def beta_scissions(rct_gras, viable_only=True):
""" find all possible beta scission reactions for these reactants
:param rct_gras: graphs for the reactants, without stereo and without
overlapping keys
:param viable_only: Filter out reactions with non-viable products?
:type viable_only: bool
:returns: a list of Reaction objects
:rtype: tuple[Reaction]
Beta scissions are enumerated by identifying all pure single bonds (single
bonds with no resonances), and looping over the results of breaking each of
them. If this gives rise to two distinct fragments, the reaction is added
to the list.
"""
assert_is_valid_reagent_graph_list(rct_gras)
rxns = []
if len(rct_gras) == 1:
rct_gra, = rct_gras
# Identify all pure single bonds
avg_bnd_ord_dct = resonance_avg_bond_orders(implicit(rct_gra))
brk_bnd_keys = dict_.keys_by_value(avg_bnd_ord_dct, lambda x: x == 1)
for brk_bnd_key in brk_bnd_keys:
prds_gra = remove_bonds(rct_gra, [brk_bnd_key])
prd_gras = connected_components(prds_gra)
if len(prd_gras) == 2:
prd_gras = sort_reagents(prd_gras)
forw_tsg = ts.graph(rct_gra,
frm_bnd_keys=[],
brk_bnd_keys=[brk_bnd_key])
back_tsg = ts.graph(prds_gra,
frm_bnd_keys=[brk_bnd_key],
brk_bnd_keys=[])
# Create the reaction object
rxns.append(Reaction(
rxn_cls=par.ReactionClass.Typ.BETA_SCISSION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=list(map(atom_keys, rct_gras)),
prds_keys=list(map(atom_keys, prd_gras)),
))
if viable_only:
rxns = filter_viable_reactions(rxns)
return ts_unique(rxns)
def additions(rct_gras, viable_only=True):
""" find all possible addition reactions for these reactants
:param rct_gras: graphs for the reactants, without stereo and without
overlapping keys
:param viable_only: Filter out reactions with non-viable products?
:type viable_only: bool
:returns: a list of Reaction objects
:rtype: tuple[Reaction]
Additions are enumerated by joining an unsaturated site on one reactant to
an unsaturated site on the other.
"""
assert_is_valid_reagent_graph_list(rct_gras)
rxns = []
if len(rct_gras) == 2:
rct_gras = sort_reagents(rct_gras)
rct1_gra, rct2_gra = rct_gras
rct1_atm_keys = unsaturated_atom_keys(rct1_gra)
rct2_atm_keys = unsaturated_atom_keys(rct2_gra)
for frm_bnd_key in itertools.product(rct1_atm_keys, rct2_atm_keys):
rcts_gra = union(rct1_gra, rct2_gra)
prd_gra = add_bonds(rcts_gra, [frm_bnd_key])
prd_gras = [prd_gra]
forw_tsg = ts.graph(rcts_gra,
frm_bnd_keys=[frm_bnd_key],
brk_bnd_keys=[])
back_tsg = ts.graph(prd_gra,
frm_bnd_keys=[],
brk_bnd_keys=[frm_bnd_key])
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.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)),
))
if viable_only:
rxns = filter_viable_reactions(rxns)
return ts_unique(rxns)
def insertions(rct_gras, viable_only=True):
""" find all possible insertion reactions for these reactants
:param rct_gras: graphs for the reactants, without stereo and without
overlapping keys
:param viable_only: Filter out reactions with non-viable products?
:type viable_only: bool
:returns: a list of Reaction objects
:rtype: tuple[Reaction]
Insertions are enumerated by looping over carbenes and multiple bonds on
one reactant, which serve as a source of potential "attacking" atoms for
the insertion, and looping over single bonds that could be inserted into on
the other reactant. For lack of a better term, we can call these "donating
atoms". The insertion then looks as follows:
A1=A2 A1
. . or .
. . . .
D1-D2 D1-D2
where two bonds are formed between the A and D atoms and the bond between
the two D atoms is broken.
