Added Ninas modifcations to ensure that getting a molecular formula includes implicit hydrogens. Addressed bug 2983334. Also updated a unit test to take into account that H's are being considered

Change-Id: I9881e31c05d0f1bfb965393bd806e562a6158a0e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Author: rajarshi

src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java

@@ -756,17 +756,25 @@ public static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer
 	 * @see                      #getMolecularFormula(IAtomContainer)
 	 */
 	@TestMethod("testGetMolecularFormula_IAtomContainer_IMolecularFormula")
-	public static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula) {
-		int charge = 0;
-		for (IAtom iAtom : atomContainer.atoms()) {
-			formula.addIsotope(iAtom);
-			charge += iAtom.getFormalCharge();
-		}
-		formula.setCharge(charge);
-		return formula;
-	}
-
-	/**
+    public static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer, IMolecularFormula formula) {
+        int charge = 0;
+        IAtom hAtom = null;
+        for (IAtom iAtom : atomContainer.atoms()) {
+            formula.addIsotope(iAtom);
+            charge += iAtom.getFormalCharge();
+
+            if (iAtom.getImplicitHydrogenCount() != null &&
+                    (iAtom.getImplicitHydrogenCount() > 0)) {
+                if (hAtom == null) hAtom =
+                        atomContainer.getBuilder().newInstance(IAtom.class, "H");
+                formula.addIsotope(hAtom, iAtom.getImplicitHydrogenCount());
+            }
+        }
+        formula.setCharge(charge);
+        return formula;
+    }
+
+    /**
 	 * Method that actually does the work of convert the IMolecularFormula
 	 * to IAtomContainer.
 	 * <p> The hydrogens must be implicit.

src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java

@@ -20,12 +20,6 @@
  */
 package org.openscience.cdk.tools.manipulator;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
 import org.junit.Assert;
 import org.junit.Test;
 import org.openscience.cdk.Atom;
@@ -46,8 +40,14 @@
 import org.openscience.cdk.io.MDLV2000Reader;
 import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
 import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.templates.MoleculeFactory;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * Checks the functionality of the MolecularFormulaManipulator.
  *
@@ -885,7 +885,7 @@ public void testSingleAtomFromSmiles() throws InvalidSmilesException {
         IAtomContainer mol = sp.parseSmiles("C");
         IMolecularFormula mf = MolecularFormulaManipulator.getMolecularFormula(mol);
         double exactMass = MolecularFormulaManipulator.getTotalExactMass(mf);
-        Assert.assertEquals(12.0000, exactMass, 0.0001);
+        Assert.assertEquals(16.0313, exactMass, 0.0001);
     }
 
     @Test
@@ -1055,4 +1055,26 @@ public void testAmericum() {
         Assert.assertNotNull(formula);
         Assert.assertEquals("Am", MolecularFormulaManipulator.getString(formula));
     }
+
+    /**
+     * @cdk.bug 2983334
+     */
+    @Test
+    public void testImplicitH() throws Exception {
+
+        CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(NoNotificationChemObjectBuilder.getInstance());
+
+        IAtomContainer mol = MoleculeFactory.makeBenzene();
+
+        IMolecularFormula f = MolecularFormulaManipulator.getMolecularFormula(mol);
+        Assert.assertEquals("C6", MolecularFormulaManipulator.getString(f));
+
+        Assert.assertEquals(6, mol.getAtomCount());
+        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
+        adder.addImplicitHydrogens(mol);
+        Assert.assertEquals(6, mol.getAtomCount());
+        f = MolecularFormulaManipulator.getMolecularFormula(mol);
+        Assert.assertEquals("C6H6", MolecularFormulaManipulator.getString(f));
+
+    }
 }