Avoid erroneous aromaticity due to abnormal valence.

Change-Id: I4abbb2e203c07c2dbec27dfb0090d20e06e49a64 Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Feb 8, 2014 · d4255b3 · d4255b3
1 parent 1a3f3d3
commit d4255b3
Show file tree

Hide file tree

Showing 2 changed files with 54 additions and 3 deletions.
diff --git a/src/main/org/openscience/cdk/aromaticity/DaylightModel.java b/src/main/org/openscience/cdk/aromaticity/DaylightModel.java
@@ -169,10 +169,13 @@ else if (nCyclicPiBonds[i] == 1) {
             }
 
             // a anion with a lone pair contributes 2 electrons - simplification
-            // here is we count the number free valence electrons
+            // here is we count the number free valence electrons but also
+            // check if the bonded valence is okay (i.e. not a radical)
             else if (charge <= 0 && charge > -3) {
-                int v = valence(element, charge);
-                if (v - bondOrderSum[i] >= 2)
+                int bondedValence = bondOrderSum[i] + container.getAtom(i).getImplicitHydrogenCount();
+                if (!normal(element, charge, bondedValence))
+                    electrons[i] = -1;
+                else if (valence(element, charge) - bondOrderSum[i] >= 2)
                     electrons[i] = 2;
                 else
                     electrons[i] = -1;
@@ -257,6 +260,39 @@ private static boolean aromaticElement(int element) {
         return false;
     }
 
+    /**
+     * The element (with only sigma bonds) has normal valence for the specified
+     * charge.
+     *
+     * @param element atomic number
+     * @param charge  formal charge
+     * @param valence bonded electrons
+     * @return acceptable for this model
+     */
+    private static boolean normal(int element, int charge, int valence) {
+        switch (element) {
+            case CARBON:
+                if (charge == -1 || charge == +1)
+                    return valence == 3;
+                return charge == 0 && valence == 4;
+            case NITROGEN:
+            case PHOSPHORUS:
+            case ARSENIC:
+                if (charge == -1)
+                    return valence == 2;
+                if (charge == +1)
+                    return valence == 4;
+                return charge == 0 && valence == 3;
+            case OXYGEN:
+            case SULPHUR:
+            case SELENIUM:
+                if (charge == +1)
+                    return valence == 3;
+                return charge == 0 && valence == 2;
+        }
+        return false;    
+    }
+
     /**
      * Lookup of the number of valence electrons for the element at a given
      * charge.

diff --git a/src/test/org/openscience/cdk/aromaticity/DaylightModelTest.java b/src/test/org/openscience/cdk/aromaticity/DaylightModelTest.java
@@ -181,6 +181,21 @@ public class DaylightModelTest {
              -1, 0, 1, 1, 2, 1, 1);
     }
 
+    @Test public void abnormalValence_carbon() throws Exception {
+        test(smiles("[C]1[C][C][C][C]1"),
+             -1, -1, -1, -1, -1);
+    }
+
+    @Test public void abnormalValence_nitrogen() throws Exception {
+        test(smiles("[N]1[N][N][N][N]1"),
+             -1, -1, -1, -1, -1);
+    }
+
+    @Test public void abnormalValence_phosphorus() throws Exception {
+        test(smiles("[P]1[P][P][P][P]1"),
+             -1, -1, -1, -1, -1);
+    }
+
     static IAtomContainer addHydrogens(IAtomContainer container) throws CDKException {
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
         CDKHydrogenAdder.getInstance(container.getBuilder()).addImplicitHydrogens(container);