def substitutions(rct_gras, prd_gras):
""" find substitutions consistent with these reactants and products
:param rct_gras: reactant graphs (must have non-overlapping keys)
:param prd_gras: product graphs (must have non-overlapping keys)
Substitutions are identified by breaking one bond in the reactants and one
bond from the products and checking for isomorphism.
"""
_assert_is_valid_reagent_graph_list(rct_gras)
_assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 2 and len(prd_gras) == 2:
rct_gra = union_from_sequence(rct_gras)
prd_gra = union_from_sequence(prd_gras)
for rgra1, rgra2 in itertools.permutations(rct_gras):
bnd_keys = bond_keys(rgra1)
rad_keys = unsaturated_atom_keys(rgra2)
for bnd_key, rad_key in itertools.product(bnd_keys, rad_keys):
gra = remove_bonds(rct_gra, [bnd_key])
for brk_key1 in bnd_key:
gra = add_bonds(gra, [(brk_key1, rad_key)])
inv_dct = isomorphism(gra, prd_gra)
if inv_dct:
brk_key2, = bnd_key - {brk_key1}
f_frm_bnd_key = (brk_key1, rad_key)
f_brk_bnd_key = (brk_key1, brk_key2)
b_frm_bnd_key = (inv_dct[brk_key1], inv_dct[brk_key2])
b_brk_bnd_key = (inv_dct[brk_key1], inv_dct[rad_key])
forw_tsg = ts.graph(rct_gra,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[f_brk_bnd_key])
back_tsg = ts.graph(prd_gra,
frm_bnd_keys=[b_frm_bnd_key],
brk_bnd_keys=[b_brk_bnd_key])
rcts_atm_keys = [atom_keys(rgra1), atom_keys(rgra2)]
prds_atm_keys = list(map(atom_keys, prd_gras))
if inv_dct[rad_key] not in prds_atm_keys[0]:
prds_atm_keys = list(reversed(prds_atm_keys))
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.SUBSTITUTION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=rcts_atm_keys,
prds_keys=prds_atm_keys,
))
return ts_unique(rxns)
def trivial(rct_gras, prd_gras):
""" find a trivial reaction, with the same reactants and products
"""
_assert_is_valid_reagent_graph_list(rct_gras)
_assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == len(prd_gras):
prd_gras = list(prd_gras)
rct_idxs = []
prd_idxs = []
# One at a time, find matches for each reactant; track the positions to
# get the right sort order
for rct_idx, rct_gra in enumerate(rct_gras):
prd_idx = next((idx for idx, prd_gra in enumerate(prd_gras)
if isomorphism(rct_gra, prd_gra)), None)
if prd_idx is not None:
rct_idxs.append(rct_idx)
prd_idxs.append(prd_idx)
prd_gras.pop(prd_idx)
else:
break
if rct_idxs and prd_idxs:
# reorder the reactants and products
rct_gras = list(map(rct_gras.__getitem__, rct_idxs))
prd_gras = list(map(prd_gras.__getitem__, prd_idxs))
rcts_gra = union_from_sequence(rct_gras)
prds_gra = union_from_sequence(prd_gras)
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.TRIVIAL,
forw_tsg=ts.graph(rcts_gra, [], []),
back_tsg=ts.graph(prds_gra, [], []),
rcts_keys=list(map(atom_keys, rct_gras)),
prds_keys=list(map(atom_keys, prd_gras)),
))
return tuple(rxns)
def ring_forming_scissions(rct_gras, prd_gras):
""" find ring-forming scissions consistent with these reactants and products
:param rct_gras: reactant graphs (must have non-overlapping keys)
:param prd_gras: product graphs (must have non-overlapping keys)
Ring-forming scissions are found by breaking ring-bonds on one product and
joining the ends to unsaturated sites on the other product
"""
_assert_is_valid_reagent_graph_list(rct_gras)
_assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 1 and len(prd_gras) == 2:
rgra, = rct_gras
pgra = union_from_sequence(prd_gras)
for pgra1, pgra2 in itertools.permutations(prd_gras):
bnd_keys = list(itertools.chain(*rings_bond_keys(pgra1)))
atm_keys = unsaturated_atom_keys(pgra2)
for bnd_key, atm_key in itertools.product(bnd_keys, atm_keys):
# Break a ring bond
gra = remove_bonds(pgra, [bnd_key])
for end_key in bnd_key:
# Add to one end of the broken ring
fgra = add_bonds(gra, [(atm_key, end_key)])
inv_dct = isomorphism(fgra, rgra)
if inv_dct:
other_end_key, = bnd_key - {end_key}
f_frm_bnd_key = (inv_dct[end_key],
inv_dct[other_end_key])
f_brk_bnd_key = (inv_dct[end_key], inv_dct[atm_key])
b_frm_bnd_key = (end_key, atm_key)
b_brk_bnd_key = (end_key, other_end_key)
forw_tsg = ts.graph(rgra,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[f_brk_bnd_key])
back_tsg = ts.graph(pgra,
frm_bnd_keys=[b_frm_bnd_key],
brk_bnd_keys=[b_brk_bnd_key])
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.RING_FORM_SCISSION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=[atom_keys(rgra)],
prds_keys=[atom_keys(pgra1),
atom_keys(pgra2)],
))
return ts_unique(rxns)
def additions(rct_gras, prd_gras):
""" find additions consistent with these reactants and products
:param rct_gras: reactant graphs (must have non-overlapping keys)
:param prd_gras: product graphs (must have non-overlapping keys)
Additions are identified by joining an unsaturated site on one reactant to
an unsaturated site on the other. If the result matches the products, this
is an addition reaction.
"""
_assert_is_valid_reagent_graph_list(rct_gras)
_assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 2 and len(prd_gras) == 1:
x_gra, y_gra = rct_gras
prd_gra, = prd_gras
x_atm_keys = unsaturated_atom_keys(x_gra)
y_atm_keys = unsaturated_atom_keys(y_gra)
for x_atm_key, y_atm_key in itertools.product(x_atm_keys, y_atm_keys):
xy_gra = add_bonds(union(x_gra, y_gra), [{x_atm_key, y_atm_key}])
iso_dct = isomorphism(xy_gra, prd_gra)
if iso_dct:
rcts_gra = union_from_sequence(rct_gras)
prds_gra = prd_gra
f_frm_bnd_key = (x_atm_key, y_atm_key)
b_brk_bnd_key = (iso_dct[x_atm_key], iso_dct[y_atm_key])
forw_tsg = ts.graph(rcts_gra,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[])
back_tsg = ts.graph(prds_gra,
frm_bnd_keys=[],
brk_bnd_keys=[b_brk_bnd_key])
# sort the reactants so that the largest species is first
rct_idxs = _argsort_reactants(rct_gras)
rct_gras = list(map(rct_gras.__getitem__, rct_idxs))
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.ADDITION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=list(map(atom_keys, rct_gras)),
prds_keys=list(map(atom_keys, prd_gras)),
))
return ts_unique(rxns)
def hydrogen_abstractions(rct_gras, prd_gras):
""" find hydrogen abstractions consistent with these reactants and products
:param rct_gras: reactant graphs (must have non-overlapping keys)
:param prd_gras: product graphs (must have non-overlapping keys)
Hydrogen abstractions are identified first by checking whether the
molecular formulas are consistent with a reaction of the form R1H + R2 =>
R2H + R1. If they do, we identify the abstraction sites by adding hydrogens
to unsaturated sites of the R1 product to see if we get the R1H reactant.
We then do the same for the R2 reactant and the R2H product.
