Aromaticity information is lost on descriptor execution unless the 'a…

…romaticity parameter' is set to true. Already perceived -- pre-perceived -- aromaticity information should not be lost automatically if this parameter is set to false. Perception of unset parameters only via the helper method in the AtomContainerManipulator rectifies this issue. Three test cases: 1) Benzene with pre-perceived aromaticity and no aromaticity perception in the descriptor. 2) Benzene with no pre-perceived aromaticity and no aromaticity perception in the descriptor. 3) Benzene with no pre-perceived aromaticity and perception in the descriptor.

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

src/main/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java

@@ -210,7 +210,7 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
         IAtomContainer ac;
         try {
             ac = (IAtomContainer) atomContainer.clone();
-            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
+            AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(ac);
             CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(ac.getBuilder());
             hAdder.addImplicitHydrogens(ac);
             AtomContainerManipulator.convertImplicitToExplicitHydrogens(ac);

src/test/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptorTest.java

@@ -28,11 +28,16 @@
 import org.junit.Ignore;
 import org.junit.Test;
 import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.aromaticity.Aromaticity;
+import org.openscience.cdk.aromaticity.ElectronDonation;
 import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.graph.Cycles;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.qsar.result.DoubleResult;
 import org.openscience.cdk.smiles.SmilesParser;
 
+import static org.hamcrest.Matchers.closeTo;
+
 /**
  * TestSuite that runs XlogP tests.
  *
@@ -267,5 +272,37 @@ public void testno1596() throws ClassNotFoundException, CDKException, java.lang.
         //logger.debug("no1822:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
         Assert.assertEquals(2.36, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
     }
+
+    @Test public void testAromaticBenzene() throws java.lang.Exception {
+        Object[] params = { false, true };
+        descriptor.setParameters(params);
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("C1=CC=CC=C1"); // benzene
+        Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), Cycles.all());
+        aromaticity.apply(mol);
+        assertAtomTypesPerceived(mol);
+        addExplicitHydrogens(mol);
+        Assert.assertThat(((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), closeTo(2.02, 0.01));
+    }
+
+    @Test public void testNonAromaticBenzene() throws java.lang.Exception {
+        Object[] params = { false, true };
+        descriptor.setParameters(params);
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("C1=CC=CC=C1"); // benzene
+        assertAtomTypesPerceived(mol);
+        addExplicitHydrogens(mol);
+        Assert.assertThat(((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), closeTo(2.08, 0.01));
+    }
+
+    @Test public void testPerceivedAromaticBenzene() throws java.lang.Exception {
+        Object[] params = { true, true };
+        descriptor.setParameters(params);
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer mol = sp.parseSmiles("C1=CC=CC=C1"); // benzene
+        assertAtomTypesPerceived(mol);
+        addExplicitHydrogens(mol);
+        Assert.assertThat(((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), closeTo(2.02, 0.01));
+    }
 }