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))
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")
