From: <eg...@us...> - 2008-07-27 12:12:44
|
Revision: 11786 http://cdk.svn.sourceforge.net/cdk/?rev=11786&view=rev Author: egonw Date: 2008-07-27 12:12:38 +0000 (Sun, 27 Jul 2008) Log Message: ----------- Moved the ConjugatedPiSystemsDetectorTest to reaction, removing the dependency of the qsar module on extra Modified Paths: -------------- cdk/trunk/src/META-INF/qsar.cdkdepends cdk/trunk/src/main/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java cdk/trunk/src/test/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java cdk/trunk/src/test/org/openscience/cdk/modulesuites/MreactionTests.java Modified: cdk/trunk/src/META-INF/qsar.cdkdepends =================================================================== --- cdk/trunk/src/META-INF/qsar.cdkdepends 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/META-INF/qsar.cdkdepends 2008-07-27 12:12:38 UTC (rev 11786) @@ -3,6 +3,5 @@ cdk-core.jar cdk-standard.jar cdk-valencycheck.jar -cdk-extra.jar cdk-reaction.jar cdk-charges.jar Modified: cdk/trunk/src/main/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/main/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -1,10 +1,6 @@ -/* - * $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ +/* $Revision$ $Author$ $Date$ * - * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project + * Copyright (C) 2004-2007 Kai Hartmann <kai...@us...> * * Contact: cdk...@li... * @@ -27,22 +23,19 @@ import java.util.List; import java.util.Stack; -import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.AtomContainerSet; -import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IBond; /** - *@author kaihartmann - * @cdk.svnrev $Revision$ - *@cdk.created 2004-09-17 - *@cdk.module extra + * @author kaihartmann + * @cdk.svnrev $Revision$ + * @cdk.created 2004-09-17 + * @cdk.module reaction * - *@cdk.todo add negatively charged atoms (e.g. O-) to the pi system + * @cdk.todo add negatively charged atoms (e.g. O-) to the pi system */ public class ConjugatedPiSystemsDetector { @@ -75,8 +68,8 @@ *@param ac The AtomContainer for which to detect conjugated pi systems *@return The set of AtomContainers with conjugated pi systems */ - public static AtomContainerSet detect(org.openscience.cdk.interfaces.IAtomContainer ac) { - AtomContainerSet piSystemSet = new AtomContainerSet(); + public static IAtomContainerSet detect(IAtomContainer ac) { + IAtomContainerSet piSystemSet = ac.getBuilder().newAtomContainerSet(); for (int i = 0; i < ac.getAtomCount(); i++) { org.openscience.cdk.interfaces.IAtom atom = ac.getAtom(i); @@ -89,8 +82,8 @@ if (firstAtom.getFlag(CDKConstants.VISITED) || checkAtom(ac, firstAtom) == -1) { continue; } - AtomContainer piSystem = new org.openscience.cdk.AtomContainer(); - Stack stack = new Stack(); + IAtomContainer piSystem = ac.getBuilder().newAtomContainer(); + Stack<IAtom> stack = new Stack<IAtom>(); piSystem.addAtom(firstAtom); stack.push(firstAtom); @@ -98,13 +91,13 @@ // Start DFS from firstAtom while (!stack.empty()) { //boolean addAtom = false; - Atom currentAtom = (Atom) stack.pop(); - List atoms = ac.getConnectedAtomsList(currentAtom); - List bonds = ac.getConnectedBondsList(currentAtom); + IAtom currentAtom = (IAtom) stack.pop(); + List<IAtom> atoms = ac.getConnectedAtomsList(currentAtom); + List<IBond> bonds = ac.getConnectedBondsList(currentAtom); for (int j = 0; j < atoms.size(); j++) { - Atom atom = (Atom) atoms.get(j); - Bond bond = (Bond) bonds.get(j); + IAtom atom = atoms.get(j); + IBond bond = bonds.get(j); if (!atom.getFlag(CDKConstants.VISITED)) { int check = checkAtom(ac, atom); if (check == 1) { @@ -144,8 +137,8 @@ */ private static int checkAtom(IAtomContainer ac, IAtom currentAtom) { int check = -1; - List atoms = ac.getConnectedAtomsList(currentAtom); - List bonds = ac.getConnectedBondsList(currentAtom); + List<IAtom> atoms = ac.getConnectedAtomsList(currentAtom); + List<IBond> bonds = ac.getConnectedBondsList(currentAtom); if (currentAtom.getFlag(CDKConstants.ISAROMATIC)) { check = 0; } else if (currentAtom.getFormalCharge() == 1 /*&& currentAtom.getSymbol().equals("C")*/) { @@ -154,7 +147,7 @@ //// NEGATIVE CHARGES WITH A NEIGHBOOR PI BOND ////////////// int counterOfPi = 0; for(int n = 0; n < atoms.size(); n++) { - Atom atom = (Atom) atoms.get(n); + IAtom atom = atoms.get(n); if(ac.getMaximumBondOrder(atom) != IBond.Order.SINGLE) { counterOfPi ++; } @@ -171,7 +164,7 @@ int singleBondCount = 0; int highOrderBondCount = 0; for (int j = 0; j < atoms.size(); j++) { - Bond bond = (Bond) bonds.get(j); + IBond bond = bonds.get(j); if (bond == null || bond.getOrder() != IBond.Order.SINGLE) { highOrderBondCount++; } else { Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -24,7 +24,6 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; -import org.openscience.cdk.AtomContainerSet; import org.openscience.cdk.Molecule; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -33,6 +32,7 @@ import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -69,7 +69,7 @@ private static final String[] names = {"protonInConjSystem"}; private boolean checkAromaticity = false; private IAtomContainer acold=null; - private AtomContainerSet acSet=null; + private IAtomContainerSet acSet=null; /** Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -21,7 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; -import org.openscience.cdk.AtomContainerSet; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -31,7 +37,12 @@ import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -40,12 +51,6 @@ import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates G3R proton descriptors used in neural networks for H1 * NMR shift. @@ -83,7 +88,7 @@ private IRingSet varRingSet = null; - private AtomContainerSet varAtomContainerSet = null; + private IAtomContainerSet varAtomContainerSet = null; private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_G3R.class); Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -21,7 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; -import org.openscience.cdk.AtomContainerSet; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -31,7 +37,12 @@ import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -40,12 +51,6 @@ import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates GDR proton descriptors used in neural networks for H1 NMR shift. * <p/> @@ -77,7 +82,7 @@ private boolean checkAromaticity = false; private IAtomContainer acold = null; private IRingSet varRingSet = null; - private AtomContainerSet varAtomContainerSet = null; + private IAtomContainerSet varAtomContainerSet = null; private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_GDR.class); private final int gdr_desc_length = 7; Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -21,7 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; -import org.openscience.cdk.AtomContainerSet; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -31,7 +37,12 @@ import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -40,13 +51,7 @@ import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates GHR proton descriptors used in neural networks for H1 NMR shift. * <p/> @@ -78,7 +83,7 @@ private boolean checkAromaticity = false; private IAtomContainer acold = null; private IRingSet varRingSet = null; - private AtomContainerSet varAtomContainerSet = null; + private IAtomContainerSet varAtomContainerSet = null; private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_GHR.class); Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -21,8 +21,14 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org._3pq.jgrapht.Edge; -import org.openscience.cdk.AtomContainerSet; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -33,7 +39,12 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.MoleculeGraphs; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -42,12 +53,6 @@ import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift. * <p/> @@ -79,7 +84,7 @@ private boolean checkAromaticity = false; private IAtomContainer acold = null; private IRingSet varRingSet = null; - private AtomContainerSet varAtomContainerSet = null; + private IAtomContainerSet varAtomContainerSet = null; private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_GHR_topol.class); private final int ghr_topol_desc_length = 15; Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -21,7 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; -import org.openscience.cdk.AtomContainerSet; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -31,7 +37,12 @@ import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -40,12 +51,6 @@ import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates GDR proton descriptors used in neural networks