Don't bond the same two atoms more than once.

cdk · Feb 4, 2016 · 2701e82 · 2701e82
1 parent fcac95e
commit 2701e82
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Showing 2 changed files with 21 additions and 2 deletions.
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
@@ -870,11 +870,19 @@ public int compare(IAtomContainer a, IAtomContainer b) {
         final IChemObjectBuilder bldr = frags.get(0).getBuilder();
 
         // make the bonds
-        final List<IBond> ionicBonds = new ArrayList<>();
+        final List<IBond> ionicBonds = new ArrayList<>(cations.size());
         for (int i = 0; i < cations.size(); i++) {
             final IAtom beg = cations.get(i);
             final IAtom end = anions.get(i);
-            ionicBonds.add(bldr.newInstance(IBond.class, beg, end));
+
+            boolean unique = true;
+            for (IBond bond : ionicBonds)
+                if (bond.getAtom(0).equals(beg) && bond.getAtom(1).equals(end) ||
+                    bond.getAtom(1).equals(beg) && bond.getAtom(0).equals(end))
+                    unique = false;
+
+            if (unique)
+                ionicBonds.add(bldr.newInstance(IBond.class, beg, end));
         }
 
         // we could merge the fragments here using union-find structures

diff --git a/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java b/tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
@@ -948,6 +948,17 @@ public void chembl12276() throws Exception {
                    closeTo(SDG.getBondLength(), 0.001));
     }
 
+    @Test
+    public void calciumOxide() throws Exception {
+        SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("[Ca+2].[O-2]");
+        layout(mol);
+        for (IAtom atom : mol.atoms())
+            assertNotNull(atom.getPoint2d());
+        assertThat(mol.getAtom(0).getPoint2d().distance(mol.getAtom(1).getPoint2d()),
+                   closeTo(SDG.getBondLength(), 0.001));
+    }
+
     // An extreme test case suggest by Roger Sayle showing Humpty Dumpty reassembly
     @Test
     public void multipleSalts() throws Exception {