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")