for H1 NMR shift. * <p/> @@ -77,7 +82,7 @@ private boolean checkAromaticity = false; private IAtomContainer acold = null; private IRingSet varRingSet = null; - private AtomContainerSet varAtomContainerSet = null; + private IAtomContainerSet varAtomContainerSet = null; private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_GSR.class); Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -20,7 +20,6 @@ */ package org.openscience.cdk.qsar.descriptors.atompair; -import org.openscience.cdk.AtomContainerSet; import org.openscience.cdk.Molecule; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; @@ -28,6 +27,7 @@ import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomPairDescriptor; @@ -75,7 +75,7 @@ private static final String[] names = {"piContact"}; private boolean checkAromaticity = false; - AtomContainerSet acSet = null; + IAtomContainerSet acSet = null; private IAtomContainer acold=null; /** Modified: cdk/trunk/src/test/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/test/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -29,13 +29,13 @@ import junit.framework.Test; import junit.framework.TestSuite; -import org.openscience.cdk.AtomContainerSet; import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemObjectBuilder; @@ -53,7 +53,7 @@ /** * Checks the functionality of the ConjugatedPiSystemsCalculator. * - * @cdk.module test-extra + * @cdk.module test-reaction */ public class ConjugatedPiSystemsDetectorTest extends CDKTestCase { @@ -81,7 +81,7 @@ CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac = acSet.getAtomContainer(0); @@ -110,7 +110,7 @@ CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac = acSet.getAtomContainer(0); @@ -139,7 +139,7 @@ CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac = acSet.getAtomContainer(0); @@ -170,7 +170,7 @@ mol = chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(2, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -214,7 +214,7 @@ CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(2, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -255,7 +255,7 @@ CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(2, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -300,7 +300,7 @@ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -334,7 +334,7 @@ lpcheck.saturate(mol); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -356,7 +356,7 @@ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -379,7 +379,7 @@ lpcheck.saturate(mol); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -403,7 +403,7 @@ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -459,7 +459,7 @@ lpcheck.saturate(mol); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -484,7 +484,7 @@ lpcheck.saturate(mol); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); @@ -508,7 +508,7 @@ lpcheck.saturate(mol); CDKHueckelAromaticityDetector.detectAromaticity(mol); - AtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); + IAtomContainerSet acSet = ConjugatedPiSystemsDetector.detect(mol); assertEquals(1, acSet.getAtomContainerCount()); IAtomContainer ac1 = acSet.getAtomContainer(0); Modified: cdk/trunk/src/test/org/openscience/cdk/modulesuites/MreactionTests.java =================================================================== --- cdk/trunk/src/test/org/openscience/cdk/modulesuites/MreactionTests.java 2008-07-27 11:44:27 UTC (rev 11785) +++ cdk/trunk/src/test/org/openscience/cdk/modulesuites/MreactionTests.java 2008-07-27 12:12:38 UTC (rev 11786) @@ -30,6 +30,7 @@ import org.openscience.cdk.ReactionCoverageTest; import org.openscience.cdk.atomtype.ResonanceStructuresTest; +import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetectorTest; import org.openscience.cdk.reaction.mechanism.AdductionLPMechanismTest; import org.openscience.cdk.reaction.mechanism.AdductionPBMechanismTest; import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanismTest; @@ -104,6 +105,7 @@ suite.addTest(new JUnit4TestAdapter(RemovingSEofNBMechanismTest.class)); suite.addTest(new JUnit4TestAdapter(SharingElectronMechanismTest.class)); suite.addTest(new JUnit4TestAdapter(TautomerizationMechanismTest.class)); + suite.addTest(ConjugatedPiSystemsDetectorTest.suite()); // from cdk.test.reaction.type suite.addTest(new JUnit4TestAdapter(ResonanceStructuresTest.class)); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |