Need to set in the map/create function of IStereoElement, also add some tests to ensure behavior is correct.

johnmay · johnmay · commit 1a17c9ce117e · 2021-02-15T19:18:07.000Z
diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java b/base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java
@@ -179,7 +179,9 @@ public IStereoElement<F, C> map(Map<IChemObject, IChemObject> chemobjs) {
         // no change, return self
         if (newfocus == focus && newcarriers == carriers)
             return this;
-        return create(newfocus, newcarriers, value);
+        IStereoElement<F, C> se = create(newfocus, newcarriers, value);
+        se.setGroupInfo(getGroupInfo());
+        return se;
     }
 
     protected abstract IStereoElement<F,C> create(F focus, List<C> carriers, int cfg);
diff --git a/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java b/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java
@@ -47,6 +47,7 @@
 import org.openscience.cdk.sgroup.Sgroup;
 import org.openscience.cdk.silent.PseudoAtom;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smiles.SmiFlavor;
 import org.openscience.cdk.smiles.SmilesGenerator;
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.stereo.TetrahedralChirality;
@@ -1289,6 +1290,18 @@ public void testSgroupSuppressionSRUCrossingBond() throws Exception {
                       "CCC[H] |Sg:n:2:n:ht|");
     }
 
+    @Test
+    public void keepStereoGroup() throws Exception {
+        assertRemoveH("C[C@]([H])(O)CC |o1:1|",
+                      "C[C@H](O)CC |o1:1|");
+    }
+
+    @Test
+    public void keepStereoGroup2() throws Exception {
+        assertAddH("C[C@H](O)CC |o1:1|",
+                   "C([C@](O[H])(C(C([H])([H])[H])([H])[H])[H])([H])([H])[H] |o1:1|");
+    }
+
     @Test
     public void molecularWeight() throws InvalidSmilesException, IOException {
         SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
@@ -1331,7 +1344,16 @@ static void assertRemoveH(String smiIn, String smiExp) throws Exception {
         SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
         IAtomContainer m = smipar.parseSmiles(smiIn);
 
-        String smiAct = new SmilesGenerator().create(AtomContainerManipulator.removeHydrogens(m));
+        String smiAct = new SmilesGenerator(SmiFlavor.Default).create(AtomContainerManipulator.removeHydrogens(m));
+
+        assertThat(smiAct, is(smiExp));
+    }
+
+    static void assertAddH(String smiIn, String smiExp) throws Exception {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer m = smipar.parseSmiles(smiIn);
+        AtomContainerManipulator.convertImplicitToExplicitHydrogens(m);
+        String smiAct = new SmilesGenerator(SmiFlavor.Default).create(m);
 
         assertThat(smiAct, is(smiExp));
     }
