For the simple cyclic pi bonds aromaticity model - don't allow atoms …

…which are next to two cyclic pi bonds. Documentation wording also improved.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

src/main/org/openscience/cdk/aromaticity/ElectronDonation.java

@@ -72,9 +72,9 @@ public static ElectronDonation cdkAtomTypes(boolean exocyclic) {
     /**
      * A very simple aromaticity model which only allows atoms adjacent to
      * cyclic pi bonds. Lone pairs are not consider and as such molecules like
-     * furan and pyrrole are not considered aromatic. The model is useful for
-     * storing aromaticity in MDL and Mol2 file formats where aromatic systems
-     * involving a lone pair can not be properly stored.
+     * furan and pyrrole are non-aromatic. The model is useful for storing
+     * aromaticity in MDL and Mol2 file formats where aromatic systems involving
+     * a lone pair can not be properly represented.
      *
      * @return electron donation model to use for aromaticity perception
      */

src/main/org/openscience/cdk/aromaticity/PiBondModel.java

@@ -37,8 +37,8 @@
 /**
  * A simple aromatic model which only allows cyclic pi-bonds to contribute to an
  * aromatic system. Lone pairs are not considered and as such molecules like
- * furan and pyrrole are not considered aromatic. This model is suitable for
- * storing aromaticity in the MDL/Mol2 file formats.
+ * furan and pyrrole are non-aromatic. This model is suitable for storing
+ * aromaticity in the MDL/Mol2 file formats.
  *
  * @author John May
  * @cdk.module standard
@@ -52,17 +52,25 @@ final class PiBondModel extends ElectronDonation {
 
         int   n         = container.getAtomCount();
         int[] electrons = new int[n];
+        int[] piBonds   = new int[n];
 
-        Arrays.fill(electrons, -1);
-
+        // count number of cyclic pi bonds
         for (IBond bond : container.bonds()) {
             int u = container.getAtomNumber(bond.getAtom(0));
             int v = container.getAtomNumber(bond.getAtom(1));
 
-            if (bond.getOrder() == DOUBLE && ringSearch.cyclic(u, v))
-                electrons[u] = electrons[v] = 1;
+            if (bond.getOrder() == DOUBLE && ringSearch.cyclic(u, v)) {
+                piBonds[u]++;
+                piBonds[v]++;
+            }
         }
 
+        // any atom which is adjacent to one (and only one) cyclic
+        // pi bond contributes 1 electron
+        for (int i = 0; i < n; i++) {
+            electrons[i] = piBonds[i] == 1 ? 1 : -1;
+        }
+
         return electrons;
     }
 }

src/test/org/openscience/cdk/aromaticity/PiBondModelTest.java

@@ -167,6 +167,18 @@ public class PiBondModelTest {
         test(smiles("O=C1NC=CC=C1"),
              -1, -1, -1, 1, 1, 1, 1);
     }
+
+    // ensures atoms next to 2 cyclic pi bonds aren't allowed
+    @Test public void cyclodecahexaene() throws Exception {
+        test(smiles("C1=CC=C=CC=C=CC=C1"),
+             1, 1, 1, -1, 1, 1, -1, 1, 1, 1);    
+    }
+
+    // similar to cyclodecahexaene but 5 pi bonds instead of 6
+    @Test public void cyclodecapentaene() throws Exception {
+        test(smiles("C1=CC=CC=CC=CC=C1"),
+             1, 1, 1, 1, 1, 1, 1, 1, 1, 1);
+    }
 
     static IAtomContainer smiles(String smi) throws Exception {
         return new SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smi);