = '[He]'
inchi = 'InChI=1S/He'
adjlist = '1 He u0 p1 c0'
adjlist_old = '1 He 0'
adjlist_intermediate = '1 He 0 1'
mol_smiles = Molecule().fromSMILES(smiles)
mol_inchi = Molecule().fromInChI(inchi)
mol = Molecule().fromAdjacencyList(adjlist)
mol_old = Molecule().fromAdjacencyList(adjlist_old)
mol_intermediate = Molecule().fromAdjacencyList(adjlist_intermediate)
# Isomorphic check
self.assertTrue(mol_smiles.isIsomorphic(mol))
self.assertTrue(mol_smiles.isIsomorphic(mol_inchi))
self.assertTrue(mol_smiles.isIsomorphic(mol_old))
self.assertTrue(mol_smiles.isIsomorphic(mol_intermediate))
# Adjlist check
self.assertEqual(mol_smiles.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_inchi.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_old.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_intermediate.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol.toSMILES(), smiles)
self.assertEqual(mol.toInChI(), 'InChI=1S/He')
def test_disconnected_molecule(self):
"""Test that we can generate an InChI for a disconnected molecule."""
mol = Molecule().fromSMILES('CCCCO.C=O')
inchi = 'InChI=1S/C4H10O.CH2O/c1-2-3-4-5;1-2/h5H,2-4H2,1H3;1H2'
self.assertEqual(mol.toInChI(), inchi)
def testHelium(self):
"""
adjlist: Test that the adjlist reading and writing works with Helium.
"""
smiles = '[He]'
inchi = 'InChI=1S/He'
adjlist = '1 He u0 p1 c0'
adjlist_old = '1 He 0'
adjlist_intermediate = '1 He 0 1'
mol_smiles = Molecule().fromSMILES(smiles)
mol_inchi = Molecule().fromInChI(inchi)
mol = Molecule().fromAdjacencyList(adjlist)
mol_old = Molecule().fromAdjacencyList(adjlist_old)
mol_intermediate = Molecule().fromAdjacencyList(adjlist_intermediate)
# Isomorphic check
self.assertTrue(mol_smiles.isIsomorphic(mol))
self.assertTrue(mol_smiles.isIsomorphic(mol_inchi))
self.assertTrue(mol_smiles.isIsomorphic(mol_old))
self.assertTrue(mol_smiles.isIsomorphic(mol_intermediate))
# Adjlist check
self.assertEqual(mol_smiles.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_inchi.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_old.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_intermediate.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol.toSMILES(),smiles)
self.assertEqual(mol.toInChI(),'InChI=1S/He')
def test_isotopic_molecule_2(self):
"""Test that we can generate an InChI for an isotopic molecule."""
mol = Molecule().fromSMILES('[13CH3]C')
inchi = 'InChI=1S/C2H6/c1-2/h1-2H3/i1+1'
self.assertEqual(mol.toInChI(), inchi)
def test_isotopic_molecule_2(self):
"""Test that we can generate an InChI for an isotopic molecule."""
mol = Molecule().fromSMILES('[13CH3]C')
inchi = 'InChI=1S/C2H6/c1-2/h1-2H3/i1+1'
self.assertEqual(mol.toInChI(), inchi)
def test_disconnected_molecule(self):
"""Test that we can generate an InChI for a disconnected molecule."""
mol = Molecule().fromSMILES('CCCCO.C=O')
inchi = 'InChI=1S/C4H10O.CH2O/c1-2-3-4-5;1-2/h5H,2-4H2,1H3;1H2'
self.assertEqual(mol.toInChI(), inchi)
def test_empty_molecule(self):
"""Test that we can safely return a blank identifier for an empty molecule."""
mol = Molecule()
self.assertEqual(mol.toSMILES(), '')
self.assertEqual(mol.toInChI(), '')
def test_empty_molecule(self):
"""Test that we can safely return a blank identifier for an empty molecule."""
mol = Molecule()
self.assertEqual(mol.toSMILES(), '')
self.assertEqual(mol.toInChI(), '')
