def test__backbone_keys():
""" test graph.backbone_keys
"""
assert graph.backbone_keys(CH2FH2H_CGR_EXP) == frozenset({0, 1, 2, 3})
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)