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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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1 parent 664a14c commit 611aaca5e9d8bc07920104bd3693da214883501d @egonw egonw committed with rajarshi Dec 12, 2011
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18 src/main/org/openscience/cdk/tools/IonizationPotentialTool.java
@@ -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;
@@ -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;
@@ -268,7 +267,7 @@ private static int getDoubleBondNumber(IAtomContainer container) {
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
@@ -347,7 +346,7 @@ private static int getDoubleBondNumber(IAtomContainer container) {
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
@@ -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>();
@@ -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
- );
- }
-
}
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12 src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -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
*
@@ -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;
@@ -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;
@@ -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;
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7 src/test/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptorTest.java
@@ -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;
@@ -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);
@@ -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);
@@ -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);
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3 src/test/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java
@@ -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;
@@ -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");
View
5 ...est/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptorTest.java
@@ -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;
@@ -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);
@@ -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

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