"""
_assert_is_valid_reagent_graph_list(rct_gras)
_assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 2 and len(prd_gras) == 2:
rct_fmls = list(map(graph_formula, rct_gras))
prd_fmls = list(map(graph_formula, prd_gras))
ret = automol.formula.reac.argsort_hydrogen_abstraction(
rct_fmls, prd_fmls)
if ret:
rct_idxs_, prd_idxs_ = ret
rct_gras = list(map(rct_gras.__getitem__, rct_idxs_))
prd_gras = list(map(prd_gras.__getitem__, prd_idxs_))
q1h_gra, q2_gra = rct_gras
q2h_gra, q1_gra = prd_gras
rets1 = _partial_hydrogen_abstraction(q1h_gra, q1_gra)
rets2 = _partial_hydrogen_abstraction(q2h_gra, q2_gra)
for ret1, ret2 in itertools.product(rets1, rets2):
f_q1h_q_atm_key, f_q1h_h_atm_key, b_q2_q_atm_key = ret1
b_q1h_q_atm_key, b_q1h_h_atm_key, f_q2_q_atm_key = ret2
# Create the forward/backward ts graphs
rcts_gra = union_from_sequence(rct_gras)
prds_gra = union_from_sequence(prd_gras)
f_frm_bnd_key = (f_q2_q_atm_key, f_q1h_h_atm_key)
f_brk_bnd_key = (f_q1h_q_atm_key, f_q1h_h_atm_key)
b_frm_bnd_key = (b_q2_q_atm_key, b_q1h_h_atm_key)
b_brk_bnd_key = (b_q1h_q_atm_key, b_q1h_h_atm_key)
forw_tsg = ts.graph(rcts_gra,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[f_brk_bnd_key])
back_tsg = ts.graph(prds_gra,
frm_bnd_keys=[b_frm_bnd_key],
brk_bnd_keys=[b_brk_bnd_key])
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.HYDROGEN_ABSTRACTION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=list(map(atom_keys, rct_gras)),
prds_keys=list(map(atom_keys, prd_gras)),
))
return ts_unique(rxns)
def eliminations(rct_gras, prd_gras):
""" find eliminations consistent with these reactants and products
:param rct_gras: reactant graphs (must have non-overlapping keys)
:param prd_gras: product graphs (must have non-overlapping keys)
Eliminations are identified by forming a bond between an attacking heavy
atom and another atom not initially bonded to it, forming a ring. The bond
adjacent to the attacked atom is then broken, along with a second bond in
the ring, downstream of the attacking heavy atom, away from the attacked
atom.
"""
_assert_is_valid_reagent_graph_list(rct_gras)
_assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 1 and len(prd_gras) == 2:
rct_gra, = rct_gras
prds_gra = union_from_sequence(prd_gras)
ngb_keys_dct = atoms_neighbor_atom_keys(rct_gra)
frm1_keys = atom_keys(rct_gra, excl_syms=('H', ))
frm2_keys = atom_keys(rct_gra)
bnd_keys = bond_keys(rct_gra)
frm_bnd_keys = [
(frm1_key, frm2_key)
for frm1_key, frm2_key in itertools.product(frm1_keys, frm2_keys)
if frm1_key != frm2_key
and not frozenset({frm1_key, frm2_key}) in bnd_keys
]
for frm1_key, frm2_key in frm_bnd_keys:
# Bond the radical atom to the hydrogen atom
gra_ = add_bonds(rct_gra, [(frm2_key, frm1_key)])
# Get keys to the ring formed by this extra bond
rng_keys = next((ks for ks in rings_atom_keys(gra_)
if frm2_key in ks and frm1_key in ks), None)
# Eliminations (as far as I can tell) only happen through TSs with
# 3- or 4-membered rings
if rng_keys is not None and len(rng_keys) < 5:
frm1_ngb_key, = ngb_keys_dct[frm1_key] & set(rng_keys)
frm2_ngb_key, = ngb_keys_dct[frm2_key] & set(rng_keys)
# Break the bonds on either side of the newly formed bond
gra_ = remove_bonds(gra_, [(frm1_key, frm1_ngb_key)])
gra_ = remove_bonds(gra_, [(frm2_key, frm2_ngb_key)])
inv_dct = isomorphism(gra_, prds_gra)
if inv_dct:
f_frm_bnd_key = (frm1_key, frm2_key)
f_brk_bnd_key1 = (frm1_key, frm1_ngb_key)
f_brk_bnd_key2 = (frm2_key, frm2_ngb_key)
inv_ = inv_dct.__getitem__
b_frm_bnd_key1 = tuple(map(inv_, f_brk_bnd_key1))
b_frm_bnd_key2 = tuple(map(inv_, f_brk_bnd_key2))
b_brk_bnd_key = tuple(map(inv_, f_frm_bnd_key))
forw_tsg = ts.graph(
rct_gra,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[f_brk_bnd_key1, f_brk_bnd_key2])
back_tsg = ts.graph(
prds_gra,
frm_bnd_keys=[b_frm_bnd_key1, b_frm_bnd_key2],
brk_bnd_keys=[b_brk_bnd_key])
rcts_atm_keys = list(map(atom_keys, rct_gras))
prds_atm_keys = list(map(atom_keys, prd_gras))
if inv_dct[frm2_key] not in prds_atm_keys[1]:
prds_atm_keys = list(reversed(prds_atm_keys))
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.ELIMINATION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=rcts_atm_keys,
prds_keys=prds_atm_keys,
))
return ts_unique(rxns)
def substitutions(rct_gras, prd_gras):
""" find substitutions consistent with these reactants and products
:param rct_gras: reactant graphs (must have non-overlapping keys)
:param prd_gras: product graphs (must have non-overlapping keys)
Substitutions are identified by breaking one bond in the reactants and one
bond from the products and checking for isomorphism.
