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 = full_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 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 = full_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 tuple(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 = full_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 tuple(rxns)
def _partial_hydrogen_abstraction(qh_gra, q_gra):
rets = []
h_atm_key = max(atom_keys(q_gra)) + 1
uns_atm_keys = unsaturated_atom_keys(q_gra)
for atm_key in uns_atm_keys:
q_gra_h = add_atom_explicit_hydrogen_keys(q_gra,
{atm_key: [h_atm_key]})
inv_atm_key_dct = full_isomorphism(q_gra_h, qh_gra)
if inv_atm_key_dct:
qh_q_atm_key = inv_atm_key_dct[atm_key]
qh_h_atm_key = inv_atm_key_dct[h_atm_key]
q_q_atm_key = atm_key
rets.append((qh_q_atm_key, qh_h_atm_key, q_q_atm_key))
return rets
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 full_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 hydrogen_migrations(rct_gras, prd_gras):
""" find hydrogen migrations 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 migrations are identified by adding a hydrogen to an unsaturated
site of the reactant and adding a hydrogen to an unsaturated site of the
product and seeing if they match up. If so, we have a hydrogen migration
between these two sites.
"""
_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) == 1:
gra1, = rct_gras
gra2, = prd_gras
# Get the keys for the reactant graph
h_atm_key1 = max(atom_keys(gra1)) + 1
atm_keys1 = unsaturated_atom_keys(gra1)
# Generate reactions for all isomorphic graphs of products
gra2_lst = (gra2, ) + isomorphic_radical_graphs(gra2)
# gra2_lst = (gra2,)
for _gra2 in gra2_lst:
# Find keys for product graph
h_atm_key2 = max(atom_keys(_gra2)) + 1
atm_keys2 = unsaturated_atom_keys(_gra2)
# Run identifier
for atm_key1, atm_key2 in itertools.product(atm_keys1, atm_keys2):
gra1_h = add_atom_explicit_hydrogen_keys(
gra1, {atm_key1: [h_atm_key1]})
gra2_h = add_atom_explicit_hydrogen_keys(
_gra2, {atm_key2: [h_atm_key2]})
iso_dct = full_isomorphism(gra1_h, gra2_h)
if iso_dct:
inv_dct = dict(map(reversed, iso_dct.items()))
f_frm_bnd_key = (atm_key1, inv_dct[h_atm_key2])
f_brk_bnd_key = (inv_dct[atm_key2], inv_dct[h_atm_key2])
b_frm_bnd_key = (atm_key2, iso_dct[h_atm_key1])
b_brk_bnd_key = (iso_dct[atm_key1], iso_dct[h_atm_key1])
forw_tsg = ts.graph(gra1,
frm_bnd_keys=[f_frm_bnd_key],
brk_bnd_keys=[f_brk_bnd_key])
back_tsg = ts.graph(_gra2,
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_MIGRATION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=[atom_keys(gra1)],
prds_keys=[atom_keys(_gra2)],
))
return tuple(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)