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_13_convertToMolecule(self):
mol2file = os.path.join(self.dataDir, 'benzamidine.mol2')
sm = SmallMol(mol2file)
mol = Molecule(mol2file)
mol_elements = mol.element.tolist()
sm_htmd = sm.toMolecule()
sm_htmd_element = sm_htmd.element.tolist()
self.assertListEqual(sm_htmd_element, mol_elements, msg="The elements found are different. The handle and convertion"
"of the SmallMol object into the htmd.Molecule one, probably "
"get wrong")
def test_13_convertToMolecule(self):
mol2file = os.path.join(self.dataDir, 'benzamidine.mol2')
sm = SmallMol(mol2file)
mol = Molecule(mol2file)
mol_elements = mol.element.tolist()
sm_htmd = sm.toMolecule()
sm_htmd_element = sm_htmd.element.tolist()
self.assertListEqual(
sm_htmd_element,
mol_elements,
msg="The elements found are different. The handle and convertion"
"of the SmallMol object into the htmd.Molecule one, probably "
"get wrong")
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")