def test4Hs(self):
hierarchy = FunctionalGroups.BuildFuncGroupHierarchy()
inName = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', 'NCI_5K_TPSA.csv')
with open(inName, 'r') as inF:
ms = [Chem.MolFromSmiles(x.split(',')[0]) for x in inF if x[0] != '#']
for m in ms:
mh = Chem.AddHs(m)
fp = FunctionalGroups.CreateMolFingerprint(m, hierarchy)
fph = FunctionalGroups.CreateMolFingerprint(mh, hierarchy)
if fp != fph:
print(Chem.MolToSmiles(m))
print(fp.ToBitString())
print(fph.ToBitString())
self.assertEqual(fp, fph)
def test4Hs(self):
hierarchy = FunctionalGroups.BuildFuncGroupHierarchy()
inName = os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data',
'NCI_5K_TPSA.csv')
inF = open(inName, 'r')
lines = inF.readlines()
ms = [
Chem.MolFromSmiles(x.split(',')[0]) for x in lines if x[0] != '#'
]
for m in ms:
mh = Chem.AddHs(m)
fp = FunctionalGroups.CreateMolFingerprint(m, hierarchy)
fph = FunctionalGroups.CreateMolFingerprint(mh, hierarchy)
if fp != fph:
print fp.ToBitString()
print fph.ToBitString()
self.failUnlessEqual(fp, fph)
def test1Basics(self):
txt = """
AcidChloride\tC(=O)Cl\tAcid Chloride
AcidChloride.Benzoyl\tC(=O)(Cl)c1ccccc1\tBenzoyl
Amine\tN\tAmine
Amine.Primary\t[N;H2]\tPrimary
Amine.Primary.Aromatic\t[N;H2][a]\tPrimary Aromatic
Amine.Aromatic\tN[a]\tAromatic
"""
hierarchy = FunctionalGroups.BuildFuncGroupHierarchy(data=txt)
self.assertTrue(hierarchy)
self.assertEqual(len(hierarchy), 2)
self.assertEqual(len(hierarchy[0]), 2)
self.assertEqual(len(hierarchy[1]), 4)
self.assertEqual(hierarchy[0].name, 'Acid Chloride')
self.assertEqual(hierarchy[0].children[0].name, 'Benzoyl')
self.assertEqual(hierarchy[0].label, 'AcidChloride')
self.assertEqual(hierarchy[0].rxnSmarts, '')
m = Chem.MolFromSmiles('ClC(=O)CCCNc1ccccc1')
fp = FunctionalGroups.CreateMolFingerprint(m, hierarchy)
self.assertEqual(fp, [1, 0, 1, 0, 0, 1])
m = Chem.MolFromSmiles('OC(=O)CCC')
fp = FunctionalGroups.CreateMolFingerprint(m, hierarchy)
self.assertEqual(fp, [0, 0, 0, 0, 0, 0])
# make sure we get the same hierarchy on the second call:
hierarchy = FunctionalGroups.BuildFuncGroupHierarchy(data=txt)
self.assertTrue(hierarchy)
self.assertEqual(len(hierarchy), 2)
self.assertEqual(len(hierarchy[0]), 2)
self.assertEqual(len(hierarchy[1]), 4)
self.assertEqual(hierarchy[0].name, 'Acid Chloride')
self.assertEqual(hierarchy[0].children[0].name, 'Benzoyl')
self.assertEqual(hierarchy[0].label, 'AcidChloride')
self.assertEqual(hierarchy[0].rxnSmarts, '')
# if we edit this hierarchy it doesn't affect the global one:
hierarchy.pop(0)
self.assertEqual(len(hierarchy[0]), 4)
hierarchy = FunctionalGroups.BuildFuncGroupHierarchy(data=txt)
self.assertTrue(hierarchy)
self.assertEqual(len(hierarchy), 2)
self.assertEqual(len(hierarchy[0]), 2)
self.assertEqual(len(hierarchy[1]), 4)
self.assertEqual(hierarchy[0].name, 'Acid Chloride')
self.assertEqual(hierarchy[0].children[0].name, 'Benzoyl')
self.assertEqual(hierarchy[0].label, 'AcidChloride')
self.assertEqual(hierarchy[0].rxnSmarts, '')
# and if we edit the global one and don't force, we get the edited one:
FunctionalGroups.hierarchy.pop(0)
self.assertEqual(len(FunctionalGroups.hierarchy[0]), 4)
hierarchy = FunctionalGroups.BuildFuncGroupHierarchy(data=txt)
self.assertTrue(hierarchy)
self.assertEqual(len(hierarchy), 1)
self.assertEqual(len(hierarchy[0]), 4)
# but a force gets us back:
hierarchy = FunctionalGroups.BuildFuncGroupHierarchy(data=txt, force=True)
self.assertEqual(len(hierarchy), 2)
self.assertEqual(len(hierarchy[0]), 2)
self.assertEqual(len(hierarchy[1]), 4)