Backmerge: #1300 Stereobond is not preserved after pasting a SMILES structure (#1324)

Author: even1024

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

@@ -81,3 +81,8 @@ C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |wU:3.12,wD:3.3,(-2.40,1.39,;-0.80,1.39,;-0.0
 atropisomer:
 C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |w:3.3,3.12|
 C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |w:3.3,3.12,(-2.40,1.39,;-0.80,1.39,;-0.00,2.77,;0.00,0.00,;1.60,0.00,;2.40,1.39,;4.00,1.39,;4.80,0.00,;6.40,0.00,;4.00,-1.39,;2.40,-1.39,;1.60,-2.77,;-0.80,-1.39,;0.00,-2.77,;-2.40,-1.39,;-3.20,-0.00,)|
+*** Suffoxides ***
+suffoxide:
+C1[S@](=O)CC(=O)C=1C
+C1[S@](=O)CC(=O)C=1C
+bond:5 stereo:6

api/tests/integration/tests/formats/smiles.py

@@ -128,3 +128,16 @@
     print(mol.smiles())
     mol.layout()
     print(mol.smiles())
+
+print("*** Suffoxides ***")
+mols_smiles = ["C1=C(C)C(=O)C[S@]1=O"]
+for sm in mols_smiles:
+    print("suffoxide:")
+    mol = indigo.loadMolecule(sm)
+    print(mol.smiles())
+    mol.layout()
+    print(mol.smiles())
+    for i in range(mol.countBonds()):
+        bs = mol.getBond(i).bondStereo()
+        if bs > 0:
+            print("bond:%d stereo:%d" % (i, bs))

core/indigo-core/molecule/src/molecule_stereocenters.cpp

@@ -1771,7 +1771,8 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx)
         for (j = 0; j < size; j++)
         {
             edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]);
-            if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getVertex(pyramid[size - 1]).degree() == 1)
+            if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondOrder(edge_idx) == BOND_SINGLE &&
+                baseMolecule.getVertex(pyramid[size - 1]).degree() == 1)
                 break;
             rotatePyramid(pyramid);
             if (size == 4)
@@ -1783,7 +1784,8 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx)
             for (j = 0; j < size; j++)
             {
                 edge_idx = baseMolecule.findEdgeIndex(atom_idx, pyramid[size - 1]);
-                if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondTopology(edge_idx) == TOPOLOGY_CHAIN && getType(pyramid[size - 1]) == 0)
+                if (baseMolecule.getBondDirection(edge_idx) == 0 && baseMolecule.getBondOrder(edge_idx) == BOND_SINGLE &&
+                    baseMolecule.getBondTopology(edge_idx) == TOPOLOGY_CHAIN && getType(pyramid[size - 1]) == 0)
                     break;
                 rotatePyramid(pyramid);
                 if (size == 4)