"""
assert_is_valid_reagent_graph_list(rct_gras)
rxns = []
if len(rct_gras) == 2:
for rct1_gra, rct2_gra in itertools.permutations(rct_gras):
rcts_gra = union(rct1_gra, rct2_gra)
# Carbenes on R1 are potential attacking atoms
atm_keys = radical_atom_keys(rct1_gra, min_valence=2.)
atm_keys = tuple(atm_keys)
# So are atoms on either side of a multiple bond
bnd_keys = dict_.keys_by_value(resonance_avg_bond_orders(rct1_gra),
lambda x: x > 1.)
bnd_keys = bond_equivalence_class_reps(rct1_gra, bnd_keys)
# Use this to form a list of attacking atom pairs for R1
att_pairs = list(map(tuple, map(sorted, bnd_keys)))
att_pairs += list(zip(atm_keys, atm_keys))
# As donor pairs, consider single bonds on R2
don_bnd_keys = dict_.keys_by_value(
resonance_avg_bond_orders(rct2_gra), lambda x: x == 1.)
don_bnd_keys = bond_equivalence_class_reps(rct2_gra, don_bnd_keys)
don_pairs = list(map(tuple, map(sorted, don_bnd_keys)))
for att_pair, don_pair in itertools.product(att_pairs, don_pairs):
if not (are_equivalent_atoms(rct1_gra, *att_pair)
or are_equivalent_atoms(rct2_gra, *don_pair)):
don_pairs_ = list(itertools.permutations(don_pair))
else:
don_pairs_ = [don_pair]
for don_pair_ in don_pairs_:
att1_key, att2_key = att_pair
don1_key, don2_key = don_pair_
prds_gra = rcts_gra
prds_gra = add_bonds(prds_gra, [(att1_key, don1_key),
(att2_key, don2_key)])
prds_gra = remove_bonds(prds_gra, [(don1_key, don2_key)])
prd_gras = connected_components(prds_gra)
if len(prd_gras) == 1:
forw_tsg = ts.graph(rcts_gra,
frm_bnd_keys=[(att1_key, don1_key),
(att2_key, don2_key)
],
brk_bnd_keys=[(don1_key, don2_key)
])
back_tsg = ts.graph(prds_gra,
frm_bnd_keys=[(don1_key, don2_key)
],
brk_bnd_keys=[(att1_key, don1_key),
(att2_key, don2_key)
])
# Create the reaction object
rcts_keys = list(map(atom_keys, [rct1_gra, rct2_gra]))
prds_keys = list(map(atom_keys, prd_gras))
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.Typ.INSERTION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=rcts_keys,
prds_keys=prds_keys,
))
if viable_only:
rxns = filter_viable_reactions(rxns)
return ts_unique(rxns)
def hydrogen_abstractions(rct_gras, viable_only=True):
""" find hydrogen abstraction reactions for these reactants
:param rct_gras: graphs for the reactants, without stereo and without
overlapping keys
:param viable_only: Filter out reactions with non-viable products?
:type viable_only: bool
:returns: a list of Reaction objects
:rtype: tuple[Reaction]
Hydrogen abstractions are enumerated by looping over unique unsaturated
atoms on one molecule and abstracting from unique atoms on the other.
