def test_05_getAtoms(self): smi = SMILE_SMI sm = SmallMol(smi) element_idx_1 = sm.get('element', 'idx 1')[0] neighbors_element_O = sm.get('neighbors', 'element O')[0] btypes_element_O = sm.get('bondtypes', 'element O', convertType=False)[0] self.assertEqual(element_idx_1, PHENOL_ELEMENT_IDX_1, 'Element of the first atom does not correspond' 'Expect: {}; Now: {}'.format(element_idx_1, PHENOL_ELEMENT_IDX_1)) self.assertListEqual(neighbors_element_O, PHENOL_ELEMENT_NEIGHBORS_OX, 'Neighbors atoms of the oxygen atom do not correspond' 'Expected: {}; Now: {}'.format(PHENOL_ELEMENT_NEIGHBORS_OX, neighbors_element_O)) self.assertListEqual(btypes_element_O, PHENOL_BTYPES_OX, 'Bondtypes of the oxygen atom do not correspond:' 'Expeected: {}; Now: {}'.format(btypes_element_O, PHENOL_BTYPES_OX))
def test_11_invertChirality(self): molsmile = CHIRAL_SMI sm = SmallMol(molsmile) aname = CHIRAL_DETAILS[0][0] chiral = CHIRAL_DETAILS[0][1] aidx = sm.get('idx', 'atomname {}'.format(aname))[0] sm.invertChirality(aidx) newchiral = sm.isChiral(returnDetails=True)[1][0][-1] self.assertNotEqual(chiral, newchiral, msg="The chirality was not formally changed") sm.generateConformers(num_confs=1, append=False) m = sm.toMolecule() fname = NamedTemporaryFile().name + '.mol2' m.write(fname) sm2 = SmallMol(fname) newchiral_confirm = sm2.isChiral(returnDetails=True)[1][0][-1] self.assertEqual(newchiral, newchiral_confirm, msg="The chirality was not structurally changed")
def test_05_getAtoms(self): smi = SMILE_SMI sm = SmallMol(smi) element_idx_1 = sm.get('element', 'idx 1')[0] neighbors_element_O = sm.get('neighbors', 'element O')[0] btypes_element_O = sm.get('bondtypes', 'element O', convertType=False)[0] self.assertEqual( element_idx_1, PHENOL_ELEMENT_IDX_1, 'Element of the first atom does not correspond' 'Expect: {}; Now: {}'.format(element_idx_1, PHENOL_ELEMENT_IDX_1)) self.assertListEqual( neighbors_element_O, PHENOL_ELEMENT_NEIGHBORS_OX, 'Neighbors atoms of the oxygen atom do not correspond' 'Expected: {}; Now: {}'.format(PHENOL_ELEMENT_NEIGHBORS_OX, neighbors_element_O)) self.assertListEqual( btypes_element_O, PHENOL_BTYPES_OX, 'Bondtypes of the oxygen atom do not correspond:' 'Expeected: {}; Now: {}'.format(btypes_element_O, PHENOL_BTYPES_OX))