Minor fix to abbreviations when the 'leaving' bond is to a '*' atom.

cdk · Aug 3, 2017 · dc73466 · dc73466
1 parent 5851070
commit dc73466
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diff --git a/app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java b/app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java
@@ -505,6 +505,8 @@ else if (attachBond.getEnd().equals(atom))
                         } else if (nbr.getAtomicNumber() > 0){
                             nbrSymbols.add(newSymbol(nbr.getAtomicNumber(), nbr.getImplicitHydrogenCount(), false));
                             xatoms.add(nbr);
+                        } else {
+                            newbonds.add(bond);
                         }
                     } else {
                         newbonds.add(bond);

diff --git a/app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java b/app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java
@@ -272,6 +272,17 @@ public void dontOverwriteExistingSgroups() throws Exception {
         assertThat(sgroups.get(0).getSubscript(), is("HOOH"));
     }
 
+    @Test public void OMeFragment() throws Exception {
+        Abbreviations factory = new Abbreviations();
+        IAtomContainer mol = smi("*OC");
+        List<Sgroup> sgroups = factory.generate(mol);
+        assertThat(sgroups.size(), is(1));
+        Sgroup sgroup = sgroups.get(0);
+        assertThat(sgroup.getAtoms().size(), is(2));
+        assertThat(sgroup.getBonds().size(), is(1));
+        assertThat(sgroup.getSubscript(), is("OMe"));
+    }
+
     @Test
     public void loadFromFile() throws Exception {
         Abbreviations factory = new Abbreviations();