def hydrogen_abstraction(xgr1, xgr2):
""" find an addition transformation
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
ret = formula.reac.argsort_hydrogen_abstraction(
list(map(convert.graph.formula, xgrs1)),
list(map(convert.graph.formula, xgrs2)))
if ret is not None:
idxs1, idxs2 = ret
q1h_xgr, q2_xgr = list(map(xgrs1.__getitem__, idxs1))
q1_xgr, q2h_xgr = list(map(xgrs2.__getitem__, idxs2))
q1_tra = _partial_hydrogen_abstraction(q1h_xgr, q1_xgr)
q2_rev_tra = _partial_hydrogen_abstraction(q2h_xgr, q2_xgr)
if q1_tra and q2_rev_tra:
xgr1_ = _union(apply(q1_tra, q1h_xgr), q2_xgr)
xgr2_ = _union(q1_xgr, q2h_xgr)
q2_tra = _reverse(q2_rev_tra, xgr2_, xgr1_)
tra = from_data('hydrogen abstraction',
frm_bnd_keys=formed_bond_keys(q2_tra),
brk_bnd_keys=broken_bond_keys(q1_tra))
return tra
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 insertion(xgr1, xgr2):
""" find an insertion transformation
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
idxs = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
if len(xgrs1) == 2 and len(xgrs2) == 1:
xgra, xgrb = xgrs1
atmsa = atoms(xgra)
atmsb = atoms(xgrb)
neighsa = atom_neighbor_keys(xgra)
neighsb = atom_neighbor_keys(xgrb)
bndsa = bond_keys(xgra)
bndsb = bond_keys(xgrb)
tra = _insertion(atmsa, neighsa, bndsa, atmsb, neighsb, xgr1, xgr2)
idxs = [0, 1]
if not tra:
tra = _insertion(atmsb, neighsb, bndsb, atmsa, neighsa, xgr1, xgr2)
if tra:
idxs = [1, 0]
else:
idxs = None
elif len(xgrs1) == 1 and len(xgrs2) == 1:
xgra = xgr1
idxs = [0]
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
bndsa = bond_keys(xgra)
tra = _insertion(atmsa, neighsa, bndsa, atmsa, neighsa, xgr1, xgr2)
return tra, idxs
def insertion(xgr1, xgr2):
""" find an insertion transformation
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
idxs = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
if len(xgrs1) == 2 and len(xgrs2) == 1:
xgrA, xgrB = xgrs1
atmsA = automol.graph.atoms(xgrA)
atmsB = automol.graph.atoms(xgrB)
neighsA = automol.graph.atom_neighbor_keys(xgrA)
neighsB = automol.graph.atom_neighbor_keys(xgrB)
bndsA = automol.graph.bond_keys(xgrA)
bndsB = automol.graph.bond_keys(xgrB)
tra = _insertion(atmsA, neighsA, bndsA, atmsB, neighsB, xgr1, xgr2)
idxs = [0, 1]
if not tra:
tra = _insertion(atmsB, neighsB, bndsB, atmsA, neighsA, xgr1, xgr2)
if tra:
idxs = [1, 0]
else:
idxs = None
elif len(xgrs1) == 1 and len(xgrs2) == 1:
xgrA = xgr1
idxs = [0]
atmsA = automol.graph.atoms(xgrA)
neighsA = automol.graph.atom_neighbor_keys(xgrA)
bndsA = automol.graph.bond_keys(xgrA)
tra = _insertion(atmsA, neighsA, bndsA, atmsA, neighsA, xgr1, xgr2)
return tra, idxs
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 substitution(xgr1, xgr2):
"""identifies substitution reactions
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
idxs = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
print('len xgrs test:', len(xgrs1), len(xgrs2))
print('xgrs test:', xgrs1, xgrs2)
if len(xgrs1) == 2 and len(xgrs2) == 2:
xgra, xgrb = xgrs1
xgrc, xgrd = xgrs2
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
bndsa = bond_keys(xgra)
