Consider implicit hydrogen counts in getNaturalExactMass.

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

base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java

@@ -204,27 +204,36 @@ public static double getTotalExactMass(IAtomContainer atomContainer) {
     }
 
     /**
-     * Returns the molecular mass of the IAtomContainer. For the calculation it uses the
-     * masses of the isotope mixture using natural abundances.
+     * Returns the molecular mass of the IAtomContainer. For the calculation it
+     * uses the masses of the isotope mixture using natural abundances.
      *
-     * @param       atomContainer
+     * @param atomContainer
      * @cdk.keyword mass, molecular
      */
     @TestMethod("testGetNaturalExactMass_IAtomContainer")
-    public static double getNaturalExactMass(IAtomContainer atomContainer) {
-		 double mass = 0.0;
-		 IsotopeFactory factory;
-		 try {
-			 factory = Isotopes.getInstance();
-		 } catch (IOException e) {
-			 throw new RuntimeException("Could not instantiate the IsotopeFactory.");
-		 }
-        for (IAtom atom : atomContainer.atoms()) {
-            IElement isotopesElement = atom.getBuilder().newInstance(IElement.class,atom.getSymbol());
-            mass += factory.getNaturalMass(isotopesElement);
+    public static double getNaturalExactMass(IAtomContainer atomContainer) {           
+        try {
+            Isotopes isotopes      = Isotopes.getInstance();
+            double   hydgrogenMass = isotopes.getNaturalMass(Elements.HYDROGEN);
+
+            double mass = 0.0;
+            for (final IAtom atom : atomContainer.atoms()) {
+
+                if (atom.getAtomicNumber() == null)
+                    throw new IllegalArgumentException("an atom had with unknown (null) atomic number");
+                if (atom.getImplicitHydrogenCount() == null)
+                    throw new IllegalArgumentException("an atom had with unknown (null) implicit hydrogens");
+
+                mass += isotopes.getNaturalMass(Elements.ofNumber(atom.getAtomicNumber()).toIElement());
+                mass += hydgrogenMass * atom.getImplicitHydrogenCount();
+            }
+            return mass;
+
+        } catch (IOException e) {
+            throw new RuntimeException("Isotopes definitions could not be loaded", e);
         }
-		 return mass;
     }
+
     /**
      * Get the summed natural abundance of all atoms in an AtomContainer
      *

base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java

@@ -530,16 +530,35 @@ private IAtomContainer getChiralMolTemplate() {
 
         Assert.assertEquals(46.96885268,totalExactMass,0.000001);
     }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void getNaturalExactMassNeedsHydrogens() {
+        IAtomContainer mol = new AtomContainer();
+        mol.addAtom(new Atom("C"));
+        AtomContainerManipulator.getNaturalExactMass(mol);    
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void getNaturalExactMassNeedsAtomicNumber() {
+        IAtomContainer mol = new AtomContainer();
+        mol.addAtom(new Atom("C"));
+        mol.getAtom(0).setAtomicNumber(null);
+        AtomContainerManipulator.getNaturalExactMass(mol);
+    }
 
     @Test public void testGetNaturalExactMass_IAtomContainer() throws Exception {
     	IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance(); 
         IAtomContainer mol = builder.newInstance(IAtomContainer.class);
         mol.addAtom(new Atom("C"));
         mol.addAtom(new Atom("Cl"));
+
+        mol.getAtom(0).setImplicitHydrogenCount(4);
+        mol.getAtom(1).setImplicitHydrogenCount(1);
 
         double expectedMass = 0.0;
         expectedMass += Isotopes.getInstance().getNaturalMass(builder.newInstance(IElement.class,"C"));
         expectedMass += Isotopes.getInstance().getNaturalMass(builder.newInstance(IElement.class,"Cl"));
+        expectedMass += 5 * Isotopes.getInstance().getNaturalMass(builder.newInstance(IElement.class,"H"));
 
     	double totalExactMass = AtomContainerManipulator.getNaturalExactMass(mol);