def atom_type(self, mol, atom_id):
atom = mol.atoms[atom_id]
atom_type = get_atomtype(atom, mol.get_bonds(atom))
if atom_type is None:
return atom_type
else:
return atom_type.label
def check_partial_charge(atom):
"""
Checks whether the partial charge attribute of the atom checks out with
the theoretical one:
"""
if atom.symbol == 'X':
return # because we can't check it.
valence = PeriodicSystem.valence_electrons[atom.symbol]
order = atom.get_total_bond_order()
theoretical = valence - order - atom.radical_electrons - 2 * atom.lone_pairs
if not (-0.301 < atom.charge - theoretical < 0.301):
# It should be 0, but -0.1 is caused by a Hydrogen bond
raise InvalidAdjacencyListError(
'Invalid valency for atom {symbol} ({type}) with {radicals} unpaired electrons, '
'{lone_pairs} pairs of electrons, {charge} charge, and bonds [{bonds}].'
.format(symbol=atom.symbol,
type=get_atomtype(atom, atom.edges).label,
radicals=atom.radical_electrons,
lone_pairs=atom.lone_pairs,
charge=atom.charge,
bonds=','.join([
str(bond.order) for bond in atom.bonds.values()
])))