[Cdk-commits] SF.net SVN: cdk: [6192] trunk/cdk/src/org/openscience/cdk/tools/manipulator

[<mig...@us...>]

Revision: 6192
Author:   miguelrojasch
Date:     2006-05-08 02:25:26 -0700 (Mon, 08 May 2006)
ViewCVS:  http://svn.sourceforge.net/cdk/?rev=6192&view=rev

Log Message:
-----------
new methods which return the total positive formal charge and negative of a atomContainer

Modified Paths:
--------------
    trunk/cdk/src/org/openscience/cdk/test/tools/manipulator/AtomContainerManipulatorTest.java
    trunk/cdk/src/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
Modified: trunk/cdk/src/org/openscience/cdk/test/tools/manipulator/AtomContainerManipulatorTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/tools/manipulator/AtomContainerManipulatorTest.java	2006-05-08 09:07:00 UTC (rev 6191)
+++ trunk/cdk/src/org/openscience/cdk/test/tools/manipulator/AtomContainerManipulatorTest.java	2006-05-08 09:25:26 UTC (rev 6192)
@@ -73,7 +73,6 @@
         mol.addBond(1,5,1);
         assertEquals(6, mol.getAtomCount());
         assertEquals(5, mol.getBondCount());
-        System.out.println(mol);
         assertEquals(0, AtomContainerManipulator.getTotalHydrogenCount(mol));
     }
         
@@ -125,6 +124,51 @@
         assertEquals("incorrect hydrogen count", 4, ac.getAtomAt(0).getHydrogenCount());
         assertEquals("incorrect hydrogen count", 4, ac.getAtomAt(1).getHydrogenCount());
     }
+    /**
+     * Test total formal charge.
+     *
+     * @throws IOException
+     * @throws ClassNotFoundException
+     * @throws CDKException
+     */
+    public void testgetTotalFormalCharge() throws IOException, ClassNotFoundException, CDKException
+    {
+        SmilesParser parser = new SmilesParser();
+        Molecule mol = parser.parseSmiles("[C-]C[C+][C+]C");
+        int totalCharge = AtomContainerManipulator.getTotalFormalCharge((IAtomContainer)mol);
+
+        assertEquals(1,totalCharge);
+    }
+    /**
+     * Test total positive formal charge.
+     *
+     * @throws IOException
+     * @throws ClassNotFoundException
+     * @throws CDKException
+     */
+    public void testgetTotalPositiveFormalCharge() throws IOException, ClassNotFoundException, CDKException
+    {
+        SmilesParser parser = new SmilesParser();
+        Molecule mol = parser.parseSmiles("[C-]C[C+][C+]C");
+        int totalCharge = AtomContainerManipulator.getTotalPositiveFormalCharge((IAtomContainer)mol);
+
+        assertEquals(2,totalCharge);
+    }
+    /**
+     * Test total negative formal charge.
+     *
+     * @throws IOException
+     * @throws ClassNotFoundException
+     * @throws CDKException
+     */
+    public void testgetTotalNegativeFormalCharge() throws IOException, ClassNotFoundException, CDKException
+    {
+        SmilesParser parser = new SmilesParser();
+        Molecule mol = parser.parseSmiles("[C-]C[C+][C+]C");
+        int totalCharge = AtomContainerManipulator.getTotalNegativeFormalCharge((IAtomContainer)mol);
+
+        assertEquals(-1,totalCharge);
+    }
 }
 
 

Modified: trunk/cdk/src/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java	2006-05-08 09:07:00 UTC (rev 6191)
+++ trunk/cdk/src/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java	2006-05-08 09:25:26 UTC (rev 6192)
@@ -101,12 +101,36 @@
      * @return The summed formal charges of all atoms in this AtomContainer.
      */
     public static int getTotalFormalCharge(IAtomContainer atomContainer) {
+        int chargeP = getTotalNegativeFormalCharge(atomContainer);
+        int chargeN = getTotalPositiveFormalCharge(atomContainer);
+        int totalCharge = chargeP + chargeN;
+        
+        return totalCharge;
+    }
+    /**
+     * @return The summed negative formal charges of all atoms in this AtomContainer. 
+     */
+    public static int getTotalNegativeFormalCharge(IAtomContainer atomContainer) {
         int charge = 0;
         for (int i = 0; i < atomContainer.getAtomCount(); i++) {
-            charge += atomContainer.getAtomAt(i).getFormalCharge();
+        	double chargeI = atomContainer.getAtomAt(i).getFormalCharge();
+        	if(chargeI < 0)
+        		charge += chargeI;
         }
         return charge;
     }
+    /**
+     * @return The summed positive formal charges of all atoms in this AtomContainer. 
+     */
+    public static int getTotalPositiveFormalCharge(IAtomContainer atomContainer) {
+        int charge = 0;
+        for (int i = 0; i < atomContainer.getAtomCount(); i++) {
+        	double chargeI = atomContainer.getAtomAt(i).getFormalCharge();
+        	if(chargeI > 0)
+        		charge += chargeI;
+        }
+        return charge;
+    }
 
     /**
      * @return The summed implicit hydrogens of all atoms in this AtomContainer.


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