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_08_generateConformers(self): mol2file = os.path.join(self.dataDir, 'benzamidine.mol2') sm = SmallMol(mol2file) current_conformer = sm.numConformers sm.generateConformers(num_confs=10, append=False) n_conformers = sm.numConformers self.assertGreater(n_conformers, current_conformer, 'The generation of conforemr should provide at least the ' 'same amount of conformer')
def test_09_writeGenerateAndWriteConformers(self): mol2file = os.path.join(self.dataDir, 'benzamidine.mol2') sm = SmallMol(mol2file) sm.generateConformers(num_confs=10, append=False) tmpdir = NamedTemporaryFile().name sm.writeConformers(savefolder=tmpdir) direxists = os.path.isdir(tmpdir) n_files = len(glob(os.path.join(tmpdir, '*.sdf'))) self.assertTrue(direxists, 'The directory where to store the conformations where not created') self.assertGreater(n_files, 1, 'None conformations were written. At least one should be present')
def test_08_generateConformers(self): mol2file = os.path.join(self.dataDir, 'benzamidine.mol2') sm = SmallMol(mol2file) current_conformer = sm.numConformers sm.generateConformers(num_confs=10, append=False) n_conformers = sm.numConformers self.assertGreater( n_conformers, current_conformer, 'The generation of conforemr should provide at least the ' 'same amount of conformer')
def test_10_removeGenerateConformer(self): molsmile = SMILE_SMI sm = SmallMol(molsmile) sm.generateConformers(num_confs=10, append=False) n_confs = sm.numConformers sm.removeConformers([0]) n_confs_del = sm.numConformers sm.removeConformers() n_confs_zero = sm.numConformers self.assertEqual(n_confs_del, n_confs - 1, "The number of conformations after the deletion was not reduced of " "exactly one unit") self.assertEqual(n_confs_zero, 0, "The number of conformations after the deletion was not reduced to 0")
def test_09_writeGenerateAndWriteConformers(self): mol2file = os.path.join(self.dataDir, 'benzamidine.mol2') sm = SmallMol(mol2file) sm.generateConformers(num_confs=10, append=False) tmpdir = NamedTemporaryFile().name sm.writeConformers(savefolder=tmpdir) direxists = os.path.isdir(tmpdir) n_files = len(glob(os.path.join(tmpdir, '*.sdf'))) self.assertTrue( direxists, 'The directory where to store the conformations where not created') self.assertGreater( n_files, 1, 'None conformations were written. At least one should be present')
def test_10_removeGenerateConformer(self): molsmile = SMILE_SMI sm = SmallMol(molsmile) sm.generateConformers(num_confs=10, append=False) n_confs = sm.numConformers sm.removeConformers([0]) n_confs_del = sm.numConformers sm.removeConformers() n_confs_zero = sm.numConformers self.assertEqual( n_confs_del, n_confs - 1, "The number of conformations after the deletion was not reduced of " "exactly one unit") self.assertEqual( n_confs_zero, 0, "The number of conformations after the deletion was not reduced to 0" )
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")