Currently it assumes that one of the reactants has a radical site that
can attack the other reactants, forming a bond and breaking another.
From the perspective of breaking and forming breaking bonds, substitutions
are equivalent with hydrogen abstractions. Hence, we remove all cases where
the forming bond involves a hydrogen atom off the reactant in which a bond
is breaking.
"""
assert_is_valid_reagent_graph_list(rct_gras)
assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 2 and len(prd_gras) == 2:
rct_gra = union_from_sequence(rct_gras)
prd_gra = union_from_sequence(prd_gras)
# Loop over both orders of reactants: A+B and B+A
for rgra1, rgra2 in itertools.permutations(rct_gras):
bnd_keys = bond_keys(rgra1)
atom_symb_dct = automol.graph.atom_symbols(rgra1)
rad_keys = unsaturated_atom_keys(rgra2)
# Break all possible bonds in total reactant
for bnd_key, rad_key in itertools.product(bnd_keys, rad_keys):
gra = remove_bonds(rct_gra, [bnd_key])
# Form all possible bonds between rad site and non-H atoms
frm_keys = ()
for key in bnd_key:
frm_symb = atom_symb_dct[key]
if frm_symb != 'H':
frm_keys += (key, )
for frm_key in frm_keys:
gra = add_bonds(gra, [(frm_key, rad_key)])
inv_dct = isomorphism(gra, prd_gra)
if inv_dct:
brk_key2, = bnd_key - {frm_key}
f_frm_bnd_key = (frm_key, rad_key)
f_brk_bnd_key = (frm_key, brk_key2)
b_frm_bnd_key = (inv_dct[frm_key], inv_dct[brk_key2])
b_brk_bnd_key = (inv_dct[frm_key], inv_dct[rad_key])
forw_tsg = ts.graph(rct_gra,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[f_brk_bnd_key])
back_tsg = ts.graph(prd_gra,
frm_bnd_keys=[b_frm_bnd_key],
brk_bnd_keys=[b_brk_bnd_key])
rcts_atm_keys = [atom_keys(rgra1), atom_keys(rgra2)]
prds_atm_keys = list(map(atom_keys, prd_gras))
if inv_dct[rad_key] not in prds_atm_keys[0]:
prds_atm_keys = list(reversed(prds_atm_keys))
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=ReactionClass.Typ.SUBSTITUTION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=rcts_atm_keys,
prds_keys=prds_atm_keys,
))
return ts_unique(rxns)
def two_bond_additions(rct_gras, prd_gras):
""" two bond additions
"""
assert_is_valid_reagent_graph_list(rct_gras)
assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 2 and len(prd_gras) == 1:
rct_gras = sort_reagents(rct_gras)
x_gra, y_gra = rct_gras
prd_gra, = prd_gras
x_atm_keys = frozenset().union(unsaturated_atom_keys(x_gra),
lone_pair_atom_keys(x_gra))
y_atm_keys = frozenset().union(unsaturated_atom_keys(y_gra),
lone_pair_atom_keys(y_gra))
print('x,y keys', x_atm_keys, y_atm_keys)
# Generate pairs of forming bonds, where each is a pair of idxs
# describing the atoms making up the forming bond:
# (frm1, frm2) = ((idx1, idx2), (idx1, idx2))
frm_bnd_pairs = tuple(itertools.product(x_atm_keys, y_atm_keys))
