def convertCycleToGroup(cycle):
"""
This function converts a list of atoms in a cycle to a functional Group object
"""
from rmgpy.molecule.group import GroupAtom, GroupBond, Group
# Create GroupAtom object for each atom in the cycle, label the first one in the cycle with a *
groupAtoms = {}
bonds = []
for atom in cycle:
groupAtoms[atom] = GroupAtom(atomType=[atom.atomType],
radicalElectrons=[0],
label='*' if cycle.index(atom)==0 else '')
group = Group(atoms=groupAtoms.values())
# Create GroupBond for each bond between atoms in the cycle, but not outside of the cycle
for atom in cycle:
for bondedAtom, bond in atom.edges.iteritems():
if bondedAtom in cycle:
# create a group bond with the same bond order as in the original molecule,
# if it hasn't already been created
if not group.hasBond(groupAtoms[atom],groupAtoms[bondedAtom]):
group.addBond(GroupBond(groupAtoms[atom],groupAtoms[bondedAtom],order=[bond.order]))
else:
pass
group.update()
return group
