Backmerge: #1182 Enhanced stereo labels on atropisomers are lost when…

… opening molfiles (#1215)

api/tests/integration/ref/formats/mol_to_ket.py.out

@@ -2,18 +2,6 @@
 1032-quadra.ket:SUCCEED
 1046-imp_hydrogen.ket:SUCCEED
 SgroupDifferent.ket:SUCCEED
-suplabel.ket:FAILED
---- 
-
-+++ 
-
-@@ -36,7 +36,7 @@
-
-                     0,
-                     1
-                 ],
--                "name": "\"sodium"
-+                "name": "sodium chloride"
-             }
-         ]
-     }
+atropisomer.ket:SUCCEED
+non_atrop.ket:SUCCEED
+suplabel.ket:SUCCEED

api/tests/integration/tests/formats/mol_to_ket.py

@@ -16,13 +16,21 @@ def find_diff(a, b):
 
 indigo = Indigo()
 indigo.setOption("json-saving-pretty", True)
+indigo.setOption("ignore-stereochemistry-errors", True)
 
 print("*** MOL to KET ***")
 
 root = joinPathPy("molecules/", __file__)
 ref_path = joinPathPy("ref/", __file__)
 
-files = ["1032-quadra", "1046-imp_hydrogen", "SgroupDifferent", "suplabel"]
+files = [
+    "1032-quadra",
+    "1046-imp_hydrogen",
+    "SgroupDifferent",
+    "suplabel",
+    "atropisomer",
+    "non_atrop",
+]
 
 files.sort()
 for filename in files:

api/tests/integration/tests/formats/molecules/atropisomer.mol

@@ -0,0 +1,48 @@
+
+     RDKit          2D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 16 17 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 25.514800 -10.612600 0.000000 0
+M  V30 2 C 28.110200 -10.611900 0.000000 0
+M  V30 3 C 26.815000 -9.862500 0.000000 0
+M  V30 4 C 28.110200 -12.113300 0.000000 0
+M  V30 5 C 25.514800 -12.120000 0.000000 0
+M  V30 6 C 26.818200 -12.862500 0.000000 0
+M  V30 7 C 26.818200 -14.362500 0.000000 0
+M  V30 8 C 28.118100 -16.609000 0.000000 0
+M  V30 9 C 28.118500 -15.112600 0.000000 0
+M  V30 10 C 26.818300 -17.360600 0.000000 0
+M  V30 11 C 25.513300 -15.117100 0.000000 0
+M  V30 12 C 25.523000 -16.617200 0.000000 0
+M  V30 13 N 29.179100 -14.051900 0.000000 0
+M  V30 14 C 29.410000 -12.862000 0.000000 0
+M  V30 15 O 24.217900 -12.873800 0.000000 0
+M  V30 16 C 26.820800 -18.860600 0.000000 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 3 1
+M  V30 2 2 4 2
+M  V30 3 1 1 5
+M  V30 4 1 2 3
+M  V30 5 2 5 6
+M  V30 6 1 6 4 CFG=1
+M  V30 7 1 6 7
+M  V30 8 2 9 7
+M  V30 9 2 10 8
+M  V30 10 1 7 11
+M  V30 11 1 8 9
+M  V30 12 2 11 12
+M  V30 13 1 12 10
+M  V30 14 1 9 13
+M  V30 15 1 4 14
+M  V30 16 1 5 15
+M  V30 17 1 10 16
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEREL1 ATOMS=(1 6)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END

api/tests/integration/tests/formats/molecules/non_atrop.mol

@@ -0,0 +1,46 @@
+
+  -INDIGO-08082300302D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 16 15 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 21.15 -11.859 0.0 0
+M  V30 2 C 21.15 -13.591 0.0 0
+M  V30 3 C 20.65 -12.725 0.0 0
+M  V30 4 C 22.15 -13.591 0.0 0
+M  V30 5 C 22.15 -11.859 0.0 0
+M  V30 6 C 22.65 -12.725 0.0 0 CFG=1
+M  V30 7 C 23.65 -12.725 0.0 0
+M  V30 8 C 25.15 -13.591 0.0 0
+M  V30 9 C 24.15 -13.591 0.0 0
+M  V30 10 C 25.65 -12.725 0.0 0
+M  V30 11 C 24.15 -11.859 0.0 0
+M  V30 12 C 25.15 -11.859 0.0 0
+M  V30 13 N 24.05 -15.0571 0.0 0
+M  V30 14 C 22.15 -14.9571 0.0 0
+M  V30 15 O 22.65 -10.9929 0.0 0
+M  V30 16 C 26.65 -12.725 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 4 2
+M  V30 2 1 1 5
+M  V30 3 1 2 3
+M  V30 4 2 5 6
+M  V30 5 1 6 4
+M  V30 6 1 6 7 CFG=1
+M  V30 7 2 9 7
+M  V30 8 2 10 8
+M  V30 9 1 7 11
+M  V30 10 1 8 9
+M  V30 11 1 12 10
+M  V30 12 1 9 13
+M  V30 13 1 4 14
+M  V30 14 1 5 15
+M  V30 15 1 10 16
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEREL1 ATOMS=(1 6)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END