def testVectorDescriptors(self):
m = Chem.MolFromSmiles('CCCc1ccccc1')
results = rdMolDescriptors.BCUT2D(m)
names = ["BCUT2D_%s"%s for s in ('MWHI',"MWLOW","CHGHI","CHGLO",
"LOGPHI","LOGPLOW","MRHI","MRLOW")]
for i,n in enumerate(names):
f = getattr(Descriptors, n)
self.assertEqual(results[i], f(m))
results = rdMolDescriptors.CalcAUTOCORR2D(m)
names = ["AUTOCORR2D_%s"%str(i+1) for i in range(192)]
for i,n in enumerate(names):
f = getattr(Descriptors, n)
self.assertEqual(results[i], f(m))
def testVectorDescriptorsInDescList(self):
# First try only bcuts should exist
descriptors = set([n for n,_ in Descriptors.descList])
names = set(["BCUT2D_%s"%str(i+1) for i in range(8)])
self.assertEqual(descriptors.intersection(names), names)
Descriptors.setupAUTOCORRDescriptors()
descriptors2 = set([n for n,_ in Descriptors.descList])
self.assertEqual(descriptors2.intersection(descriptors), descriptors)
names = ["AUTOCORR2D_%s"%str(i+1) for i in range(192)]
self.assertEqual(descriptors.intersection(names), names)
def testBCUT(self):
smiles = ("c1ccccc1S", "c1cscc1", "CC(=S)C", "CSC", "CS(=O)C",
"CP(C)C", "CP=O", "CP(C)(C)=O", "C[PH](C)=O")
expected = [
[
32.11691025659743, 10.3711255714102, 1.7258015589384423,
-1.813025067747632, 2.0032623406582895, -1.5648237280483932,
7.798895708674262, 1.480463460412681
],
[
32.133385673916855, 10.690498814349603, 1.5812862454321042,
-1.3924158848795094, 1.9109090827066813, -1.1624011856503906,
7.073072952311218, 2.0294988143496093
],
[
32.09203038492705, 10.585642854940236, 1.5531725323483636,
-1.6095571920399787, 1.6095355058255407, -1.6264025009240035,
7.798379459554676, 1.8522004089765778
],
[
32.16623472793675, 11.912765272063261, 1.3229624149945334,
-1.5095023144073105, 1.699644712375421, -1.2539447123754206,
7.974132068991219, 2.370867931008784
],
[
32.19696040763111, 11.912196087574864, 1.571634336328628,
-1.5986639964786287, 1.4708186703193278, -1.7011978973115978,
7.829987043024966, 0.6900118228151252
],
[
31.130920829765557, 11.856079170234391, 1.652795743173261,
-1.8120831465729346, 2.1415709560249625, -1.4818709560249614,
7.546153955380794, 2.12884604461921
],
[
31.059700934072303, 11.958086319851176, 1.271920282698931,
-1.2044337292760101, 1.6734005705339297, -0.9875941256320955,
7.220415332975225, 0.601201124030627
],
[
31.163638790374048, 11.855143433013291, 1.8876168729214116,
-1.862911092419536, 2.279553713445213, -1.6070814330824321,
7.610231826377116, 0.5859042224902173
],
[
31.111807418763107, 11.906469225329653, 1.5848247701762241,
-1.5909887821270712, 2.0038391834918317, -1.3277290609201042,
7.422700514979134, 0.5941465179281992
]
]
for i, smi in enumerate(smiles):
mol = Chem.MolFromSmiles(smi)
res = rdMD.BCUT2D(mol)
self.assertEqual(len(res), 8)
for rv, ev in zip(res, expected[i]):
self.assertAlmostEqual(rv, ev)
def testVectorDescriptors(self):
m = Chem.MolFromSmiles('CCCc1ccccc1')
results = rdMolDescriptors.BCUT2D(m)
names = [
"BCUT2D_%s" % s for s in ('MWHI', "MWLOW", "CHGHI", "CHGLO",
"LOGPHI", "LOGPLOW", "MRHI", "MRLOW")
]
for i, n in enumerate(names):
f = getattr(Descriptors, n)
self.assertEqual(results[i], f(m))
results = rdMolDescriptors.CalcAUTOCORR2D(m)
names = ["AUTOCORR2D_%s" % str(i + 1) for i in range(192)]
for i, n in enumerate(names):
f = getattr(Descriptors, n)
self.assertEqual(results[i], f(m))
def testBCUTUserProps(self):
m = Chem.MolFromSmiles("CCCCCC")
props = []
for a in m.GetAtoms():
a.SetDoubleProp("prop", a.GetIdx() + 1)
props.append(float(a.GetIdx() + 1))
bcut1 = rdMD.BCUT2D(m, "prop")
m = Chem.MolFromSmiles("CCCCCC")
bcut2 = rdMD.BCUT2D(m, props)
bcut3 = rdMD.BCUT2D(m, tuple(props))
# might need feq
self.assertEqual(list(bcut1), list(bcut2))
self.assertEqual(list(bcut3), list(bcut2))
props.append(0.0)
try:
bcut2 = rdMD.BCUT2D(m, props)
self.assertTrue(0, "Failed to handle bad prop size")
except RuntimeError as e:
self.assertTrue("tom_props.size() == num_atoms" in str(e))
try:
bcut2 = rdMD.BCUT2D(m, "property not existing on the atom")
self.assertTrue(0, "Failed to handle not existing properties")
except KeyError as e:
self.assertEqual(e.args, ("property not existing on the atom", ))
for atom in m.GetAtoms():
atom.SetProp("bad_prop", "not a double")
break
try:
bcut2 = rdMD.BCUT2D(m, "bad_prop")
self.assertTrue(0, "Failed to handle bad prop (not a double)")
except RuntimeError as e:
self.assertTrue("boost::bad_any_cast" in str(e))