def test__from_local_stereo():
""" test graph.from_local_stereo
"""
gra = graph.explicit(C3H5_SGR)
loc_gra = graph.to_local_stereo(gra)
assert gra == graph.from_local_stereo(loc_gra)
for gra in C2H2CL2F2_SGRS:
gra = graph.explicit(gra)
loc_gra = graph.to_local_stereo(gra)
assert gra == graph.from_local_stereo(loc_gra)
for gra in C3H3CL2F3_SGRS:
gra = graph.explicit(gra)
loc_gra = graph.to_local_stereo(gra)
assert gra == graph.from_local_stereo(loc_gra)
for gra in C3H5N3_SGRS:
gra = graph.explicit(gra)
loc_gra = graph.to_local_stereo(gra)
assert gra == graph.from_local_stereo(loc_gra)
for gra in C8H13O_SGRS:
gra = graph.explicit(gra)
loc_gra = graph.to_local_stereo(gra)
assert gra == graph.from_local_stereo(loc_gra)
def test__atom_stereo_coordinates():
""" test graph.atom_stereo_coordinates
"""
for sgr in C2H2CL2F2_SGRS:
sgr = graph.explicit(sgr)
cgr = graph.without_stereo_parities(sgr)
atm_xyz_dct = graph.atom_stereo_coordinates(sgr)
assert graph.set_stereo_from_atom_coordinates(cgr, atm_xyz_dct) == sgr
for sgr in C3H5N3_SGRS:
sgr = graph.explicit(sgr)
cgr = graph.without_stereo_parities(sgr)
atm_xyz_dct = graph.atom_stereo_coordinates(sgr)
assert graph.set_stereo_from_atom_coordinates(cgr, atm_xyz_dct) == sgr
for sgr in C3H3CL2F3_SGRS:
sgr = graph.explicit(sgr)
cgr = graph.without_stereo_parities(sgr)
atm_xyz_dct = graph.atom_stereo_coordinates(sgr)
assert graph.set_stereo_from_atom_coordinates(cgr, atm_xyz_dct) == sgr
for sgr in C8H13O_SGRS:
sgr = graph.explicit(sgr)
cgr = graph.without_stereo_parities(sgr)
atm_xyz_dct = graph.atom_stereo_coordinates(sgr)
assert graph.set_stereo_from_atom_coordinates(cgr, atm_xyz_dct) == sgr
def test__to_index_based_stereo():
""" test graph.to_index_based_stereo
"""
sgr = graph.explicit(C3H5_SGR)
idx_sgr = graph.to_index_based_stereo(sgr)
assert sgr == graph.from_index_based_stereo(idx_sgr)
for sgr in C2H2CL2F2_SGRS:
sgr = graph.explicit(sgr)
idx_sgr = graph.to_index_based_stereo(sgr)
assert sgr == graph.from_index_based_stereo(idx_sgr)
for sgr in C3H3CL2F3_SGRS:
sgr = graph.explicit(sgr)
idx_sgr = graph.to_index_based_stereo(sgr)
assert sgr == graph.from_index_based_stereo(idx_sgr)
for sgr in C3H5N3_SGRS:
sgr = graph.explicit(sgr)
idx_sgr = graph.to_index_based_stereo(sgr)
assert sgr == graph.from_index_based_stereo(idx_sgr)
for sgr in C8H13O_SGRS:
sgr = graph.explicit(sgr)
idx_sgr = graph.to_index_based_stereo(sgr)
assert sgr == graph.from_index_based_stereo(idx_sgr)
def test__trans__form_dummy_bonds():
""" test graph.trans.from_dummy_bonds
"""
cgr1 = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('C', 1, None),
3: ('C', 2, None),
4: ('C', 1, None),
5: ('C', 2, None),
6: ('C', 2, None),
7: ('O', 1, None)
}, {
frozenset({4, 6}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
cgr2 = ({
0: ('C', 2, None),
1: ('C', 3, None),
2: ('C', 1, None),
3: ('C', 2, None),
4: ('C', 1, None),
5: ('C', 2, None),
6: ('C', 2, None),
7: ('O', 2, None)
}, {
frozenset({4, 6}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
cgr1 = graph.explicit(cgr1)
cgr2 = graph.explicit(cgr2)
tra = graph.trans.hydrogen_abstraction(cgr1, cgr2)
dum_cgr1 = graph.trans.form_dummy_bonds(tra, cgr1)
assert graph.rotational_bond_keys(dum_cgr1) == frozenset({
frozenset({4, 6}),
frozenset({10, 7}),
frozenset({0, 2}),
frozenset({5, 6}),
frozenset({3, 5}),
frozenset({1, 3})
})
bnd_key = frozenset({10, 7})
atm1_key = 7
atm2_key = 10
print(graph.branch_atom_keys(dum_cgr1, atm1_key, bnd_key))
print(graph.branch_atom_keys(dum_cgr1, atm2_key, bnd_key))
def test__trans__is_stereo_compatible():
""" test graph.trans.is_stereo_compatible
"""
cgr1 = ({
0: ('C', 1, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('F', 0, None),
5: ('F', 0, None),
6: ('O', 1, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
cgr2 = ({
0: ('C', 1, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('F', 0, None),
5: ('F', 0, None),
6: ('O', 1, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({3, 6}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
cgr1 = graph.explicit(cgr1)
cgr2 = graph.explicit(cgr2)
ich1 = graph.inchi(cgr1)
ich2 = graph.inchi(cgr2)
smi1 = automol.inchi.smiles(ich1)
