def addition(xgr1, xgr2):
""" find an addition transformation
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
if len(xgrs1) == 2 and len(xgrs2) == 1:
x_xgr, y_xgr = xgrs1
xgr2, = xgrs2
x_atm_keys = _unsaturated_atom_keys(x_xgr)
y_atm_keys = _unsaturated_atom_keys(y_xgr)
# xgeo = geometry(xgr2)
for x_atm_key, y_atm_key in itertools.product(x_atm_keys, y_atm_keys):
xy_xgr = add_bonds(_union(x_xgr, y_xgr), [{x_atm_key, y_atm_key}])
# xgeo = geometry(xy_xgr)
atm_key_dct = _full_isomorphism(xy_xgr, xgr2)
if atm_key_dct:
tra = from_data('addition',
frm_bnd_keys=[{x_atm_key, y_atm_key}],
brk_bnd_keys=[])
return tra
def proton_migration(xgr1, xgr2):
""" find a proton migration transformation
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tras = []
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
h_atm_key1 = max(_atom_keys(xgr1)) + 1
h_atm_key2 = max(_atom_keys(xgr2)) + 1
if len(xgrs1) == 1 and len(xgrs2) == 1:
xgr1, = xgrs1
xgr2, = xgrs2
atm_keys1 = _unsaturated_atom_keys(xgr1)
atm_keys2 = _unsaturated_atom_keys(xgr2)
for atm_key1, atm_key2 in itertools.product(atm_keys1, atm_keys2):
xgr1_h = _add_atom_explicit_hydrogen_keys(xgr1,
{atm_key1: [h_atm_key1]})
xgr2_h = _add_atom_explicit_hydrogen_keys(xgr2,
{atm_key2: [h_atm_key2]})
inv_atm_key_dct = _full_isomorphism(xgr2_h, xgr1_h)
if inv_atm_key_dct:
tras.append(
from_data(
frm_bnd_keys=[{atm_key1, inv_atm_key_dct[h_atm_key2]}],
brk_bnd_keys=[{
inv_atm_key_dct[atm_key2],
inv_atm_key_dct[h_atm_key2]
}]))
if len(tras) < 1:
tras = None
return tras
def is_stereo_compatible(tra, sgr1, sgr2):
""" is this transformation compatible with the reactant/product stereo
assignments?
"""
cgr1 = without_stereo_parities(sgr1)
cgr2 = without_stereo_parities(sgr2)
atm_key_dct = _full_isomorphism(apply(tra, cgr1), cgr2)
# determine the stereo centers which are preserved in the transformation
sgr1 = _relabel(sgr1, atm_key_dct)
atm_keys = sorted(atom_stereo_keys(sgr1) & atom_stereo_keys(sgr2))
bnd_keys = sorted(bond_stereo_keys(sgr1) & bond_stereo_keys(sgr2))
atm_pars1 = dict_.values_by_key(atom_stereo_parities(sgr1), atm_keys)
atm_pars2 = dict_.values_by_key(atom_stereo_parities(sgr2), atm_keys)
bnd_pars1 = dict_.values_by_key(bond_stereo_parities(sgr1), bnd_keys)
bnd_pars2 = dict_.values_by_key(bond_stereo_parities(sgr2), bnd_keys)
atm_ngb_keys_dct1 = atom_neighbor_keys(sgr1)
atm_ngb_keys_dct2 = atom_neighbor_keys(sgr2)
ret = True
for atm_key, par1, par2 in zip(atm_keys, atm_pars1, atm_pars2):
atm_ngb_keys1 = stereo_sorted_atom_neighbor_keys(
sgr1, atm_key, atm_ngb_keys_dct1[atm_key])
atm_ngb_keys2 = stereo_sorted_atom_neighbor_keys(
sgr2, atm_key, atm_ngb_keys_dct2[atm_key])
if _permutation_parity(atm_ngb_keys1, atm_ngb_keys2):
ret &= (par1 == par2)
else:
ret &= (par1 != par2)
for bnd_key, par1, par2 in zip(bnd_keys, bnd_pars1, bnd_pars2):
atm1_key, atm2_key = bnd_key
atm1_ngb_key1 = stereo_sorted_atom_neighbor_keys(
sgr1, atm1_key, atm_ngb_keys_dct1[atm1_key] - {atm2_key})[0]
atm2_ngb_key1 = stereo_sorted_atom_neighbor_keys(
sgr1, atm2_key, atm_ngb_keys_dct1[atm2_key] - {atm1_key})[0]
atm1_ngb_key2 = stereo_sorted_atom_neighbor_keys(
sgr2, atm1_key, atm_ngb_keys_dct2[atm1_key] - {atm2_key})[0]
atm2_ngb_key2 = stereo_sorted_atom_neighbor_keys(
sgr2, atm2_key, atm_ngb_keys_dct2[atm2_key] - {atm1_key})[0]
if not ((atm1_ngb_key1 != atm1_ngb_key2) ^
(atm2_ngb_key1 != atm2_ngb_key2)):
ret &= (par1 == par2)
else:
ret &= (par1 != par2)
return ret
def _reverse(tra, xgr1, xgr2):
frm_bnd_keys = formed_bond_keys(tra)
brk_bnd_keys = broken_bond_keys(tra)
atm_key_dct = _full_isomorphism(apply(tra, xgr1), xgr2)
rev_frm_bnd_keys = [
frozenset(map(atm_key_dct.__getitem__, bnd_key))
for bnd_key in brk_bnd_keys
]
rev_brk_bnd_keys = [
frozenset(map(atm_key_dct.__getitem__, bnd_key))
for bnd_key in frm_bnd_keys
]
rev_tra = from_data(frm_bnd_keys=rev_frm_bnd_keys,
brk_bnd_keys=rev_brk_bnd_keys)
return rev_tra
