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
for atom in atoms[s0:]:
atom.props['inRing'] = True
# Label atoms
atoms[0].label = '*1'
if a > 1:
atoms[1].label = '*4'
if a > 2:
atoms[-1].label = '*5'
if a > 3:
for i, atom in enumerate(atoms[2:-1]):
atom.label = '*{0}'.format(i + 6)
# Add to group
for atom in reversed(atoms):
new_group.addAtom(atom)
# Add bond to newly added atoms
new_group.addBond(
GroupBond(new_group.atoms[1], atoms[-1], order=[1, 2, 3, 1.5]))
# Create bonds
if a > 1:
bonds = [
GroupBond(atoms[i], atoms[i + 1], order=[1, 2, 3, 1.5])
for i in range(a - 1)
]
for bond in bonds:
new_group.addBond(bond)
# Add remaining atoms
if b > 0:
# Create atoms
atoms = [
GroupAtom(atomType=['R!H'],
radicalElectrons=None,