smi2 = automol.inchi.smiles(ich2)
print(smi1)
print(smi2)
cgr1s = graph.connected_components(cgr1)
cgr2s = graph.connected_components(cgr2)
tras, _, _ = graph.reac.addition(cgr1s, cgr2s)
for tra in tras:
assert graph.backbone_isomorphic(graph.trans.apply(tra, cgr1), cgr2)
sgr1 = graph.stereomers(cgr1)[0]
print(sgr1)
for sgr2 in graph.stereomers(cgr2):
print(sgr2)
print(graph.trans.is_stereo_compatible(tra, sgr1, sgr2))
def test__reac__beta_scission():
""" test graph.reac.beta_scission
"""
rct_cgr = ({
0: ('C', 1, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('F', 0, None),
5: ('F', 0, None),
6: ('O', 1, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({3, 6}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
prd_cgr = ({
0: ('C', 1, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('F', 0, None),
5: ('F', 0, None),
6: ('O', 1, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.beta_scission(rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
print("beta scission")
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
def test__trans__hydrogen_abstraction():
""" test graph.trans.hydrogen_abstraction
"""
cgr1 = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('C', 1, None),
3: ('C', 2, None),
4: ('C', 1, None),
5: ('C', 2, None),
6: ('C', 2, None),
7: ('O', 1, None)
}, {
frozenset({4, 6}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
cgr2 = ({
0: ('C', 2, None),
1: ('C', 3, None),
2: ('C', 1, None),
3: ('C', 2, None),
4: ('C', 1, None),
5: ('C', 2, None),
6: ('C', 2, None),
7: ('O', 2, None)
}, {
frozenset({4, 6}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
cgr1 = graph.explicit(cgr1)
cgr2 = graph.explicit(cgr2)
tra = graph.trans.hydrogen_abstraction(cgr1, cgr2)
assert graph.backbone_isomorphic(graph.trans.apply(tra, cgr1), cgr2)
tra = graph.trans.hydrogen_abstraction(cgr2, cgr1)
assert graph.backbone_isomorphic(graph.trans.apply(tra, cgr2), cgr1)
def test__trans__addition():
""" test graph.trans.addition
"""
cgr1 = ({
0: ('C', 1, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('F', 0, None),
5: ('F', 0, None),
6: ('O', 1, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
cgr2 = ({
0: ('C', 1, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('F', 0, None),
5: ('F', 0, None),
6: ('O', 1, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({3, 6}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
cgr1 = graph.explicit(cgr1)
cgr2 = graph.explicit(cgr2)
tra = graph.trans.addition(cgr1, cgr2)
assert graph.backbone_isomorphic(graph.trans.apply(tra, cgr1), cgr2)
def test__reac__substitution():
""" test graph.reac.substitution
"""
# CH3OOH + CH3 => CH3OCH3 + OH
rct_cgr = ({
0: ('C', 3, None),
1: ('O', 1, None),
2: ('O', 0, None),
3: ('C', 3, None)
}, {
frozenset({0, 2}): (1, None),
frozenset({1, 2}): (1, None)
})
prd_cgr = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('O', 0, None),
3: ('O', 1, None)
}, {
frozenset({0, 2}): (1, None),
frozenset({1, 2}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.substitution(rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
print("substitution")
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
def test__heavy_atom_count():
""" test graph.explicit_hydrogen_count
"""
cgr = graph.explicit(C8H13O_CGR)
assert graph.heavy_atom_count(cgr) == 9
def _are_all_explicit(gras):
return all(gra == explicit(gra) for gra in gras)
def test__reac__hydrogen_migration():
""" test graph.reac.hydrogen_migration
"""
# first test a radical site migration
rct_cgr = ({
0: ('C', 1, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('C', 1, None),
5: ('O', 0, None)
}, {
frozenset({3, 4}): (1, None),
frozenset({2, 3}): (1, None),
frozenset({1, 2}): (1, None),
frozenset({4, 5}): (1, None),
frozenset({0, 1}): (1, None)
})
prd_cgr = ({
0: ('C', 2, None),
1: ('C', 1, None),
2: ('C', 1, None),
3: ('C', 1, None),
4: ('C', 0, None),
5: ('O', 0, None)
}, {
frozenset({3, 4}): (1, None),
frozenset({2, 3}): (1, None),
frozenset({1, 2}): (1, None),
frozenset({4, 5}): (1, None),
frozenset({0, 1}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_migration(
rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