frm_bnds_lst = ()
for pair in itertools.product(frm_bnd_pairs, frm_bnd_pairs):
# Preclude pairs with same idxs (formind same bond twice)
if pair[0] != pair[1]:
# Preclude multiple bonds formed to same atom X---A---Y
if pair[0][0] != pair[1][0] and pair[0][1] != pair[1][1]:
# Preclude the reverse
if pair[::-1] not in frm_bnds_lst:
frm_bnds_lst += (pair, )
for frm_bnd_keys in frm_bnds_lst:
xy_gra = add_bonds(union(x_gra, y_gra),
[set(frm_bnd_keys[0]),
set(frm_bnd_keys[1])])
iso_dct = isomorphism(xy_gra, prd_gra)
if iso_dct:
rcts_gra = union_from_sequence(rct_gras)
prds_gra = prd_gra
b_brk_bnd_keys = [[
iso_dct[frm_bnd_keys[0][0]], iso_dct[frm_bnd_keys[0][1]]
], [iso_dct[frm_bnd_keys[1][0]], iso_dct[frm_bnd_keys[1][1]]]]
forw_tsg = ts.graph(rcts_gra,
frm_bnd_keys=frm_bnd_keys,
brk_bnd_keys=[])
back_tsg = ts.graph(prds_gra,
frm_bnd_keys=[],
brk_bnd_keys=b_brk_bnd_keys)
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=ReactionClass.Typ.ADDITION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=list(map(atom_keys, rct_gras)),
prds_keys=list(map(atom_keys, prd_gras)),
))
return ts_unique(rxns)
def eliminations(rct_gras, prd_gras):
""" find eliminations consistent with these reactants and products
:param rct_gras: reactant graphs (must have non-overlapping keys)
:param prd_gras: product graphs (must have non-overlapping keys)
Eliminations are identified by forming a bond between an attacking heavy
atom and another atom not initially bonded to it, forming a ring. The bond
adjacent to the attacked atom is then broken, along with a second bond in
the ring, downstream of the attacking heavy atom, away from the attacked
atom.
"""
def _identify(frm1_keys, frm2_keys, bnd_keys):
""" Try and identify elmination from some set of keys
"""
_rxns = []
frm_bnd_keys = [
(frm1_key, frm2_key)
for frm1_key, frm2_key in itertools.product(frm1_keys, frm2_keys)
if frm1_key != frm2_key
and not frozenset({frm1_key, frm2_key}) in bnd_keys
]
for frm1_key, frm2_key in frm_bnd_keys:
prds_gra_ = add_bonds(rct_gra, [(frm2_key, frm1_key)])
# Get keys of all bonds in the ring formed by this extra bond
rng_bnd_keys = next((ks for ks in rings_bond_keys(prds_gra_)
if frozenset({frm1_key, frm2_key}) in ks),
None)
if rng_bnd_keys is not None:
# Elims break two bonds of the ring formed by the forming bond
# Loop over all ring bond-pairs, break bonds, see if prods form
# Ensure to preclude the forming-bond from this set
brk_bnds = tuple(
bond for bond in itertools.combinations(rng_bnd_keys, 2)
if frozenset({frm1_key, frm2_key}) not in bond)
for brk_bnd_1, brk_bnd_2 in brk_bnds:
prds_gra_2_ = prds_gra_
prds_gra_2_ = remove_bonds(prds_gra_2_, [brk_bnd_1])
prds_gra_2_ = remove_bonds(prds_gra_2_, [brk_bnd_2])
