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_06_isChiral(self):
smi = CHIRAL_SMI
sm = SmallMol(smi)
ischiral, details = sm.isChiral(returnDetails=True)
self.assertListEqual(
details, CHIRAL_DETAILS, 'chiral atom does not match.'
'Expected: {}; Now: {}'.format(CHIRAL_DETAILS, details))
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_06_isChiral(self):
smi = CHIRAL_SMI
sm = SmallMol(smi)
ischiral, details = sm.isChiral(returnDetails=True)
self.assertListEqual(details, CHIRAL_DETAILS, 'chiral atom does not match.'
'Expected: {}; Now: {}'.format(CHIRAL_DETAILS, details))