print("hydrogen migration")
rct_cgr = graph.union_from_sequence(rct_cgrs)
prd_cgr = graph.union_from_sequence(prd_cgrs)
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_migration(
prd_cgrs, rct_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
# then test a tautomerization
rct_cgr = ({
0: ('C', 2, None),
1: ('C', 1, None),
2: ('O', 1, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({1, 2}): (1, None)
})
prd_cgr = ({
0: ('C', 3, None),
1: ('C', 1, None),
2: ('O', 0, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({1, 2}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_migration(
rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_migration(
prd_cgrs, rct_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
def test__reac__insertion():
""" test graph.reac.insertion
"""
# CH2CH2 + HOO => CH3CH3OO
rct_cgr = ({
0: ('C', 2, None),
1: ('C', 2, None),
2: ('O', 1, None),
3: ('O', 0, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({2, 3}): (1, None)
})
prd_cgr = ({
0: ('C', 3, None),
1: ('C', 2, None),
2: ('O', 0, None),
3: ('O', 0, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({1, 3}): (1, None),
frozenset({2, 3}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.insertion(rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
print("insertion")
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
# CH3CH3 + :C=O => CH3C(=O)CH3 (CO insertion)
rct_cgr = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('C', 0, None),
3: ('O', 0, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({2, 3}): (1, None)
})
prd_cgr = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('C', 0, None),
3: ('O', 0, None)
}, {
frozenset({0, 2}): (1, None),
frozenset({2, 3}): (1, None),
frozenset({1, 2}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.insertion(rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
# CH3CH3 + O=C=O => CH3C(=O)OCH3 (CO2 insertion)
rct_cgr = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('C', 0, None),
3: ('O', 0, None),
4: ('O', 0, None)
}, {
frozenset({0, 1}): (1, None),
frozenset({2, 3}): (1, None),
frozenset({2, 4}): (1, None)
})
prd_cgr = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('C', 0, None),
3: ('O', 0, None),
4: ('O', 0, None)
}, {
frozenset({0, 2}): (1, None),
frozenset({1, 4}): (1, None),
frozenset({2, 3}): (1, None),
frozenset({2, 4}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.insertion(rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
def test__explicit():
""" test graph.explicit
"""
assert CH2FH2H_CGR_EXP == graph.explicit(CH2FH2H_CGR_IMP)
def test__explicit():
""" test graph.explicit
"""
assert graph.explicit(CH2FH2H_CGR) == CH2FH2H_CGR_EXP
def test__implicit():
""" test graph.implicit
"""
assert CH2FH2H_CGR_IMP == graph.implicit(graph.explicit(CH2FH2H_CGR_IMP))
def test__reac__hydrogen_abstraction():
""" test graph.reac.hydrogen_abstraction
"""
rct_cgr = ({
0: ('C', 3, None),
1: ('C', 3, None),
2: ('C', 1, None),
3: ('C', 2, None),
4: ('C', 1, None),
5: ('C', 2, None),
6: ('C', 2, None),
7: ('O', 1, None)
}, {
frozenset({4, 6}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
prd_cgr = ({
0: ('C', 2, None),
1: ('C', 3, None),
2: ('C', 1, None),
3: ('C', 2, None),
4: ('C', 1, None),
5: ('C', 2, None),
6: ('C', 2, None),
7: ('O', 2, None)
}, {
frozenset({4, 6}): (1, None),
frozenset({0, 2}): (1, None),
frozenset({2, 4}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({3, 5}): (1, None),
frozenset({1, 3}): (1, None)
})
rct_cgr = graph.explicit(rct_cgr)
prd_cgr = graph.explicit(prd_cgr)
rct_cgrs = graph.connected_components(rct_cgr)
prd_cgrs = graph.connected_components(prd_cgr)
tras, rct_idxs, prd_idxs = graph.reac.hydrogen_abstraction(
rct_cgrs, prd_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
print("hydrogen abstraction")
rct_cgr = graph.union_from_sequence(rct_cgrs)
print(rct_cgr)
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, rct_cgr),
prd_cgr)
tras, prd_idxs, rct_idxs = graph.reac.hydrogen_abstraction(
prd_cgrs, rct_cgrs)
assert tras
assert rct_idxs
assert prd_idxs
for tra in tras:
print(tra)
assert graph.backbone_isomorphic(graph.trans.apply(tra, prd_cgr),
rct_cgr)
