When new tetrahedral elements are created, e.g. adding/removing hydrogens make sure the stereo group info is copied accross.

johnmay · johnmay · commit 45aeef33cb5c · 2021-02-15T19:11:39.000Z
diff --git a/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -657,7 +657,9 @@ public static void convertImplicitToExplicitHydrogens(IAtomContainer atomContain
 
                 if (hydrogen != null) {
                     replaceAtom(carriers, focus, hydrogen);
-                    stereos.add(new TetrahedralChirality(focus, carriers, tc.getStereo()));
+                    TetrahedralChirality newStereo = new TetrahedralChirality(focus, carriers, tc.getStereo());
+                    newStereo.setGroupInfo(tc.getGroupInfo());
+                    stereos.add(newStereo);
                 } else {
                     stereos.add(stereo);
                 }
@@ -967,7 +969,9 @@ public static IAtomContainer suppressHydrogens(IAtomContainer org) {
                 if (!updated) {
                     elements.add(tc);
                 } else {
-                    elements.add(new TetrahedralChirality(focus, neighbors, tc.getStereo()));
+                    TetrahedralChirality e = new TetrahedralChirality(focus, neighbors, tc.getStereo());
+                    e.setGroupInfo(tc.getGroupInfo());
+                    elements.add(e);
                 }
             } else if (se instanceof ExtendedTetrahedral) {
                 ExtendedTetrahedral tc = (ExtendedTetrahedral) se;
