[Cdk-commits] SF.net SVN: cdk: [10305] branches/miguelrojasch/reaction/src

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

Revision: 10305
          http://cdk.svn.sourceforge.net/cdk/?rev=10305&view=rev
Author:   miguelrojasch
Date:     2008-03-05 00:25:36 -0800 (Wed, 05 Mar 2008)

Log Message:
-----------
update the isomorphism to QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer to distinguish between aromatics compounds

Modified Paths:
--------------
    branches/miguelrojasch/reaction/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java
    branches/miguelrojasch/reaction/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java

Modified: branches/miguelrojasch/reaction/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java
===================================================================
--- branches/miguelrojasch/reaction/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java	2008-03-05 07:57:54 UTC (rev 10304)
+++ branches/miguelrojasch/reaction/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java	2008-03-05 08:25:36 UTC (rev 10305)
@@ -231,24 +231,18 @@
 	 * @return   			 True, if the atomContainer is contained
 	 */
 	private boolean existAC(IAtomContainerSet set, IAtomContainer atomContainer) {
-//		atomContainer = setID(atomContainer);
 		for(int i = 0 ; i < atomContainer.getAtomCount(); i++)
 			atomContainer.getAtom(i).setID(""+atomContainer.getAtomNumber(atomContainer.getAtom(i)));
 		QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(atomContainer);
 		for(int i = 0 ; i < set.getAtomContainerCount(); i++){
-//			IAtomContainer ac = setID(set.getAtomContainer(i));
 			IAtomContainer ss = set.getAtomContainer(i);
 			for(int j = 0 ; j < ss.getAtomCount(); j++)
 				ss.getAtom(j).setID(""+ss.getAtomNumber(ss.getAtom(j)));
-//			QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(ac);
-//			QueryAtomContainer qAC = QueryAtomContainerCreator.createAnyAtomContainer(atomContainer,false);
 			try {
 				if(UniversalIsomorphismTester.isIsomorph(ss,qAC)){
-//					logger.debug("exist");
-//					SmilesGenerator sg = new SmilesGenerator();
-//					System.out.println(sg.createSMILES((IMolecule) atomContainer));
-//					System.out.println(sg.createSMILES((IMolecule) ss));
-					return true;
+					QueryAtomContainer qAC2 = QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(atomContainer);
+					if(UniversalIsomorphismTester.isIsomorph(ss,qAC2))
+						return true;
 				}
 			} catch (CDKException e1) {
 				System.err.println(e1);

Modified: branches/miguelrojasch/reaction/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java	2008-03-05 07:57:54 UTC (rev 10304)
+++ branches/miguelrojasch/reaction/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java	2008-03-05 08:25:36 UTC (rev 10305)
@@ -51,7 +51,6 @@
 import org.openscience.cdk.reaction.type.RearrangementLonePairReaction;
 import org.openscience.cdk.reaction.type.RearrangementRadicalReaction;
 import org.openscience.cdk.reaction.type.SharingLonePairReaction;
-import org.openscience.cdk.smiles.SmilesGenerator;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 /**
@@ -772,7 +771,7 @@
 		StructureResonanceGenerator gRI = new StructureResonanceGenerator();
 		IMoleculeSet resonanceStructures = gRI.getStructures(molecule);
 		
-		Assert.assertEquals(4,resonanceStructures.getAtomContainerCount());
+		Assert.assertEquals(5,resonanceStructures.getAtomContainerCount());
 	}
 	/**
 	 * 
@@ -808,8 +807,7 @@
 		AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
 		LonePairElectronChecker lpChecker = new LonePairElectronChecker();
 		lpChecker.saturate(molecule);
-		SmilesGenerator sg = new SmilesGenerator();
-		System.out.println(sg.createSMILES(molecule));
+		
 		Assert.assertEquals(18, molecule.getAtomCount());
 
 		StructureResonanceGenerator gRI = new StructureResonanceGenerator();
@@ -821,10 +819,7 @@
 		gRI.setReactions(newReactionList);
 		
 		IMoleculeSet resonanceStructures = gRI.getStructures(molecule);
-
-//		SmilesGenerator sg = new SmilesGenerator();
-		for(int i = 0; i < resonanceStructures.getMoleculeCount(); i++)
-			System.out.println(sg.createSMILES((IMolecule) resonanceStructures.getMolecule(i)));
+		
 		Assert.assertEquals(2,resonanceStructures.getAtomContainerCount());
 	}
 	


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