Resolve #495

cdk · Oct 25, 2018 · a64b2e0 · a64b2e0
1 parent 04dfa04
commit a64b2e0
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Showing 2 changed files with 24 additions and 5 deletions.
diff --git a/...ain/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java b/...ain/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java
@@ -192,11 +192,15 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
             // looking for suitable oxygen atoms
             else if (atom.getSymbol().equals("O") && atom.getFormalCharge() <= 0) {
                 //excluding oxygens that are adjacent to a nitrogen or to an aromatic carbon
-                List<IAtom> neighbours = ac.getConnectedAtomsList(atom);
-                for (IAtom neighbour : neighbours)
-                    if (neighbour.getSymbol().equals("N")
-                            || (neighbour.getSymbol().equals("C") && neighbour.getFlag(CDKConstants.ISAROMATIC)))
-                        continue atomloop;
+                List<IBond> neighbours = ac.getConnectedBondsList(atom);
+                for (IBond bond : neighbours) {
+                    IAtom neighbor = bond.getOther(atom);
+                    if (neighbor.getSymbol().equals("N") ||
+                        (neighbor.getSymbol().equals("C") &&
+                         neighbor.isAromatic() &&
+                         bond.getOrder() != IBond.Order.DOUBLE))
+                        continue atomloop;;
+                }
                 hBondAcceptors++;
             }
         }

diff --git a/...java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptorTest.java b/...java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptorTest.java
@@ -20,11 +20,13 @@
 
 import javax.vecmath.Point3d;
 
+import org.hamcrest.CoreMatchers;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -119,4 +121,17 @@ public void testCID9257() throws CDKException {
         descriptor.setParameters(params);
         Assert.assertEquals(2, ((IntegerResult) descriptor.calculate(mol).getValue()).intValue());
     }
+
+    /**
+     * @see <a href="https://github.com/cdk/cdk/issues/495">Issue 495</a>
+     */
+    @Test
+    public void exocyclicOxygenInAromaticRing() throws InvalidSmilesException {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IAtomContainer m = sp.parseSmiles("Cn1c2nc([nH]c2c(=O)n(c1=O)C)C1CCCC1");
+
+        HBondAcceptorCountDescriptor hbond_acceptor_desc = new HBondAcceptorCountDescriptor();
+        int actual = ((IntegerResult)hbond_acceptor_desc.calculate(m).getValue()).intValue();
+        Assert.assertThat(actual, CoreMatchers.is(3));
+    }
 }