def _substitution(atmsA, neighsA, bndsA, atmsB, neighsB, xgr1, xgr2):
for atmi in atmsA:
if _is_heavy(atmi, atmsA):
i_neighs = neighsA[atmi]
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bndsA)
new_xgr = automol.graph.remove_bonds(xgr1, [bnd_break_key_ij])
for atmk in atmsB:
if atmk != atmi and atmk != atmj: # and not atmi in neighsB[atmk] and not atmj in neighsB[atmk]:
bnd_form_key_ik = frozenset({atmi, atmk})
newnew_xgr = automol.graph.add_bonds(
new_xgr, [bnd_form_key_ik])
atm_key_dct = _full_isomorphism(newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_ik], [bnd_break_key_ij]]
return tra
def _substitution(atmsa, neighsa, bndsa, atmsb, xgr1, xgr2):
ret_tra = None
for atmi in atmsa:
if _is_heavy(atmi, atmsa):
i_neighs = neighsa[atmi]
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bndsa)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
for atmk in atmsb:
if atmk not in (atmi, atmj):
bnd_form_key_ik = frozenset({atmi, atmk})
newnew_xgr = add_bonds(new_xgr, [bnd_form_key_ik])
atm_key_dct = _full_isomorphism(newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_ik], [bnd_break_key_ij]]
ret_tra = tra
return ret_tra
def _partial_hydrogen_abstraction(qh_xgr, q_xgr):
tra = None
h_atm_key = max(_atom_keys(q_xgr)) + 1
#rad_atm_keys = _resonance_dominant_radical_atom_keys(q_xgr)
uns_atm_keys = automol.graph.unsaturated_atom_keys(q_xgr)
for atm_key in uns_atm_keys:
#for atm_key in rad_atm_keys:
q_xgr_h = _add_atom_explicit_hydrogen_keys(q_xgr,
{atm_key: [h_atm_key]})
inv_atm_key_dct = _full_isomorphism(q_xgr_h, qh_xgr)
if inv_atm_key_dct:
brk_bnd_keys = [
frozenset(
{inv_atm_key_dct[atm_key], inv_atm_key_dct[h_atm_key]})
]
tra = from_data(frm_bnd_keys=[], brk_bnd_keys=brk_bnd_keys)
return tra
def _insertion(atmsA, neighsA, bndsA, atmsB, neighsB, xgr1, xgr2):
"""Do the insertion for an order of reactants
"""
for i in atmsA:
if _is_heavy(i, atmsA):
i_neighs = neighsA[i]
for j in i_neighs:
bnd_break_key_ij = _get_bnd_key(i, j, bndsA)
new_xgr = automol.graph.remove_bonds(xgr1, [bnd_break_key_ij])
for k in atmsB:
if _is_heavy(
k,
atmsB) and k != i and k != j and not i in neighsB[
k] and not j in neighsB[k]:
bnd_form_key_ik = {i, k}
bnd_form_key_jk = {j, k}
newnew_xgr = automol.graph.add_bonds(
new_xgr, [bnd_form_key_ik, bnd_form_key_jk])
atm_key_dct = _full_isomorphism(newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_ik, bnd_form_key_jk],
[bnd_break_key_ij]]
return tra
def _insertion(atmsa, neighsa, bndsa, atmsb, neighsb, xgr1, xgr2):
"""Do the insertion for an order of reactants
"""
ret_tra = None
for i in atmsa:
if _is_heavy(i, atmsa):
i_neighs = neighsa[i]
for j in i_neighs:
bnd_break_key_ij = _get_bnd_key(i, j, bndsa)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
for k in atmsb:
if _is_heavy(k, atmsb) and (k != i and k != j
and i not in neighsb[k]
and j not in neighsb[k]):
bnd_form_key_ik = {i, k}
bnd_form_key_jk = {j, k}
newnew_xgr = add_bonds(
new_xgr, [bnd_form_key_ik, bnd_form_key_jk])
atm_key_dct = _full_isomorphism(newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_ik, bnd_form_key_jk],
[bnd_break_key_ij]]
ret_tra = tra
return ret_tra
def elimination(xgr1, xgr2):
"""identifies elimination reactions
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
tras = []
if len(xgrs1) == 1 and len(xgrs2) == 2:
atms = atoms(xgr1)
neighs = atom_neighbor_keys(xgr1)
bnds = bond_keys(xgr1)
radicals = _resonance_dominant_radical_atom_keys(xgr1)
lonepairs = atom_lone_pair_counts(xgr1)
for atmi in atms:
i_neighs = neighs[atmi]
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bnds)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
new_xgrs = _connected_components(new_xgr)
if len(new_xgrs) == 2:
xgra, xgrb = new_xgrs
atmsa = atoms(xgra)
if atmi not in atmsa.keys():
xgrb, xgra = xgra, xgrb
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
atmsb = atoms(xgrb)
neighs_i = neighsa[atmi]
