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 testFacade(self):
parts = "CNO"
mol = pybel.readstring("smi", ">".join(parts)).OBMol
facade = ob.OBReactionFacade(mol)
# basic test - copy out each component
comps = [ob.REACTANT, ob.AGENT, ob.PRODUCT]
for part, comp in zip(parts, comps):
nmol = ob.OBMol()
facade.GetComponent(nmol, comp, 0)
nsmi = pybel.Molecule(nmol).write("smi").rstrip()
self.assertEqual(nsmi, part)
nmol = ob.OBMol()
facade.GetComponent(nmol, ob.NO_REACTIONROLE, 0)
self.assertEqual(0, nmol.NumAtoms())
# Reassign role
facade.ReassignComponent(ob.AGENT, 0, ob.NO_REACTIONROLE)
nsmi = pybel.Molecule(mol).write("smi").rstrip()
self.assertEqual("C>>O", nsmi)
# ...and back again
facade.ReassignComponent(ob.NO_REACTIONROLE, 0, ob.AGENT)
# Add a new reactant
molb = pybel.readstring("smi", "S").OBMol
facade.AddComponent(molb, ob.REACTANT)
nsmi = pybel.Molecule(mol).write("smi").rstrip()
self.assertEqual("C.S>N>O", nsmi)
# ...and copy it back out
nmol = ob.OBMol()
facade.GetComponent(nmol, ob.REACTANT, 1)
nsmi = pybel.Molecule(nmol).write("smi").rstrip()
self.assertEqual("S", nsmi)
# ...and also copy the O
facade.GetComponent(nmol, ob.PRODUCT, 0)
nmol.SetIsReaction()
nsmi = pybel.Molecule(nmol).write("smi").rstrip()
self.assertEqual("S>>O", nsmi)