Merge pull request #556 from avcopan/dev

Fix for double bridgehead pairs
Auto-Mech · Aug 16, 2024 · 57a02d1 · 57a02d1
2 parents c243af0 + ccee237
commit 57a02d1
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diff --git a/automol/graph/base/_11stereo.py b/automol/graph/base/_11stereo.py
@@ -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
 

diff --git a/automol/tests/test_graph_ts.py b/automol/tests/test_graph_ts.py
@@ -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),
@@ -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",
@@ -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):
@@ -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])