Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix for double bridgehead pairs #556

Merged
merged 2 commits into from
Aug 16, 2024
Merged

Fix for double bridgehead pairs #556

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4ec146e
Fix: Prevent crash due to duplicate removal
avcopan Aug 16, 2024
ccee237
Test: Adds double bridgehead test case
avcopan Aug 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions automol/graph/base/_11stereo.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -184,6 +184,7 @@ def _remove_strained_stereoisomers_from_expansion(gps, cand_dct):
is_strained = not par1 ^ par2 ^ sgn1 ^ sgn2
if is_strained:
gps.remove((gra, pri_dct))
break

return gps

Expand Down
54 changes: 50 additions & 4 deletions automol/tests/test_graph_ts.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -785,7 +785,7 @@
# OO[C@@H]1CC=C[CH]1 => C=1[C@H]2C[C@H](C=1)O2 + [OH]
# * * * *
# [* marks a pair of bridgehead stereo atoms]
C5H6O_TSG = (
C5H7O2_TSG = (
{
0: ("O", 0, None),
1: ("O", 0, None),
Expand Down Expand Up @@ -821,6 +821,50 @@
},
)

# Double Bridgehead Atom Pair
# [O]OC1CCC2C1O2 => OOC1[CH]CC2C1O2
# ^ ^ * * ^ ^ * *
# [* marks the first pair of bridgehead stereo atoms]
# [^ marks the first pair of bridgehead stereo atoms]
C5H7O3_TSG = (
{
0: ("O", 0, None),
1: ("O", 0, None),
2: ("C", 0, None),
3: ("C", 0, None),
4: ("C", 0, None),
5: ("C", 0, None),
6: ("C", 0, None),
7: ("O", 0, None),
8: ("H", 0, None),
9: ("H", 0, None),
10: ("H", 0, None),
11: ("H", 0, None),
12: ("H", 0, None),
13: ("H", 0, None),
14: ("H", 0, None),
},
{
frozenset({8, 2}): (1, None),
frozenset({2, 3}): (1, None),
frozenset({9, 3}): (0.9, None),
frozenset({2, 6}): (1, None),
frozenset({4, 5}): (1, None),
frozenset({0, 1}): (1, None),
frozenset({6, 7}): (1, None),
frozenset({6, 14}): (1, None),
frozenset({5, 13}): (1, None),
frozenset({5, 7}): (1, None),
frozenset({0, 9}): (0.1, None),
frozenset({3, 4}): (1, None),
frozenset({1, 2}): (1, None),
frozenset({4, 12}): (1, None),
frozenset({10, 3}): (1, None),
frozenset({5, 6}): (1, None),
frozenset({11, 4}): (1, None),
},
)


@pytest.mark.parametrize(
"formula,tsg,geo,npars1,npars2",
Expand Down Expand Up @@ -928,7 +972,8 @@ def _test(formula, tsg):
("C2H4O2", C2H4O2_TSG, [1, 1]),
("C4H4F2", C4H4F2_TSG, [1, 1, 1, 1]),
("C8H14", C8H14_TSG, [1, 1, 1, 1]),
("C5H6O", C5H6O_TSG, [1, 1]),
("C5H7O2", C5H7O2_TSG, [1, 1]),
("C5H7O3", C5H7O3_TSG, [1, 1, 1, 1]),
],
)
def test__ts__expand_reaction_stereo(formula, ts_gra, ts_counts):
Expand Down Expand Up @@ -1370,10 +1415,11 @@ def test__zmatrix():
# test__ts__reagents_graph()
# test__rotational_bond_keys()
# test__ts__expand_reaction_stereo()
test__amchi("CH4CLFNO", CH4CLFNO_TSG)
# test__amchi("CH4CLFNO", CH4CLFNO_TSG)
# test__ts__fleeting_stereocenter_keys()
# test__linear_atom_keys()
# test__radical_atom_keys()
# test__geometry()
# test__ts__expand_reaction_stereo("C5H6O", C5H6O_TSG, [1, 1])
# test__zmatrix()
# test__ts__expand_reaction_stereo("C5H6O", C5H6O_TSG, [1, 1])
test__ts__expand_reaction_stereo("C5H7O3", C5H7O3_TSG, [1, 1, 1, 1])