inv_dct = isomorphism(prds_gra_2_, prds_gra)
if inv_dct:
f_frm_bnd_key = (frm1_key, frm2_key)
inv_ = inv_dct.__getitem__
b_frm_bnd_key1 = tuple(map(inv_, brk_bnd_1))
b_frm_bnd_key2 = tuple(map(inv_, brk_bnd_2))
b_brk_bnd_key = tuple(map(inv_, f_frm_bnd_key))
forw_tsg = ts.graph(
rct_gra,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[brk_bnd_1, brk_bnd_2])
back_tsg = ts.graph(
prds_gra,
frm_bnd_keys=[b_frm_bnd_key1, b_frm_bnd_key2],
brk_bnd_keys=[b_brk_bnd_key])
rcts_atm_keys = list(map(atom_keys, rct_gras))
prds_atm_keys = list(map(atom_keys, prd_gras))
if inv_dct[frm1_key] not in prds_atm_keys[1]:
prds_atm_keys = list(reversed(prds_atm_keys))
assert inv_dct[frm1_key] in prds_atm_keys[1]
assert inv_dct[frm2_key] in prds_atm_keys[1]
# Create the reaction object
_rxns.append(
Reaction(
rxn_cls=ReactionClass.Typ.ELIMINATION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=rcts_atm_keys,
prds_keys=prds_atm_keys,
))
return _rxns
assert_is_valid_reagent_graph_list(rct_gras)
assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 1 and len(prd_gras) == 2:
rct_gra, = rct_gras
prds_gra = union_from_sequence(prd_gras)
# ngb_keys_dct = atoms_neighbor_atom_keys(rct_gra)
# Generate keys all bonds and 1/2 the forming bond
frm1_keys = atom_keys(rct_gra)
bnd_keys = bond_keys(rct_gra)
frm2_keys = unsaturated_atom_keys(rct_gra)
rct_symbs = atom_symbols(rct_gra)
frm2_keys_o = frozenset(key for key in frm2_keys
if rct_symbs[key] == 'O')
rxns.extend(_identify(frm1_keys, frm2_keys_o, bnd_keys))
# OLD WAY. More IDs but more mistakes
# To make the function general, try to ID reaction
# with different types of keys for the attacking atom
# (1) unsaturated atom sites
# frm2_keys = unsaturated_atom_keys(rct_gra)
# rxns.extend(_identify(frm1_keys, frm2_keys, bnd_keys))
# if not rxns:
# # (2) remaining saturated atom sites
# frm2_keys = atom_keys(rct_gra, excl_syms=('H',)) - frm2_keys
# rxns.extend(_identify(frm1_keys, frm2_keys, bnd_keys))
# # if not rxns: # Ignoring H2 formation for now for speed
# # # (3) H atoms
# # frm1_keys = atom_keys(rct_gra, sym='H')
# # rxns.extend(_identify(frm1_keys, frm2_keys, bnd_keys))
return ts_unique(rxns)
def eliminations(rct_gras, prd_gras):
""" find eliminations consistent with these reactants and products
:param rct_gras: reactant graphs (must have non-overlapping keys)
:param prd_gras: product graphs (must have non-overlapping keys)
Eliminations are identified by forming a bond between an attacking heavy
atom and another atom not initially bonded to it, forming a ring. The bond
adjacent to the attacked atom is then broken, along with a second bond in
the ring, downstream of the attacking heavy atom, away from the attacked
atom.