"""
assert_is_valid_reagent_graph_list(rct_gras)
rxns = []
if len(rct_gras) == 2:
for q1h_gra, q2_gra in itertools.permutations(rct_gras):
hyd_keys = atom_keys(q1h_gra, sym='H')
# Identify unique heavy atoms as potential donors
don_keys = atom_keys(q1h_gra, excl_syms=('H', ))
don_keys = atom_equivalence_class_reps(q1h_gra, don_keys)
# Identify unique unsaturated atoms as potential attackers
att_keys = unsaturated_atom_keys(q2_gra)
att_keys = atom_equivalence_class_reps(q2_gra, att_keys)
for don_key, att_key in itertools.product(don_keys, att_keys):
hyd_key = atom_neighbor_atom_key(q1h_gra,
don_key,
symbs_first=['H'],
symbs_last=[])
if hyd_key in hyd_keys:
# Remove a hydrogen from the donor site
q1_gra = remove_atoms(q1h_gra, {hyd_key})
# Add a hydrogen atom to the attacker site
q2h_gra = add_bonded_atom(q2_gra,
'H',
att_key,
bnd_atm_key=hyd_key)
rcts_gra = union(q1h_gra, q2_gra)
prds_gra = union(q2h_gra, q1_gra)
forw_tsg = ts.graph(rcts_gra,
frm_bnd_keys=[(att_key, hyd_key)],
brk_bnd_keys=[(don_key, hyd_key)])
back_tsg = ts.graph(prds_gra,
frm_bnd_keys=[(don_key, hyd_key)],
brk_bnd_keys=[(att_key, hyd_key)])
rcts_atm_keys = list(map(atom_keys, [q1h_gra, q2_gra]))
prds_atm_keys = list(map(atom_keys, [q2h_gra, q1_gra]))
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.Typ.HYDROGEN_ABSTRACTION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=rcts_atm_keys,
prds_keys=prds_atm_keys,
))
if viable_only:
rxns = filter_viable_reactions(rxns)
return ts_unique(rxns)
def hydrogen_migrations(rct_gras, viable_only=True):
""" find all possible hydrogen migration reactions for these reactants
:param rct_gras: graphs for the reactants, without stereo and without
overlapping keys
:param viable_only: Filter out reactions with non-viable products?
:type viable_only: bool
:returns: a list of Reaction objects
:rtype: tuple[Reaction]
Hydrogen migrations are enumerated looping over unsaturated sites, adding
hydrogens to them, and looping over non-equivalent heavy atoms and removing
hydrgens from them.
"""
assert_is_valid_reagent_graph_list(rct_gras)
rxns = []
if len(rct_gras) == 1:
rct_gra, = rct_gras
# Identify unsaturated sites
rct_add_key = max(atom_keys(rct_gra)) + 1
rct_rad_keys = unsaturated_atom_keys(rct_gra)
rct_hyd_keys = atom_keys(rct_gra, sym='H')
for rct_rad_key in rct_rad_keys:
# Add a hydrogen to the radical/unsaturated site
rct_h_gra = add_bonded_atom(rct_gra,
'H',
rct_rad_key,
bnd_atm_key=rct_add_key)
# Identify donor sites
rct_don_keys = backbone_keys(rct_h_gra) - {rct_rad_key}
for rct_don_key in rct_don_keys:
rct_hyd_key = atom_neighbor_atom_key(rct_gra,
rct_don_key,
symbs_first=['H'],
symbs_last=[])
if rct_hyd_key in rct_hyd_keys:
prd_gra = remove_atoms(rct_h_gra, {rct_hyd_key})
prd_gra = relabel(prd_gra, {rct_add_key: rct_hyd_key})
forw_tsg = ts.graph(rct_gra,
frm_bnd_keys=[(rct_rad_key,
rct_hyd_key)],
brk_bnd_keys=[(rct_don_key,
rct_hyd_key)])
back_tsg = ts.graph(prd_gra,
frm_bnd_keys=[(rct_don_key,
rct_hyd_key)],
brk_bnd_keys=[(rct_rad_key,
rct_hyd_key)])
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.Typ.HYDROGEN_MIGRATION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=[atom_keys(rct_gra)],
prds_keys=[atom_keys(prd_gra)],
))
if viable_only:
rxns = filter_viable_reactions(rxns)
return ts_unique(rxns)
def eliminations(rct_gras, viable_only=True):
""" find all possible elimination reactions for these reactants
:param rct_gras: graphs for the reactants, without stereo and without
overlapping keys
:param viable_only: Filter out reactions with non-viable products?
:type viable_only: bool
:returns: a list of Reaction objects
:rtype: tuple[Reaction]
Eliminations are enumerated 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 from the attacking heavy atom, away from the attacked
atom.
