def test__relabel():
""" test graph.relabel
"""
assert graph.relabel(C3H3_CGR, {0: 10, 1: 11, 2: 12}) == (
{10: ('C', 1, None), 11: ('C', 1, None), 12: ('C', 1, None)},
{frozenset({10, 11}): (1, None), frozenset({11, 12}): (1, None),
frozenset({12, 10}): (1, None)})
def test__backbone_isomorphism():
""" test graph.backbone_isomorphism
"""
cgr = C8H13O_CGR
natms = len(graph.atoms(cgr))
for _ in range(10):
pmt_dct = dict(enumerate(numpy.random.permutation(natms)))
cgr_pmt = graph.relabel(cgr, pmt_dct)
assert graph.backbone_isomorphism(cgr, cgr_pmt) == pmt_dct
def test__atom_inchi_numbers():
""" test graph.atom_inchi_numbers
"""
cgr = C8H13O_CGR
natms = len(graph.atoms(cgr))
for _ in range(10):
pmt_dct = dict(enumerate(numpy.random.permutation(natms)))
cgr_pmt = graph.relabel(cgr, pmt_dct)
inv_pmt_dct = dict(map(reversed, pmt_dct.items()))
assert graph.atom_inchi_numbers(cgr_pmt) == inv_pmt_dct
def test__from_dictionaries():
""" test graph.from_dictionaries
"""
assert graph.from_dictionaries(
graph.atom_symbols(CH2FH2H_CGR_EXP),
graph.bond_keys(CH2FH2H_CGR_EXP)
) == CH2FH2H_CGR_EXP
assert graph.from_dictionaries(
graph.atom_symbols(C8H13O_RGRS[0]),
graph.bond_keys(C8H13O_RGRS[0]),
atm_imp_hyd_vlc_dct=graph.atom_implicit_hydrogen_valences(
C8H13O_RGRS[0]),
bnd_ord_dct=graph.bond_orders(C8H13O_RGRS[0])
) == C8H13O_RGRS[0]
assert graph.from_dictionaries(
graph.atom_symbols(C8H13O_SGRS[0]),
graph.bond_keys(C8H13O_SGRS[0]),
atm_imp_hyd_vlc_dct=graph.atom_implicit_hydrogen_valences(
C8H13O_SGRS[0]),
atm_ste_par_dct=graph.atom_stereo_parities(C8H13O_SGRS[0]),
bnd_ste_par_dct=graph.bond_stereo_parities(C8H13O_SGRS[0])
) == C8H13O_SGRS[0]
# a litte ridiculous, but make sure we get the keys right
sgr_ref = C8H13O_SGRS[0]
natms = len(graph.atoms(sgr_ref))
for _ in range(10):
pmt_dct = dict(enumerate(numpy.random.permutation(natms)))
sgr = graph.relabel(sgr_ref, pmt_dct)
assert graph.from_dictionaries(
graph.atom_symbols(sgr),
graph.bond_keys(sgr),
atm_imp_hyd_vlc_dct=graph.atom_implicit_hydrogen_valences(sgr),
atm_ste_par_dct=graph.atom_stereo_parities(sgr),
bnd_ste_par_dct=graph.bond_stereo_parities(sgr)
) == sgr
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)
