Fix phenol hbond acceptor count

johnmay · egonw · commit dfbc32822e7d · 2021-11-25T10:38:30.000+01:00
diff --git a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java
@@ -192,15 +192,27 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
             }
             // looking for suitable oxygen atoms
             else if (atom.getAtomicNumber() == IElement.O && atom.getFormalCharge() <= 0) {
-                //excluding oxygens that are adjacent to a nitrogen or to an aromatic carbon
+
                 List<IBond> neighbours = ac.getConnectedBondsList(atom);
+
+                // get the "true" degree
+                int degree = 0;
+                for (IBond bond : neighbours) {
+                    IAtom nbor = bond.getOther(atom);
+                    if (nbor.getAtomicNumber() != IAtom.H)
+                        degree++;
+                }
+
                 for (IBond bond : neighbours) {
                     IAtom neighbor = bond.getOther(atom);
-                    if (neighbor.getAtomicNumber() == IElement.N ||
-                        (neighbor.getAtomicNumber() == IElement.C &&
-                         neighbor.isAromatic() &&
-                         bond.getOrder() != IBond.Order.DOUBLE))
-                        continue atomloop;;
+                    // adjacent to a nitrogen => reject
+                    if (neighbor.getAtomicNumber() == IElement.N)
+                        continue atomloop;
+                    // adjacent to an aromatic carbon and degree != 1
+                    if (neighbor.getAtomicNumber() == IElement.C &&
+                        neighbor.isAromatic() &&
+                        degree != 1)
+                        continue atomloop;
                 }
                 hBondAcceptors++;
             }
diff --git a/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptorTest.java b/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptorTest.java
@@ -134,4 +134,15 @@ public void exocyclicOxygenInAromaticRing() throws InvalidSmilesException {
         int actual = ((IntegerResult)hbond_acceptor_desc.calculate(m).getValue()).intValue();
         org.hamcrest.MatcherAssert.assertThat(actual, CoreMatchers.is(3));
     }
+
+    @Test
+    public void testPhenol() throws CDKException {
+        Object[] params = {new Boolean(true)};
+        descriptor.setParameters(params);
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        // original molecule O=N(=O)c1cccc2cn[nH]c12 - correct kekulisation will give
+        // the same result. this test though should depend on kekulisation working
+        IAtomContainer mol = sp.parseSmiles("Oc1ccccc1");
+        Assert.assertEquals(1, ((IntegerResult) descriptor.calculate(mol).getValue()).intValue());
+    }
 }
