def radical_groups(gra):
""" returns a list of lists of groups attached each radical
"""
gra = without_fractional_bonds(gra)
groups = []
rads = sing_res_dom_radical_atom_keys(gra)
for rad in rads:
groups.append(atom_groups(gra, rad))
return groups
def one_resonance_dominant_bond_orders(rgr):
""" resonance-dominant bond orders, by bond
"""
rgr = without_fractional_bonds(rgr)
bnd_keys = list(bond_keys(rgr))
bnd_ords_by_res = [
dict_.values_by_key(bond_orders(dom_rgr), bnd_keys)
for dom_rgr in dominant_resonances(rgr)
]
first_bnd_ords = [bnd_ords_by_res[0]]
bnd_ords_lst = list(map(frozenset, zip(*first_bnd_ords)))
bnd_dom_res_ords_dct = dict(zip(bnd_keys, bnd_ords_lst))
return bnd_dom_res_ords_dct
def resonance_avg_bond_orders(rgr):
""" resonance-dominant bond orders, by bond
"""
rgr = without_fractional_bonds(rgr)
bnd_keys = list(bond_keys(rgr))
bnd_ords_by_res = [
dict_.values_by_key(bond_orders(dom_rgr), bnd_keys)
for dom_rgr in dominant_resonances(rgr)
]
nres = len(bnd_ords_by_res)
bnd_ords_lst = zip(*bnd_ords_by_res)
avg_bnd_ord_lst = [sum(bnd_ords) / nres for bnd_ords in bnd_ords_lst]
avg_bnd_ord_dct = dict(zip(bnd_keys, avg_bnd_ord_lst))
return avg_bnd_ord_dct
def nonresonant_radical_atom_keys(rgr):
""" keys for radical atoms that are not in resonance
"""
rgr = without_fractional_bonds(rgr)
atm_keys = list(atom_keys(rgr))
atm_rad_vlcs_by_res = [
dict_.values_by_key(atom_unsaturated_valences(dom_rgr), atm_keys)
for dom_rgr in dominant_resonances(rgr)
]
atm_rad_vlcs = [min(rad_vlcs) for rad_vlcs in zip(*atm_rad_vlcs_by_res)]
atm_rad_keys = frozenset(
atm_key for atm_key, atm_rad_vlc in zip(atm_keys, atm_rad_vlcs)
if atm_rad_vlc)
return atm_rad_keys
def sing_res_dom_radical_atom_keys(rgr):
""" resonance-dominant radical atom keys,for one resonance
"""
rgr = without_fractional_bonds(rgr)
atm_keys = list(atom_keys(rgr))
atm_rad_vlcs_by_res = [
dict_.values_by_key(atom_unsaturated_valences(dom_rgr), atm_keys)
for dom_rgr in dominant_resonances(rgr)
]
first_atm_rad_val = [atm_rad_vlcs_by_res[0]]
atm_rad_vlcs = [max(rad_vlcs) for rad_vlcs in zip(*first_atm_rad_val)]
atm_rad_keys = frozenset(
atm_key for atm_key, atm_rad_vlc in zip(atm_keys, atm_rad_vlcs)
if atm_rad_vlc)
return atm_rad_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 radical_group_dct(gra):
""" return a dictionary of lists of groups attached each radical
"""
gra = without_fractional_bonds(gra)
groups = {}
rads = list(sing_res_dom_radical_atom_keys(gra))
atms = atoms(gra)
for rad in rads:
key = atms[rad][0]
if key in groups:
groups[atms[rad][0]] += atom_groups(gra, rad)
else:
groups[atms[rad][0]] = atom_groups(gra, rad)
return groups
def resonance_dominant_radical_atom_keys(rgr):
""" resonance-dominant radical atom keys
(keys of resonance-dominant radical sites)
"""
rgr = without_fractional_bonds(rgr)
atm_keys = list(atom_keys(rgr))
atm_rad_vlcs_by_res = [
dict_.values_by_key(atom_unsaturated_valences(dom_rgr), atm_keys)
for dom_rgr in dominant_resonances(rgr)
]
atm_rad_vlcs = [max(rad_vlcs) for rad_vlcs in zip(*atm_rad_vlcs_by_res)]
atm_rad_keys = frozenset(
atm_key for atm_key, atm_rad_vlc in zip(atm_keys, atm_rad_vlcs)
if atm_rad_vlc)
return atm_rad_keys
def resonance_dominant_atom_centered_cumulene_keys(rgr):
""" resonance dominant keys for atom-centered cumulenes
the bond-centered cumulenes are described by
(frozenset({end_atm_key1, end_atm_key2}), cent_atm_key)
where the first pair contains the sp2 atoms at the cumulene ends and
`cent_atm_key` is the key of the central atom
"""
rgr = without_fractional_bonds(rgr)
cum_chains = _cumulene_chains(rgr)
cum_keys = set()
for cum_chain in cum_chains:
size = len(cum_chain)
if size % 2 == 1:
cum_keys.add((frozenset({cum_chain[0],
cum_chain[-1]}), cum_chain[size // 2]))
cum_keys = frozenset(cum_keys)
return cum_keys
def radical_dissociation_prods(gra, pgra1):
""" given a dissociation product, determine the other product
"""
gra = without_fractional_bonds(gra)
pgra2 = None
rads = sing_res_dom_radical_atom_keys(gra)
adj_atms = atoms_neighbor_atom_keys(gra)
# adj_idxs = tuple(adj_atms[rad] for rad in rads)
for rad in rads:
for adj in adj_atms[rad]:
for group in atom_groups(gra, adj):
if full_isomorphism(explicit(group), explicit(pgra1)):
pgra2 = remove_atoms(gra, atom_keys(group))
# pgra2 = remove_bonds(pgra2, bond_keys(group))
if bond_keys(group) in pgra2:
pgra2 = remove_bonds(pgra2, bond_keys(group))
return (pgra1, pgra2)
def linear_atom_keys(rgr, dummy=True):
""" atoms forming linear bonds, based on their hybridization
:param rgr: the graph
:param dummy: whether or not to consider atoms connected to dummy atoms as
linear, if different from what would be predicted based on their
hybridization
:returns: the linear atom keys
:rtype: tuple[int]
"""
rgr = without_fractional_bonds(rgr)
atm_hyb_dct = resonance_dominant_atom_hybridizations(implicit(rgr))
lin_atm_keys = set(dict_.keys_by_value(atm_hyb_dct, lambda x: x == 1))
if dummy:
dum_ngb_key_dct = dummy_atoms_neighbor_atom_key(rgr)
lin_atm_keys |= set(dum_ngb_key_dct.values())
lin_atm_keys = tuple(sorted(lin_atm_keys))
return lin_atm_keys
