Additional guard against trying to write molecules in an inconsistent…

… state.
johnmay · Nov 9, 2016 · 974b385 · 974b385
1 parent b5ff6c4
commit 974b385
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Showing 2 changed files with 16 additions and 2 deletions.
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java
@@ -248,7 +248,11 @@ static Edge toBeamEdge(IBond b, int flavour, Map<IAtom, Integer> indices) throws
      */
     private static Bond toBeamEdgeLabel(IBond b, int flavour) throws CDKException {
 
-        if (SmiFlavor.isSet(flavour, SmiFlavor.UseAromaticSymbols) && b.getFlag(CDKConstants.ISAROMATIC)) return Bond.AROMATIC;
+        if (SmiFlavor.isSet(flavour, SmiFlavor.UseAromaticSymbols) && b.isAromatic()) {
+            if (!b.getAtom(0).isAromatic() || !b.getAtom(1).isAromatic())
+                throw new IllegalStateException("Aromatic bond connects non-aromatic atomic atoms");
+            return Bond.AROMATIC;
+        }
 
         if (b.getOrder() == null) throw new CDKException("A bond had undefined order, possible query bond?");
 
@@ -264,7 +268,7 @@ private static Bond toBeamEdgeLabel(IBond b, int flavour) throws CDKException {
             case QUADRUPLE:
                 return Bond.QUADRUPLE;
             default:
-                if (!SmiFlavor.isSet(flavour, SmiFlavor.UseAromaticSymbols) && b.getFlag(CDKConstants.ISAROMATIC))
+                if (!SmiFlavor.isSet(flavour, SmiFlavor.UseAromaticSymbols) && b.isAromatic())
                     throw new CDKException("Cannot write Kekulé SMILES output due to aromatic bond with unset bond order - molecule should be Kekulized");
                 throw new CDKException("Unsupported bond order: " + order);
         }

diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java
@@ -1228,6 +1228,16 @@ public void assignDbStereo() throws Exception {
         assertThat(smigen.create(r2), is(smigen.create(r3)));
     }
 
+    @Test(expected = IllegalStateException.class)
+    public void inconsistentAromaticState() throws Exception {
+        SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer mol = smipar.parseSmiles("c1ccccc1");
+        for (IAtom atom : mol.atoms())
+            atom.setIsAromatic(false);
+        SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.UseAromaticSymbols);
+        smigen.create(mol);
+    }
+
     static ITetrahedralChirality anticlockwise(IAtomContainer container, int central, int a1, int a2, int a3, int a4) {
         return new TetrahedralChirality(container.getAtom(central), new IAtom[]{container.getAtom(a1),
                                                                                 container.getAtom(a2), container.getAtom(a3), container.getAtom(a4)},