Special handling of atom type 'X', leave hydrogens alone unless the v…

…alue is null and we then set it to 0. Note this conditional was only added recently to ensure pseudo atoms don't have an unset hydrogen count. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jul 22, 2014 · a952ead · a952ead
1 parent 3836141
commit a952ead
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Showing 2 changed files with 31 additions and 1 deletion.
diff --git a/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java b/base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java
@@ -36,11 +36,13 @@
 import org.openscience.cdk.PseudoAtom;
 import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
 import org.openscience.cdk.config.Elements;
+import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemFile;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IElement;
 import org.openscience.cdk.interfaces.IMolecularFormula;
 import org.openscience.cdk.io.MDLV2000Reader;
@@ -51,6 +53,9 @@
 import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
 import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
 
+import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.MatcherAssert.assertThat;
+
 /**
  * Tests CDK's hydrogen adding capabilities in terms of
  * example molecules.
@@ -781,6 +786,30 @@ public void testPseudoAtom() throws Exception {
         }
         Assert.assertEquals(1, hCount);
     }
+
+    @Test public void unknownAtomTypeLeavesHydrogenCountAlone() throws Exception {
+        IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+        CDKHydrogenAdder   hydrogenAdder = CDKHydrogenAdder.getInstance(bldr);
+        IAtomContainer container = bldr.newInstance(IAtomContainer.class);
+        IAtom atom = bldr.newInstance(IAtom.class, "C");
+        atom.setImplicitHydrogenCount(3);
+        atom.setAtomTypeName("X");
+        container.addAtom(atom);
+        hydrogenAdder.addImplicitHydrogens(container);
+        assertThat(atom.getImplicitHydrogenCount(), is(3));
+    }
+
+    @Test public void unknownAtomTypeLeavesHydrogenCountAloneUnlessNull() throws Exception {
+        IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+        CDKHydrogenAdder   hydrogenAdder = CDKHydrogenAdder.getInstance(bldr);
+        IAtomContainer container = bldr.newInstance(IAtomContainer.class);
+        IAtom atom = bldr.newInstance(IAtom.class, "C");
+        atom.setImplicitHydrogenCount(null);
+        atom.setAtomTypeName("X");
+        container.addAtom(atom);
+        hydrogenAdder.addImplicitHydrogens(container);
+        assertThat(atom.getImplicitHydrogenCount(), is(0));
+    }
 
     private void findAndConfigureAtomTypesForAllAtoms(IAtomContainer container) throws Exception {
     	Iterator<IAtom> atoms = container.atoms().iterator();

diff --git a/base/valencycheck/src/main/java/org/openscience/cdk/tools/CDKHydrogenAdder.java b/base/valencycheck/src/main/java/org/openscience/cdk/tools/CDKHydrogenAdder.java
@@ -125,7 +125,8 @@ public void addImplicitHydrogens(IAtomContainer container, IAtom atom) throws CD
 			throw new CDKException("IAtom is not typed! " + atom.getSymbol());
 
 		if ("X".equals(atom.getAtomTypeName())) {
-			atom.setImplicitHydrogenCount(0);
+            if (atom.getImplicitHydrogenCount() == null)
+			    atom.setImplicitHydrogenCount(0);
 			return; 
 		}