"""
assert_is_valid_reagent_graph_list(rct_gras)
rxns = []
if len(rct_gras) == 1:
rct_gra, = rct_gras
ngb_keys_dct = atoms_neighbor_atom_keys(rct_gra)
# frm1_keys = atom_keys(rct_gra, excl_syms=('H',))
frm1_keys = unsaturated_atom_keys(rct_gra)
rct_symbs = atom_symbols(rct_gra)
frm1_keys_o = frozenset(key for key in frm1_keys
if rct_symbs[key] == 'O')
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_o, 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
prds_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(prds_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
prds_gra = remove_bonds(prds_gra, [(frm1_key, frm1_ngb_key)])
prds_gra = remove_bonds(prds_gra, [(frm2_key, frm2_ngb_key)])
prd_gras = connected_components(prds_gra)
if len(prd_gras) == 2:
forw_tsg = ts.graph(rct_gra,
frm_bnd_keys=[(frm1_key, frm2_key)],
brk_bnd_keys=[(frm1_key, frm1_ngb_key),
(frm2_key, frm2_ngb_key)
])
back_tsg = ts.graph(prds_gra,
frm_bnd_keys=[(frm1_key, frm1_ngb_key),
(frm2_key, frm2_ngb_key)
],
brk_bnd_keys=[(frm1_key, frm2_key)])
rcts_atm_keys = list(map(atom_keys, rct_gras))
prds_atm_keys = list(map(atom_keys, prd_gras))
if 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.Typ.ELIMINATION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=rcts_atm_keys,
prds_keys=prds_atm_keys,
))
if viable_only:
rxns = filter_viable_reactions(rxns)
return ts_unique(rxns)
def ring_forming_scissions(rct_gras, viable_only=True):
""" find all possible ring-forming scission reactions for these reactants
:param rct_gras: graphs for the reactants, without stereo and without
overlapping keys
:param viable_only: Filter out reactions with non-viable products?
:type viable_only: bool
:returns: a list of Reaction objects
:rtype: tuple[Reaction]
Right now it takes the lazy, chemically specific approach of finding
C-O-O-H groups and forming a bond between the O of the C-O bond
and radical sites of the species, while breaking the O-O bond.
"""
assert_is_valid_reagent_graph_list(rct_gras)
rxns = []
if len(rct_gras) == 1:
rct_gra, = rct_gras
# Identify the radical sites and COOH groups
rad_keys = radical_atom_keys(rct_gra)
cooh_grps = hydroperoxy_groups(rct_gra)
# Get the bnd keys for filtering
bnd_keys = bond_keys(rct_gra)
# Set the forming and breaking bonds by looping over COOH groups
rxn_bnd_keys = ()
for cooh_grp in cooh_grps:
brk_bnd_key = frozenset(cooh_grp[1:3])
for rad_key in rad_keys:
frm_bnd_key = frozenset({rad_key, cooh_grp[1]})
# Only includ frm bnd if it does not exist
# e.g., CC[C]OO already has frm bnd -> no rxn possible
if frm_bnd_key not in bnd_keys:
rxn_bnd_keys += ((frm_bnd_key, brk_bnd_key), )
# Form reactions with all combinations of frm and brk bnds
for frm_bnd_key, brk_bnd_key in rxn_bnd_keys:
prds_gra = rct_gra
prds_gra = add_bonds(prds_gra, [frm_bnd_key])
prds_gra = remove_bonds(prds_gra, [brk_bnd_key])
prd_gras = connected_components(prds_gra)
if len(prd_gras) == 2:
prd_gras = sort_reagents(prd_gras)
forw_tsg = ts.graph(rct_gra,
frm_bnd_keys=[frm_bnd_key],
brk_bnd_keys=[brk_bnd_key])
back_tsg = ts.graph(prds_gra,
frm_bnd_keys=[brk_bnd_key],
brk_bnd_keys=[frm_bnd_key])
# Create the reaction object
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.Typ.RING_FORM_SCISSION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=list(map(atom_keys, rct_gras)),
prds_keys=list(map(atom_keys, prd_gras)),
))
if viable_only:
rxns = filter_viable_reactions(rxns)
return ts_unique(rxns)