for atmk in atmsb:
if atmk in radicals:
for atml in neighs_i:
neighs_l = neighsa[atml]
if atml != atmj:
bnd_break_key_il = _get_bnd_key(
atmi, atml, bnds)
bnd_form_key_kl = frozenset({atmk, atml})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_il])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_kl])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_kl],
[
bnd_break_key_ij,
bnd_break_key_il
]]
return tra
for atmm in neighs_l:
if atmm != atmi:
bnd_break_key_lm = _get_bnd_key(
atml, atmm, bnds)
bnd_form_key_km = frozenset(
{atmk, atmm})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_lm])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_km])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tras.append([[bnd_form_key_km],
[
bnd_break_key_ij,
bnd_break_key_lm
]])
for atmi in atms:
i_neighs = neighs[atmi]
print('atmi test:', atmi)
print('i_neighs test:', i_neighs)
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bnds)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
new_xgrs = _connected_components(new_xgr)
if len(new_xgrs) == 2:
xgra, xgrb = new_xgrs
atmsa = atoms(xgra)
if atmi not in atmsa.keys():
xgrb, xgra = xgra, xgrb
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
atmsb = atoms(xgrb)
neighs_i = neighsa[atmi]
print('len atmsb test:', len(atmsb))
for atmk in atmsb:
if lonepairs[atmk] > 0 or len(atmsb) == 1:
# if lonepairs[atmk] > 0:
for atml in neighs_i:
neighs_l = neighsa[atml]
if atml != atmj:
bnd_break_key_il = _get_bnd_key(
atmi, atml, bnds)
bnd_form_key_kl = frozenset({atmk, atml})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_il])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_kl])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_kl],
[
bnd_break_key_ij,
bnd_break_key_il
]]
return tra
for atmm in neighs_l:
if atmm != atmi:
bnd_break_key_lm = _get_bnd_key(
atml, atmm, bnds)
bnd_form_key_km = frozenset(
{atmk, atmm})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_lm])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_km])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tras.append([[bnd_form_key_km],
[
bnd_break_key_ij,
bnd_break_key_lm
]])
if len(tras) < 1:
tras = None
return tras
def elimination(xgr1, xgr2):
"""identifies elimination reactions
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
tras = []
if len(xgrs1) == 1 and len(xgrs2) == 2:
atms = automol.graph.atoms(xgr1)
neighs = automol.graph.atom_neighbor_keys(xgr1)
bnds = automol.graph.bond_keys(xgr1)
lonepairs = automol.graph.atom_lone_pair_counts(xgr1)
for atmi in atms:
i_neighs = neighs[atmi]
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bnds)
new_xgr = automol.graph.remove_bonds(xgr1, [bnd_break_key_ij])
new_xgrs = _connected_components(new_xgr)
if len(new_xgrs) == 2:
xgrA, xgrB = new_xgrs
atmsA = automol.graph.atoms(xgrA)
if atmi not in atmsA.keys():
xgrB, xgrA = xgrA, xgrB
atmsA = automol.graph.atoms(xgrA)
neighsA = automol.graph.atom_neighbor_keys(xgrA)
atmsB = automol.graph.atoms(xgrB)
neighs_i = neighsA[atmi]
for atmk in atmsB:
if lonepairs[atmk] > 0:
for atml in neighs_i:
neighs_l = neighsA[atml]
if atml != atmj:
bnd_break_key_il = _get_bnd_key(
atmi, atml, bnds)
bnd_form_key_kl = frozenset({atmk, atml})
newnew_xgr = automol.graph.remove_bonds(
new_xgr, [bnd_break_key_il])
newnew_xgr = automol.graph.add_bonds(
newnew_xgr, [bnd_form_key_kl])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_kl],
[
bnd_break_key_ij,
bnd_break_key_il
]]
return tra
for atmm in neighs_l:
if atmm != atmi:
bnd_break_key_lm = _get_bnd_key(
atml, atmm, bnds)
bnd_form_key_km = frozenset(
{atmk, atmm})
newnew_xgr = automol.graph.remove_bonds(
new_xgr, [bnd_break_key_lm])
newnew_xgr = automol.graph.add_bonds(
newnew_xgr, [bnd_form_key_km])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tras.append([[bnd_form_key_km],
[
bnd_break_key_ij,
bnd_break_key_lm
]])
if len(tras) < 1:
tras = None
return tras
