[Cdk-commits] SF.net SVN: cdk: [9933] branches/miguelrojasch/reaction/src/org/openscience /cdk

[<eg...@us...>]

Revision: 9933
          http://cdk.svn.sourceforge.net/cdk/?rev=9933&view=rev
Author:   egonw
Date:     2008-01-20 12:33:20 -0800 (Sun, 20 Jan 2008)

Log Message:
-----------
Fixed test: testing was inconsistent with comment, and with results which did match the comments

Modified Paths:
--------------
    branches/miguelrojasch/reaction/src/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java
    branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java

Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java	2008-01-20 19:22:52 UTC (rev 9932)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java	2008-01-20 20:33:20 UTC (rev 9933)
@@ -41,7 +41,10 @@
     }
     public void setOperator(String str){}
     public boolean matches(IAtom atom) {
-        return this.getSymbol().equals(atom.getSymbol())&&this.getFormalCharge()==atom.getFormalCharge();
+    	int requiredCharge = this.getFormalCharge() == null ? 0 : this.getFormalCharge();
+    	int foundCharge = atom.getFormalCharge() == null ? 0 : atom.getFormalCharge();
+        return this.getSymbol().equals(atom.getSymbol()) &&
+               requiredCharge == foundCharge;
     };
 
     public String toString() {

Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java	2008-01-20 19:22:52 UTC (rev 9932)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/BreakingBondReactionTest.java	2008-01-20 20:33:20 UTC (rev 9933)
@@ -33,6 +33,7 @@
 import org.openscience.cdk.Atom;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.Molecule;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IBond;
@@ -141,8 +142,11 @@
         /*[H-] + [C+](H)=O*/
 		molecule2 = builder.newMolecule();//Smiles("C=O");
         molecule2.addAtom(builder.newAtom("C"));
+        molecule2.getAtom(0).setFormalCharge(+1);
         molecule2.addAtom(builder.newAtom("O"));
 	    molecule2.addBond(0, 1, IBond.Order.DOUBLE);
+	    molecule2.addAtom(builder.newAtom("H"));
+	    molecule2.addBond(0, 2, IBond.Order.SINGLE);
         
 	    qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
 		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
@@ -150,13 +154,10 @@
 		product = setOfReactions.getReaction(2).getProducts().getMolecule(0);
         /*[H+] + [C-](H)=O*/
 		molecule2.getAtom(0).setFormalCharge(-1);
-		molecule2.addAtom(new Atom("H"));
-	    molecule2.addBond(0, 2, IBond.Order.SINGLE);
         qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
 		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
-		
-		
 	}
+
 	/**
 	 * A unit test suite for JUnit. Reaction: C=O => [C+]-[O-]
 	 * Manually put of the reactive center.


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