The formal charge of the IAtomcontainer is transfered to IMolecularFo…

…rmula Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
egonw · May 18, 2009 · 2f30841 · 2f30841
1 parent b72fa58
commit 2f30841
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diff --git a/src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java b/src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
@@ -728,10 +728,12 @@ public static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer
 	 */
 	@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;
 	}
 	/**

diff --git a/src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java b/src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
@@ -660,6 +660,26 @@ public void testGetMolecularFormula_IAtomContainer(){
 		Assert.assertEquals(MolecularFormulaManipulator.getElementCount(mf2, elemH), MolecularFormulaManipulator.getElementCount(mf1,elemH));
 
 	}
+
+    /**
+	 * A unit test suite for JUnit.
+	 *
+	 * @return    The test suite
+	 */
+	@Test 
+    public void testGetMolecularFormula_IAtomContainer_withCharge(){
+		IAtomContainer ac = builder.newAtomContainer();
+		ac.addAtom(builder.newAtom("C"));
+		ac.getAtom(0).setFormalCharge(1);
+		ac.addAtom(builder.newAtom("C"));
+		ac.addAtom(builder.newAtom("H"));
+		ac.addAtom(builder.newAtom("H"));
+		ac.addAtom(builder.newAtom("H"));
+
+		IMolecularFormula mf1 = MolecularFormulaManipulator.getMolecularFormula(ac);		
+
+		Assert.assertEquals(1, mf1.getCharge(),0.000);
+	}
 	/**
 	 * A unit test suite for JUnit.
 	 *