def update_molecule(mol, to_single_bonds=False):
"""
Returns a copy of the current molecule with updated atomTypes
if to_single_bonds is True, the returned mol contains only single bonds.
This is useful for isomorphism comparison
"""
new_mol = Molecule()
try:
atoms = mol.atoms
except AttributeError:
return None
atom_mapping = dict()
for atom1 in atoms:
new_atom = new_mol.addAtom(Atom(atom1.element))
atom_mapping[atom1] = new_atom
for atom1 in atoms:
for atom2 in atom1.bonds.keys():
bond_order = 1.0 if to_single_bonds else atom1.bonds[
atom2].getOrderNum()
bond = Bond(atom_mapping[atom1], atom_mapping[atom2], bond_order)
new_mol.addBond(bond)
try:
new_mol.updateAtomTypes()
except AtomTypeError:
pass
new_mol.multiplicity = mol.multiplicity
return new_mol
