def radical_atom_keys(gra, single_res=False, min_valence=1.):
""" Radical atom keys for this molecular graph
Radical atoms are based on the lowest-spin resonance structures for this
graph. If the `single_res` flag is set, a single low-spin resonance
structure will be chosen when there are multiple such structures.
This function should eventually replace both
`resonance_dominant_radical_atom_keys` and
`sing_res_dom_radical_atom_keys` for a more user-friendly interface.
Note that this function ignores the bond orders in `gra`. If you wish to
identify radical atom keys based on the bond orders in `gra`, this can be
done by using the `atom_unsaturated_valences` function.
:param gra: the molecular graph
:param single_res: only include radical keys for a single (arbitrary)
resonance structure, or include all atoms that are radicals in any of
the low-spin resonance structures?
:type single_res: bool
:param min_valence: optionally, specify that only sites with at least a
certain number of radical electrons be included
:type min_valence: int
:returns: the radical atom keys
:rtype: frozenset[int]
"""
gra = without_fractional_bonds(gra)
atm_keys = list(atom_keys(gra))
if single_res:
atm_rad_vlcs = dict_.values_by_key(
atom_unsaturated_valences(dominant_resonance(gra)), atm_keys)
else:
atm_rad_vlcs_by_res = [
dict_.values_by_key(atom_unsaturated_valences(dom_gra), atm_keys)
for dom_gra in dominant_resonances(gra)
]
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 >= min_valence)
return atm_rad_keys
def _bond_capacities(rgr):
""" the number of electron pairs available for further pi-bonding, by bond
"""
rgr = without_dummy_bonds(rgr)
atm_unsat_vlc_dct = atom_unsaturated_valences(rgr)
def _pi_capacities(bnd_key):
return min(map(atm_unsat_vlc_dct.__getitem__, bnd_key))
bnd_keys = list(bond_keys(rgr))
bnd_caps = tuple(map(_pi_capacities, bnd_keys))
bnd_cap_dct = dict(zip(bnd_keys, bnd_caps))
return bnd_cap_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
TODO: DEPRECATE
"""
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 resonance_dominant_radical_atom_keys(rgr):
""" resonance-dominant radical atom keys
TODO: DEPRECATE
(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 subresonances(rgr):
""" this connected graph and its lower-spin (more pi-bonded) resonances
"""
rgr = without_fractional_bonds(rgr)
# get the bond capacities (room for increasing bond order), filtering out
# the negative ones to avoid complications with hypervalent atoms in TSs
bnd_cap_dct = dict_.by_value(_bond_capacities(rgr), lambda x: x > 0)
ret_rgrs = []
if bnd_cap_dct:
bnd_keys, bnd_caps = zip(*bnd_cap_dct.items())
atm_keys = list(functools.reduce(frozenset.union, bnd_keys))
# Loop over all possible combinations of bond order increments (amounts
# by which to increase the bond order), filtering out combinations that
# exceed the valences of the atoms involved.
# (Note that we are only testing the bonds with available pi electrons,
# so this is compatible with having hypervalent atoms elsewhere in the
# molecule)
bnd_ord_inc_ranges = [range(bnd_cap + 1) for bnd_cap in bnd_caps]
for bnd_ord_incs in itertools.product(*bnd_ord_inc_ranges):
bnd_ord_inc_dct = dict(zip(bnd_keys, bnd_ord_incs))
ret_rgr = _add_pi_bonds(rgr, bnd_ord_inc_dct)
max_bnd_ord = max(bond_orders(ret_rgr).values())
atm_unsat_vlcs = dict_.values_by_key(
atom_unsaturated_valences(ret_rgr), atm_keys)
if not any(atm_unsat_vlc < 0 for atm_unsat_vlc in atm_unsat_vlcs):
if max_bnd_ord < 4:
ret_rgrs.append(ret_rgr)
if not ret_rgrs:
ret_rgrs = (rgr, )
else:
ret_rgrs = tuple(ret_rgrs)
return ret_rgrs
def radical_atom_keys_from_resonance(rgr, min_valence=1.):
""" Radical atom keys for a resonance molecular graph
Assumes the graph has already been assinged to a resonance structure.
:param rgr: a resonance-structure molecular graph
:param min_valence: optionally, specify that only sites with at least a
certain number of radical electrons be included
:type min_valence: int
:returns: the radical atom keys
:rtype: frozenset[int]
"""
rgr = without_fractional_bonds(rgr)
atm_keys = list(atom_keys(rgr))
atm_rad_vlcs = dict_.values_by_key(atom_unsaturated_valences(rgr),
atm_keys)
atm_rad_keys = frozenset(
atm_key for atm_key, atm_rad_vlc in zip(atm_keys, atm_rad_vlcs)
if atm_rad_vlc >= min_valence)
return atm_rad_keys