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Replaced more IMolecule by IAtomContainer, fixing more unit test regr…
…essions

Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
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egonw authored and rajarshi committed Dec 12, 2011
1 parent 664a14c commit 611aaca
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Showing 5 changed files with 13 additions and 32 deletions.
18 changes: 4 additions & 14 deletions src/main/org/openscience/cdk/tools/IonizationPotentialTool.java
Expand Up @@ -36,7 +36,6 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.reaction.IReactionProcess;
Expand Down Expand Up @@ -182,7 +181,7 @@ private static boolean familyBond(IAtomContainer container, IBond bond) {
return false;

StructureResonanceGenerator gRN = new StructureResonanceGenerator();
IAtomContainer ac = gRN.getContainer((IMolecule) container, bond);
IAtomContainer ac = gRN.getContainer(container, bond);

if(ac == null)
return true;
Expand Down Expand Up @@ -268,7 +267,7 @@ public static double[] getQSARs(IAtomContainer container, IAtom atom) throws CD
else
results[5] = 0.0;
// numberResonance
IAtomContainer acR = gRI.getContainer(asMolecule(container), atom);
IAtomContainer acR = gRI.getContainer(container, atom);
if(acR != null){
results[6] = acR.getAtomCount();
// numberAromaticAtoms
Expand Down Expand Up @@ -347,7 +346,7 @@ public static double[] getQSARs(IAtomContainer container, IBond bond) throws CD
else
results[5] += 0.0;
// numberResonance
IAtomContainer acR = gRI.getContainer((IMolecule) container, atom);
IAtomContainer acR = gRI.getContainer(container, atom);
if(acR != null){
results[6] += acR.getAtomCount();
// numberAromaticAtoms
Expand Down Expand Up @@ -484,7 +483,7 @@ private static IAtomContainer initiateIonization(IAtomContainer container,
IReactionProcess reactionNBE = new ElectronImpactNBEReaction();

IAtomContainerSet setOfReactants = container.getBuilder().newInstance(IAtomContainerSet.class);
setOfReactants.addAtomContainer(asMolecule(container));
setOfReactants.addAtomContainer(container);

atom.setFlag(CDKConstants.REACTIVE_CENTER,true);
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
Expand All @@ -503,13 +502,4 @@ private static IAtomContainer initiateIonization(IAtomContainer container,
return null;
}

private static IMolecule asMolecule(IAtomContainer container) {
if (container instanceof IMolecule)
return (IMolecule) container;

return container.getBuilder().newInstance(
IMolecule.class, container
);
}

}
@@ -1,9 +1,4 @@
/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project
/* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project
*
* Contact: cdk-devel@lists.sourceforge.net
*
Expand Down Expand Up @@ -49,7 +44,6 @@
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IStereoElement;

Expand Down Expand Up @@ -361,7 +355,7 @@ public static IAtomContainer removeHydrogens(IAtomContainer atomContainer)
List<IAtom> remove = new ArrayList<IAtom>(); // lists removed Hs.

// Clone atoms except those to be removed.
IMolecule mol = atomContainer.getBuilder().newInstance(IMolecule.class);
IAtomContainer mol = atomContainer.getBuilder().newInstance(IAtomContainer.class);
int count = atomContainer.getAtomCount();
for (int i = 0;
i < count;
Expand Down Expand Up @@ -489,7 +483,7 @@ private static IAtomContainer removeHydrogens(IAtomContainer ac, List<IAtom> pre
// lists removed Hs.

// Clone atoms except those to be removed.
IMolecule mol = ac.getBuilder().newInstance(IMolecule.class);
IAtomContainer mol = ac.getBuilder().newInstance(IAtomContainer.class);
int count = ac.getAtomCount();
for (int i = 0;
i < count;
Expand Down
Expand Up @@ -29,7 +29,6 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
Expand Down Expand Up @@ -76,7 +75,7 @@ public void testIPAtomicLearningDescriptor() throws Exception {
@Test
public void testIPDescriptor0() throws ClassNotFoundException, CDKException, java.lang.Exception{

IMolecule mol = builder.newInstance(IMolecule.class);
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class,"C"));
mol.addAtom(builder.newInstance(IAtom.class,"C"));
mol.addBond(0, 1, IBond.Order.SINGLE);
Expand Down Expand Up @@ -107,7 +106,7 @@ public void testIPDescriptor0() throws ClassNotFoundException, CDKException, jav
@Test
public void testIPDescriptor1() throws Exception{

IMolecule mol = builder.newInstance(IMolecule.class);
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class,"C"));
mol.addAtom(builder.newInstance(IAtom.class,"C"));
mol.addBond(0, 1, IBond.Order.SINGLE);
Expand Down Expand Up @@ -542,7 +541,7 @@ public void testIPPySystemWithHeteroatomDescriptor1() throws Exception{
@Test
public void testFluorobenzene() throws Exception {

IMolecule molecule = builder.newInstance(IMolecule.class);
IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
molecule.addAtom(builder.newInstance(IAtom.class,"F"));
molecule.addAtom(builder.newInstance(IAtom.class,"C"));
molecule.addBond(0, 1, IBond.Order.SINGLE);
Expand Down
Expand Up @@ -25,7 +25,6 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
Expand Down Expand Up @@ -59,7 +58,7 @@ public void setUp() throws Exception {
*/
@Test public void test() throws Exception {
IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
IAtom a1 = builder.newInstance(IAtom.class,"N");
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class,"N");
Expand Down
Expand Up @@ -30,7 +30,6 @@
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
Expand Down Expand Up @@ -75,7 +74,7 @@ public void testIPMolecularLearningDescriptor() throws Exception {
*/
@Test public void testIPDescriptor0() throws Exception{

IMolecule mol = builder.newInstance(IMolecule.class);
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class,"C"));
mol.addAtom(builder.newInstance(IAtom.class,"C"));
mol.addBond(0, 1, IBond.Order.SINGLE);
Expand Down Expand Up @@ -249,7 +248,7 @@ public void testIPMolecularLearningDescriptor() throws Exception {
*/
@Test
public void testBug_2787332_triclosan() throws Exception {
IMolecule mol = builder.newInstance(IMolecule.class);
IAtomContainer mol = builder.newInstance(IAtomContainer.class);
mol.addAtom(builder.newInstance(IAtom.class,"C"));//0
mol.addAtom(builder.newInstance(IAtom.class,"C"));//1
mol.addAtom(builder.newInstance(IAtom.class,"C"));//2
Expand Down

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