Consider implicit hydrogens in exact mass utility.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Apr 6, 2014 · 0e85729 · 0e85729
1 parent 7433ac1
commit 0e85729
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Showing 2 changed files with 15 additions and 5 deletions.
diff --git a/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -196,11 +196,21 @@ public static double getTotalCharge(IAtomContainer atomContainer) {
      */
     @TestMethod("testGetTotalExactMass_IAtomContainer")
     public static double getTotalExactMass(IAtomContainer atomContainer) {
-        double mass = 0.0;
-        for (IAtom atom : atomContainer.atoms()) {
-            mass += atom.getExactMass();
+        try {
+
+            Isotopes isotopes = Isotopes.getInstance();
+            double mass = 0.0;
+            double hExactMass = isotopes.getMajorIsotope(1).getExactMass();
+            for (IAtom atom : atomContainer.atoms()) {
+                if (atom.getImplicitHydrogenCount() == null)
+                    throw new IllegalArgumentException("an atom had with unknown (null) implicit hydrogens");                
+                mass += atom.getExactMass();
+                mass += atom.getImplicitHydrogenCount() * hExactMass; 
+            }
+            return mass;
+        } catch (IOException e) {
+            throw new RuntimeException("Isotopes definitions could not be loaded", e);
         }
-        return mass;
     }
 
     /**

diff --git a/...ard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java b/...ard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java
@@ -528,7 +528,7 @@ private IAtomContainer getChiralMolTemplate() {
         mol.getAtom(1).setExactMass(34.96885268);
         double totalExactMass = AtomContainerManipulator.getTotalExactMass(mol);
 
-        Assert.assertEquals(46.96885268,totalExactMass,0.000001);
+        Assert.assertEquals(49.992327775,totalExactMass,0.000001);
     }
 
     @Test(expected = IllegalArgumentException.class)