"""
_assert_is_valid_reagent_graph_list(rct_gras)
_assert_is_valid_reagent_graph_list(prd_gras)
rxns = []
if len(rct_gras) == 1 and len(prd_gras) == 2:
rgra, = rct_gras
pgra = union_from_sequence(prd_gras)
rngb_keys = atoms_sorted_neighbor_atom_keys(rgra)
frm1_keys = atom_keys(rgra, excl_syms=('H', ))
frm2_keys = atom_keys(rgra)
bnd_keys = bond_keys(rgra)
frm_bnd_keys = [
(frm1_key, frm2_key)
for frm1_key, frm2_key in itertools.product(frm1_keys, frm2_keys)
if frm1_key != frm2_key
and not frozenset({frm1_key, frm2_key}) in bnd_keys
]
for frm1_key, frm2_key in frm_bnd_keys:
# Bond the radical atom to the hydrogen atom
rgra_ = add_bonds(rgra, [(frm2_key, frm1_key)])
# Get keys to the ring formed by this extra bond
rng_keys = next((ks for ks in rings_atom_keys(rgra_)
if frm2_key in ks and frm1_key in ks), None)
if rng_keys is not None:
for nfrm2_key in rngb_keys[frm2_key]:
# Break the bond between the attacked atom and its neighbor
rgra_ = remove_bonds(rgra_, [(frm2_key, nfrm2_key)])
# Sort the ring keys so that they start with the radical
# atom and end with the hydrogen atom
keys = cycle_ring_atom_key_to_front(rng_keys,
frm1_key,
end_key=frm2_key)
# Break one ring bond at a time, starting from the rind,
# and see what we get
for brk_key1, brk_key2 in mit.windowed(keys[:-1], 2):
gra = remove_bonds(rgra_, [(brk_key1, brk_key2)])
inv_dct = full_isomorphism(gra, pgra)
if inv_dct:
f_frm_bnd_key = (frm2_key, frm1_key)
f_brk_bnd_key1 = (frm2_key, nfrm2_key)
f_brk_bnd_key2 = (brk_key1, brk_key2)
b_frm_bnd_key1 = (inv_dct[frm2_key],
inv_dct[nfrm2_key])
b_frm_bnd_key2 = (inv_dct[brk_key1],
inv_dct[brk_key2])
b_brk_bnd_key = (inv_dct[frm2_key],
inv_dct[frm1_key])
forw_tsg = ts.graph(
rgra,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[f_brk_bnd_key1, f_brk_bnd_key2])
back_tsg = ts.graph(
pgra,
frm_bnd_keys=[b_frm_bnd_key1, b_frm_bnd_key2],
brk_bnd_keys=[b_brk_bnd_key])
rcts_atm_keys = list(map(atom_keys, rct_gras))
prds_atm_keys = list(map(atom_keys, prd_gras))
if inv_dct[frm2_key] not in prds_atm_keys[1]:
prds_atm_keys = list(reversed(prds_atm_keys))
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.ELIMINATION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=rcts_atm_keys,
prds_keys=prds_atm_keys,
))
return tuple(rxns)
def test__reac__hydrogen_migration():
""" test graph.reac.hydrogen_migration
"""
# first test a radical site migration
rct_cgr = ({
0: ('C', 1, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('C', 1, None),
5: ('O', 0, None)
}, {
frozenset({3, 4}): (1, None),
frozenset({2, 3}): (1, None),
frozenset({1, 2}): (1, None),
frozenset({4, 5}): (1, None),
frozenset({0, 1}): (1, None)
})
prd_cgr = ({
0: ('C', 2, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('C', 0, None),
5: ('O', 0, None)
}, {
frozenset({3, 4}): (1, None),
frozenset({2, 3}): (1, None),
frozenset({1, 2}): (1, None),
frozenset({4, 5}): (1, None),
frozenset({0, 1}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_migration(
rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
print("hydrogen migration")
rct_cgr = graph.union_from_sequence(rct_cgrs)
prd_cgr = graph.union_from_sequence(prd_cgrs)
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_migration(
prd_cgrs, rct_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
# then test a tautomerization
rct_cgr = ({
0: ('C', 2, None),
1: ('C', 1, None),
2: ('O', 1, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({1, 2}): (1, None)
})
prd_cgr = ({
0: ('C', 3, None),
1: ('C', 1, None),
2: ('O', 0, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({1, 2}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_migration(
rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_migration(
prd_cgrs, rct_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
def test__reac__hydrogen_abstraction():
""" test graph.reac.hydrogen_abstraction
"""
rct_cgr = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('C', 1, None),
3: ('C', 2, None),
4: ('C', 1, None),
5: ('C', 2, None),
6: ('C', 2, None),
7: ('O', 1, None)
}, {
frozenset({4, 6}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
prd_cgr = ({
0: ('C', 2, None),
1: ('C', 3, None),
2: ('C', 1, None),
3: ('C', 2, None),
4: ('C', 1, None),
5: ('C', 2, None),
6: ('C', 2, None),
7: ('O', 2, None)
}, {
frozenset({4, 6}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_abstraction(
rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
print("hydrogen abstraction")
rct_cgr = graph.union_from_sequence(rct_cgrs)
print(rct_cgr)
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
tras, prd_idxs, rct_idxs = graph.reac.hydrogen_abstraction(
prd_cgrs, rct_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, prd_cgr),
rct_cgr)
