def ring_arc_complement_atom_keys(gra, rng):
""" non-intersecting arcs from a ring that shares segments with a graph
"""
gra_atm_bnd_dct = atoms_bond_keys(gra)
rng_atm_bnd_dct = atoms_bond_keys(rng)
# 1. find divergence points, given by the atom at which the divergence
# occurs and the bond followed by the ring as it diverges
div_dct = {}
for atm_key in atom_keys(gra) & atom_keys(rng):
div = rng_atm_bnd_dct[atm_key] - gra_atm_bnd_dct[atm_key]
if div:
bnd_key, = div
div_dct[atm_key] = bnd_key
# 2. cycle through the ring atoms; if you meet a starting divergence, start
# an arc; extend the arc until you meet an ending divergence; repeat until
# all divergences are accounted for
atm_keys = sorted_ring_atom_keys_from_bond_keys(bond_keys(rng))
arcs = []
arc = []
for atm_key, next_atm_key in mit.windowed(itertools.cycle(atm_keys), 2):
bnd_key = frozenset({atm_key, next_atm_key})
# if we haven't started an arc, see if we are at a starting divergence;
# if so, start the arc now and cross the divergence from our list
if not arc:
if atm_key in div_dct and div_dct[atm_key] == bnd_key:
div_dct.pop(atm_key)
arc.append(atm_key)
# if we've started an arc, extend it; then, check if we are at an
# ending divergence; if so, end the arc and cross the divergence from
# our list; add it to our list of arcs
else:
arc.append(atm_key)
if next_atm_key in div_dct and div_dct[next_atm_key] == bnd_key:
div_dct.pop(next_atm_key)
arc.append(next_atm_key)
arcs.append(arc)
arc = []
# if no divergences are left, break out of the loop
if not div_dct:
break
arcs = tuple(map(tuple, arcs))
return arcs
def branch_bond_keys(gra, atm_key, bnd_key):
""" bond keys for branch extending along `bnd_key` away from `atm_key`
"""
# bnd_key is the set of atom indices for the bond of interest
# atm_bnd_keys_dct is a dictionary of atoms that are connected to each atom
bnd_key = frozenset(bnd_key)
assert atm_key in bnd_key
atm_bnd_keys_dct = atoms_bond_keys(gra)
bnch_bnd_keys = {bnd_key}
seen_bnd_keys = set()
excl_bnd_keys = atm_bnd_keys_dct[atm_key] - {bnd_key}
new_bnd_keys = {bnd_key}
bnd_ngb_keys_dct = bonds_neighbor_bond_keys(gra)
while new_bnd_keys:
new_bnd_ngb_keys = set(
itertools.chain(
*dict_.values_by_key(bnd_ngb_keys_dct, new_bnd_keys)))
bnch_bnd_keys.update(new_bnd_ngb_keys - excl_bnd_keys)
seen_bnd_keys.update(new_bnd_keys)
new_bnd_keys = bnch_bnd_keys - seen_bnd_keys
return frozenset(bnch_bnd_keys)
def sigma_radical_atom_keys(rgr):
""" keys for sigma radical atoms
"""
rgr = without_fractional_bonds(rgr)
atm_rad_keys = nonresonant_radical_atom_keys(rgr)
bnd_ords_dct = resonance_dominant_bond_orders(rgr)
atm_bnd_keys_dct = atoms_bond_keys(rgr)
atm_sig_keys = []
for atm_key in atm_rad_keys:
for bnd_key in atm_bnd_keys_dct[atm_key]:
if 3 in bnd_ords_dct[bnd_key]:
atm_sig_keys.append(atm_key)
break
atm_sig_keys = frozenset(atm_sig_keys)
return atm_sig_keys
def sigma_radical_atom_keys(rgr):
""" keys for sigma radical atoms
:param rgr: the molecular graph
:returns: the sigma radical atom keys
:rtype: frozenset[int]
"""
rgr = without_fractional_bonds(rgr)
atm_rad_keys = nonresonant_radical_atom_keys(rgr)
bnd_ords_dct = resonance_dominant_bond_orders(rgr)
atm_bnd_keys_dct = atoms_bond_keys(rgr)
atm_sig_keys = []
for atm_key in atm_rad_keys:
for bnd_key in atm_bnd_keys_dct[atm_key]:
if 3 in bnd_ords_dct[bnd_key]:
atm_sig_keys.append(atm_key)
break
atm_sig_keys = frozenset(atm_sig_keys)
return atm_sig_keys