atmsb = atoms(xgrb)
neighsb = atom_neighbor_keys(xgrb)
bndsb = bond_keys(xgrb)
atmsc = atoms(xgrc)
neighsc = atom_neighbor_keys(xgrc)
bndsc = bond_keys(xgrc)
atmsd = atoms(xgrd)
neighsd = atom_neighbor_keys(xgrd)
bndsd = bond_keys(xgrd)
tra = _substitution(atmsa, neighsa, bndsa, atmsb, xgr1, xgr2)
# tra = _substitution(
# atmsa, neighsa, bndsa, atmsb, neighsb, xgr1, xgr2)
idxs = [[0, 1], [0, 1]]
if not tra:
tra = _substitution(atmsb, neighsb, bndsb, atmsa, xgr1, xgr2)
# atmsb, neighsb, bndsb, atmsa, neighsa, xgr1, xgr2)
idxs = [[0, 1], [1, 0]]
if not tra:
tra = _substitution(atmsc, neighsc, bndsc, atmsd, xgr2, xgr1)
# atmsc, neighsc, bndsc, atmsd, neighsd, xgr2, xgr1)
idxs = [[1, 0], [0, 1]]
if not tra:
tra = _substitution(atmsd, neighsd, bndsd, atmsc, xgr2,
xgr1)
# atmsd, neighsd, bndsd, atmsc, neighsc, xgr2, xgr1)
idxs = [[1, 0], [1, 0]]
if not tra:
idxs = None
# return not substitution for radical + unsaturated reactions
unsat_atm_keys = _unsaturated_atom_keys(xgra)
# print('unsat test:', tra[0][0], unsat_atm_keys)
tra_list = list(tra[0])
for key in unsat_atm_keys:
if key in tra_list[0]:
pass
# tra = None
# commented out the tra = None and added pass to run CO + HO2
return tra, idxs
def substitution(xgr1, xgr2):
"""identifies substitution reactions
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
idxs = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
if len(xgrs1) == 2 and len(xgrs2) == 2:
xgrA, xgrB = xgrs1
xgrC, xgrD = xgrs2
atmsA = automol.graph.atoms(xgrA)
neighsA = automol.graph.atom_neighbor_keys(xgrA)
bndsA = automol.graph.bond_keys(xgrA)
atmsB = automol.graph.atoms(xgrB)
neighsB = automol.graph.atom_neighbor_keys(xgrB)
bndsB = automol.graph.bond_keys(xgrB)
atmsC = automol.graph.atoms(xgrC)
neighsC = automol.graph.atom_neighbor_keys(xgrC)
bndsC = automol.graph.bond_keys(xgrC)
atmsD = automol.graph.atoms(xgrD)
neighsD = automol.graph.atom_neighbor_keys(xgrD)
bndsD = automol.graph.bond_keys(xgrD)
tra = _substitution(atmsA, neighsA, bndsA, atmsB, neighsB, xgr1, xgr2)
idxs = [[0, 1], [0, 1]]
if not tra:
tra = _substitution(atmsB, neighsB, bndsB, atmsA, neighsA, xgr1,
xgr2)
idxs = [[0, 1], [1, 0]]
if not tra:
tra = _substitution(atmsC, neighsC, bndsC, atmsD, neighsD,
xgr2, xgr1)
idxs = [[1, 0], [0, 1]]
if not tra:
tra = _substitution(atmsD, neighsD, bndsD, atmsC, neighsC,
xgr2, xgr1)
idxs = [[1, 0], [1, 0]]
if not tra:
idxs = None
# return not substitution for radical + unsaturated reactions
unsat_atm_keys = automol.graph.unsaturated_atom_keys(xgrB)
for key in unsat_atm_keys:
if key in tra[0]:
tra = None
return tra, idxs
def _atom_coordinates(sgr):
""" non-stereo-specific coordinates for a molecular graph
"""
atm_xyz_dct = {}
for idx, cnn_sgr in enumerate(_connected_components(sgr)):
shift = 20. * idx
cnn_atm_xyz_dct = _connected_graph_atom_coordinates(cnn_sgr)
atm_keys = list(cnn_atm_xyz_dct.keys())
atm_xyzs = numpy.array(list(cnn_atm_xyz_dct.values()))
atm_xyzs += numpy.array([0., 0., shift])
atm_xyz_dct.update(dict(zip(atm_keys, map(tuple, atm_xyzs))))
return atm_xyz_dct
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