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")