def json_to_pybel(data, infer_bonds=False):
"""Converts python data structure to pybel.Molecule.
This will infer bond data if not specified.
Args:
data: The loaded json data of a molecule, as a Python object
infer_bonds (Optional): If no bonds specified in input, infer them
Returns:
An instance of `pybel.Molecule`
"""
obmol = ob.OBMol()
obmol.BeginModify()
for atom in data['atoms']:
obatom = obmol.NewAtom()
obatom.SetAtomicNum(table.GetAtomicNum(str(atom['element'])))
obatom.SetVector(*atom['location'])
if 'label' in atom:
pd = ob.OBPairData()
pd.SetAttribute('_atom_site_label')
pd.SetValue(atom['label'])
obatom.CloneData(pd)
# If there is no bond data, try to infer them
if 'bonds' not in data or not data['bonds']:
if infer_bonds:
obmol.ConnectTheDots()
obmol.PerceiveBondOrders()
# Otherwise, use the bonds in the data set
else:
for bond in data['bonds']:
if 'atoms' not in bond:
continue
obmol.AddBond(bond['atoms'][0] + 1, bond['atoms'][1] + 1,
bond['order'])
# Check for unit cell data
if 'unitcell' in data:
uc = ob.OBUnitCell()
uc.SetData(*(ob.vector3(*v) for v in data['unitcell']))
uc.SetSpaceGroup('P1')
obmol.CloneData(uc)
obmol.EndModify()
mol = pybel.Molecule(obmol)
# Add partial charges
if 'charge' in data['atoms'][0]:
mol.OBMol.SetPartialChargesPerceived()
for atom, pyatom in zip(data['atoms'], mol.atoms):
pyatom.OBAtom.SetPartialCharge(atom['charge'])
return mol
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 add_property(mol, prop_name, prop_value):
newData = openbabel.OBPairData()
newData.SetAttribute(prop_name)
newData.SetValue(prop_value)
mol.OBMol.CloneData(newData)
