def testWhetherAllElementsAreSupported(self):
"""Check whether a new element has been correctly added"""
N = 0
while ob.GetSymbol(N+1):
N += 1
# Is the symbol parsed?
symbol = ob.GetSymbol(N)
self.assertEqual(N, ob.GetAtomicNum(symbol))
self.assertEqual(N, ob.GetAtomicNum(symbol.lower())) # test lowercase version
# Has an exact mass been set?
self.assertNotEqual(0.0, ob.GetExactMass(N))
# Has the symbol been added to the SMILES parser?
numatoms = pybel.readstring("smi", "[%s]" % symbol).OBMol.NumAtoms()
self.assertEqual(numatoms, 1)
# Check whether the element is available as a constant
self.assertEqual(N, getattr(ob, ob.GetName(N)))
self.assertTrue(N > 100)
def get_mass(types):
m = []
if OB_version == 3:
for value in types:
a = ob.GetAtomicNum(value)
print("debug readFiles.py: get_mass - a -", a)
c = ob.GetMass(a)
m.append(c)
elif OB_version == 2:
etab = ob.OBElementTable()
for value in types:
a = etab.GetAtomicNum(value)
c = etab.GetMass(a)
m.append(c)
else:
raise Exception("Unknown openbabel version")
return m
def testHydrogenIsotopes(self):
"""Are D and T supported by GetAtomicNum?"""
for symbol in "DT":
self.assertEqual(1, ob.GetAtomicNum(symbol))