def test__equivalent_atoms():
""" test graph.equivalent_atoms
"""
# central carbon
assert graph.equivalent_atoms(C4H10_GRA, 3) == {3}
# central hydrogen
assert graph.equivalent_atoms(C4H10_GRA, 13) == {13}
# terminal carbons
assert graph.equivalent_atoms(C4H10_GRA, 0) == {0, 1, 2}
assert graph.equivalent_atoms(C4H10_GRA, 1) == {0, 1, 2}
assert graph.equivalent_atoms(C4H10_GRA, 2) == {0, 1, 2}
# terminal hydrogens
assert graph.equivalent_atoms(C4H10_GRA,
4) == {4, 5, 6, 7, 8, 9, 10, 11, 12}
assert graph.equivalent_atoms(C4H10_GRA,
5) == {4, 5, 6, 7, 8, 9, 10, 11, 12}
assert graph.equivalent_atoms(C4H10_GRA,
6) == {4, 5, 6, 7, 8, 9, 10, 11, 12}
assert graph.equivalent_atoms(C4H10_GRA,
11) == {4, 5, 6, 7, 8, 9, 10, 11, 12}
assert graph.equivalent_atoms(C4H10_GRA,
12) == {4, 5, 6, 7, 8, 9, 10, 11, 12}
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:
rct_gra, = rct_gras
prd_gra, = prd_gras
# Find keys for reactant graph
rct_h_key = max(atom_keys(rct_gra)) + 1
rct_rad_keys = unsaturated_atom_keys(rct_gra)
# Find keys for product graph
prd_h_key = max(atom_keys(prd_gra)) + 1
prd_rad_keys = unsaturated_atom_keys(prd_gra)
for rct_rad_key, prd_rad_key in (itertools.product(
rct_rad_keys, prd_rad_keys)):
# Add hydrogens to each radical site and see if the result matches
rct_h_gra = add_bonded_atom(rct_gra,
'H',
rct_rad_key,
bnd_atm_key=rct_h_key)
prd_h_gra = add_bonded_atom(prd_gra,
'H',
prd_rad_key,
bnd_atm_key=prd_h_key)
iso_dct = isomorphism(rct_h_gra, prd_h_gra)
if iso_dct:
inv_dct = dict(map(reversed, iso_dct.items()))
rct_don_key = inv_dct[prd_rad_key]
prd_don_key = iso_dct[rct_rad_key]
# Check equivalent donor atoms for other possible TSs
rct_don_keys = equivalent_atoms(rct_h_gra, rct_don_key)
prd_don_keys = equivalent_atoms(prd_h_gra, prd_don_key)
for rct_don_key, prd_don_key in (itertools.product(
rct_don_keys, prd_don_keys)):
rct_hyd_key = atom_neighbor_atom_key(rct_gra,
rct_don_key,
symbs_first=('H', ),
symbs_last=())
prd_hyd_key = atom_neighbor_atom_key(prd_gra,
prd_don_key,
symbs_first=('H', ),
symbs_last=())
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=[(prd_rad_key,
prd_hyd_key)],
brk_bnd_keys=[(prd_don_key,
prd_hyd_key)])
if isomorphism(forw_tsg, ts.reverse(back_tsg)):
rxns.append(
Reaction(
rxn_cls=par.ReactionClass.HYDROGEN_MIGRATION,
forw_tsg=forw_tsg,
back_tsg=back_tsg,
rcts_keys=[atom_keys(rct_gra)],
prds_keys=[atom_keys(prd_gra)],
))
return ts_unique(rxns)