def test__backbone_isomorphic():
""" test graph.backbone_isomorphic
"""
assert graph.backbone_isomorphic(CH2FH2H_CGR_IMP, CH2FH2H_CGR_EXP)
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_isomorphic(cgr, cgr_pmt)
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__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__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__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__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)