def testInvalidRxn(self):
"""IsValid() should flag up invalid reaction data"""
mol = pybel.readstring("smi", "CC>>O").OBMol
facade = ob.OBReactionFacade(mol)
self.assertTrue(facade.IsValid())
mol.SetIsReaction(False)
self.assertFalse(facade.IsValid())
mol.SetIsReaction()
self.assertTrue(facade.IsValid())
atom = mol.GetAtom(1)
facade.SetRole(atom, 4)
self.assertFalse(facade.IsValid()) # invalid role
facade.SetRole(atom, ob.REACTANT)
self.assertTrue(facade.IsValid())
data = atom.GetData("rxncomp")
ob.toPairInteger(data).SetValue(-1)
self.assertFalse(facade.IsValid()) # invalid rxn component id
atom.DeleteData(data)
self.assertFalse(atom.HasData("rxncomp"))
self.assertFalse(facade.IsValid()) # data missing
newdata = ob.OBPairData()
newdata.SetAttribute("rxncomp")
newdata.SetValue("1")
atom.CloneData(newdata)
self.assertTrue(atom.HasData("rxncomp"))
self.assertFalse(facade.IsValid()) # wrong type of data
# Connected component should not belong to two different
# rxn components or two different reaction roles
mol = pybel.readstring("smi", "CC>>O").OBMol
facade = ob.OBReactionFacade(mol)
self.assertTrue(facade.IsValid())
atom = mol.GetAtom(1)
facade.SetComponentId(atom, 99)
self.assertFalse(facade.IsValid())
facade.SetComponentId(atom, 1)
self.assertTrue(facade.IsValid())
facade.SetRole(atom, ob.AGENT)
self.assertFalse(facade.IsValid())
def testInvalidRxn(self):
"""IsValid() should flag up invalid reaction data"""
mol = pybel.readstring("smi", "CC>>O").OBMol
facade = ob.OBReactionFacade(mol)
self.assertTrue(facade.IsValid())
mol.SetIsReaction(False)
self.assertFalse(facade.IsValid())
mol.SetIsReaction()
self.assertTrue(facade.IsValid())
atom = mol.GetAtom(1)
facade.SetRole(atom, 4)
self.assertFalse(facade.IsValid()) # invalid role
facade.SetRole(atom, ob.REACTANT)
self.assertTrue(facade.IsValid())
data = atom.GetData("rxncomp")
ob.toPairInteger(data).SetValue(-1)
self.assertFalse(facade.IsValid()) # invalid rxn component id
atom.DeleteData(data)
self.assertFalse(atom.HasData("rxncomp"))
self.assertFalse(facade.IsValid()) # data missing
newdata = ob.OBPairData()
newdata.SetAttribute("rxncomp")
newdata.SetValue("1")
atom.CloneData(newdata)
self.assertTrue(atom.HasData("rxncomp"))
self.assertFalse(facade.IsValid()) # wrong type of data
# Connected component should not belong to two different
# rxn components or two different reaction roles
mol = pybel.readstring("smi", "CC>>O").OBMol
facade = ob.OBReactionFacade(mol)
self.assertTrue(facade.IsValid())
atom = mol.GetAtom(1)
facade.SetComponentId(atom, 99)
self.assertFalse(facade.IsValid())
facade.SetComponentId(atom, 1)
self.assertTrue(facade.IsValid())
facade.SetRole(atom, ob.AGENT)
self.assertFalse(facade.IsValid())
def testSMILES(self):
mol = pybel.readstring("smi", "C[CH3:6]")
atom = mol.OBMol.GetAtom(2)
data = atom.GetData("Atom Class")
self.assertTrue(data)
self.assertEqual(6, ob.toPairInteger(data).GetGenericValue())
atom.DeleteData("Atom Class")
ac = ob.OBPairInteger()
ac.SetAttribute("Atom Class")
ac.SetValue(2)
mol.OBMol.GetAtom(1).CloneData(ac)
out = mol.write("smi", opt={"a": True, "n": True, "nonewline": True})
self.assertEqual("[CH3:2]C", out)
def testSMILES(self):
mol = pybel.readstring("smi", "C[CH3:6]")
atom = mol.OBMol.GetAtom(2)
data = atom.GetData("Atom Class")
self.assertTrue(data)
self.assertEqual(6, ob.toPairInteger(data).GetGenericValue())
atom.DeleteData("Atom Class")
ac = ob.obpairtemplateint()
ac.SetAttribute("Atom Class")
ac.SetValue(2)
mol.OBMol.GetAtom(1).CloneData(ac)
out = mol.write("smi", opt={"a":True, "n":True, "nonewline":True})
self.assertEqual("[CH3:2]C", out)