def test__remove_atoms():
""" test graph.remove_atoms
"""
assert graph.remove_atoms(C3H3_CGR, (0, )) == ({
1: ('C', 1, None),
2: ('C', 1, None)
}, {
frozenset({1, 2}): (1, None)
})
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)