def stereogenic_atom_keys(gra, assigned=False):
""" Find stereogenic atoms in this graph.
If the `assigned` flag is set to `False`, only unassigned stereogenic
atoms will be detected.
:param gra: the graph
:param assigned: Include atoms that already have stereo assignments?
:param assigned: bool
:returns: the stereogenic atom keys
:rtype: frozenset
"""
gra = without_bond_orders(gra)
gra = explicit(gra) # for simplicity, add the explicit hydrogens back in
atm_keys = dict_.keys_by_value(atom_bond_valences(gra), lambda x: x == 4)
if not assigned:
# Remove assigned stereo keys
atm_keys -= atom_stereo_keys(gra)
atm_ngb_keys_dct = atoms_neighbor_atom_keys(gra)
def _is_stereogenic(atm_key):
atm_ngb_keys = list(atm_ngb_keys_dct[atm_key])
pri_vecs = [
stereo_priority_vector(gra, atm_key, atm_ngb_key)
for atm_ngb_key in atm_ngb_keys
]
ret = not any(pv1 == pv2
for pv1, pv2 in itertools.combinations(pri_vecs, r=2))
return ret
ste_gen_atm_keys = frozenset(filter(_is_stereogenic, atm_keys))
return ste_gen_atm_keys
def stereogenic_bond_keys(gra, assigned=False):
""" Find stereogenic bonds in this graph.
If the `assigned` flag is set to `False`, only unassigned stereogenic
bonds will be detected.
:param gra: the graph
:param assigned: Include bonds that already have stereo assignments?
:param assigned: bool
:returns: the stereogenic bond keys
:rtype: frozenset
"""
gra = without_bond_orders(gra)
gra = explicit(gra) # for simplicity, add the explicit hydrogens back in
# get candidates: planar bonds
bnd_keys = sp2_bond_keys(gra)
if not assigned:
# remove bonds that already have stereo assignments
bnd_keys -= bond_stereo_keys(gra)
bnd_keys -= functools.reduce( # remove double bonds in small rings
frozenset.union, filter(lambda x: len(x) < 8, rings_bond_keys(gra)),
frozenset())
atm_ngb_keys_dct = atoms_neighbor_atom_keys(gra)
def _is_stereogenic(bnd_key):
atm1_key, atm2_key = bnd_key
def _is_symmetric_on_bond(atm_key, atm_ngb_key):
atm_ngb_keys = list(atm_ngb_keys_dct[atm_key] - {atm_ngb_key})
if not atm_ngb_keys: # C=:O:
ret = True
elif len(atm_ngb_keys) == 1: # C=N:-X
ret = False
else:
assert len(atm_ngb_keys) == 2 # C=C(-X)-Y
ret = (stereo_priority_vector(
gra, atm_key, atm_ngb_keys[0]) == stereo_priority_vector(
gra, atm_key, atm_ngb_keys[1]))
return ret
return not (_is_symmetric_on_bond(atm1_key, atm2_key)
or _is_symmetric_on_bond(atm2_key, atm1_key))
ste_gen_bnd_keys = frozenset(filter(_is_stereogenic, bnd_keys))
return ste_gen_bnd_keys
def sp2_bond_keys(gra):
""" determine the sp2 bonds in this graph
"""
gra = without_bond_orders(gra)
bnd_keys = dict_.keys_by_value(resonance_dominant_bond_orders(gra),
lambda x: 2 in x)
# make sure both ends are sp^2 (excludes cumulenes)
atm_hyb_dct = resonance_dominant_atom_hybridizations(gra)
sp2_atm_keys = dict_.keys_by_value(atm_hyb_dct, lambda x: x == 2)
bnd_keys = frozenset(
{bnd_key
for bnd_key in bnd_keys if bnd_key <= sp2_atm_keys})
return bnd_keys
def resonances(rgr):
""" all resonance graphs with this connectivity
"""
return subresonances(without_bond_orders(rgr))
