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Some IMolecule/IAtomContainer fixes, to get things to compile here
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@egonw
egonw committed Dec 10, 2011
1 parent f74a3ad commit c950448
Showing 1 changed file with 29 additions and 30 deletions.
59 changes: 29 additions & 30 deletions src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,13 +36,11 @@
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.IMoleculeSet;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction;
import org.openscience.cdk.reaction.type.HyperconjugationReaction;
Expand All @@ -54,6 +52,7 @@
import org.openscience.cdk.reaction.type.SharingLonePairReaction;
import org.openscience.cdk.reaction.type.parameters.IParameterReact;
import org.openscience.cdk.reaction.type.parameters.SetReactionCenter;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

Expand Down Expand Up @@ -379,7 +378,7 @@ public StructureResonanceGeneratorTest() {
addExplicitHydrogens(molecule);

StructureResonanceGenerator sRG = new StructureResonanceGenerator();
IMoleculeSet setOfMolecules = sRG.getStructures(molecule);
IAtomContainerSet setOfMolecules = sRG.getStructures(molecule);

Assert.assertEquals(4,setOfMolecules.getAtomContainerCount());

Expand Down Expand Up @@ -428,7 +427,7 @@ public StructureResonanceGeneratorTest() {
reaction.setParameterList(paramList);
}

IMoleculeSet setOfMolecules = sRG.getStructures(molecule);
IAtomContainerSet setOfMolecules = sRG.getStructures(molecule);

Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());

Expand Down Expand Up @@ -474,7 +473,7 @@ public StructureResonanceGeneratorTest() {
addExplicitHydrogens(molecule);

StructureResonanceGenerator gR = new StructureResonanceGenerator();
IMoleculeSet setOfMolecules = gR.getStructures(molecule);
IAtomContainerSet setOfMolecules = gR.getStructures(molecule);

Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());

Expand All @@ -491,7 +490,7 @@ public StructureResonanceGeneratorTest() {
addExplicitHydrogens(molecule2);

QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getMolecule(1),qAC));
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));
}
/**
* A unit test suite for JUnit: Resonance Formic acid C(=O)O <=> [C+](-[O-])O <=> C([O-])=[O+]
Expand All @@ -515,7 +514,7 @@ public StructureResonanceGeneratorTest() {
List<IReactionProcess> reactionList = gR.getReactions();
reactionList.add(new HeterolyticCleavagePBReaction());
gR.setReactions(reactionList);
IMoleculeSet setOfMolecules = gR.getStructures(molecule);
IAtomContainerSet setOfMolecules = gR.getStructures(molecule);

Assert.assertEquals(3,setOfMolecules.getAtomContainerCount());

Expand All @@ -532,7 +531,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule2);

QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getMolecule(1),qAC));
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));

}

Expand All @@ -555,7 +554,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule);

StructureResonanceGenerator gR = new StructureResonanceGenerator();
IMoleculeSet setOfMolecules = gR.getStructures(molecule);
IAtomContainerSet setOfMolecules = gR.getStructures(molecule);

Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());

Expand All @@ -572,7 +571,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule1);

QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule1);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getMolecule(1),qAC));
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));
}
/**
* A unit test suite for JUnit: Resonance Fluorobenzene Fc1ccccc1 <=> ...
Expand Down Expand Up @@ -604,7 +603,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule);

StructureResonanceGenerator gRI = new StructureResonanceGenerator();
IMoleculeSet setOfMolecules = gRI.getStructures(molecule);
IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);

Assert.assertEquals(5,setOfMolecules.getAtomContainerCount());

Expand All @@ -630,7 +629,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule1);

QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule1);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getMolecule(2),qAC));
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(2),qAC));

IMolecule molecule2 = builder.newInstance(IMolecule.class);
molecule2.addAtom(builder.newInstance(IAtom.class,"F"));
Expand All @@ -653,7 +652,7 @@ public StructureResonanceGeneratorTest() {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule2);
lpcheck.saturate(molecule2);

IMolecule product2 = setOfMolecules.getMolecule(4);
IAtomContainer product2 = setOfMolecules.getAtomContainer(4);
qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product2,qAC));

Expand Down Expand Up @@ -723,7 +722,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule);

StructureResonanceGenerator gRI = new StructureResonanceGenerator(true);
IMoleculeSet setOfMolecules = gRI.getStructures(molecule);
IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);

Assert.assertEquals(3,setOfMolecules.getAtomContainerCount());

Expand All @@ -749,7 +748,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule1);

QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule1);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getMolecule(1),qAC));
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),qAC));

IMolecule molecule2 = builder.newInstance(IMolecule.class);
molecule2.addAtom(builder.newInstance(IAtom.class,"F"));
Expand All @@ -772,7 +771,7 @@ public StructureResonanceGeneratorTest() {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule2);
lpcheck.saturate(molecule2);

IMolecule product2 = setOfMolecules.getMolecule(2);
IAtomContainer product2 = setOfMolecules.getAtomContainer(2);
qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(product2,qAC));

Expand Down Expand Up @@ -805,7 +804,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule);

StructureResonanceGenerator gRI = new StructureResonanceGenerator();
IMoleculeSet setOfMolecules = gRI.getStructures(molecule);
IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);

Assert.assertEquals(5,setOfMolecules.getAtomContainerCount());
}
Expand Down Expand Up @@ -837,7 +836,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule);

StructureResonanceGenerator gRI = new StructureResonanceGenerator(true);
IMoleculeSet setOfMolecules = gRI.getStructures(molecule);
IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);

Assert.assertEquals(3,setOfMolecules.getAtomContainerCount());
}
Expand All @@ -864,7 +863,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule);

StructureResonanceGenerator gRI = new StructureResonanceGenerator();
IMoleculeSet resonanceStructures = gRI.getStructures(molecule);
IAtomContainerSet resonanceStructures = gRI.getStructures(molecule);

Assert.assertEquals(4,resonanceStructures.getAtomContainerCount());
}
Expand Down Expand Up @@ -892,7 +891,7 @@ public StructureResonanceGeneratorTest() {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);

StructureResonanceGenerator gRI = new StructureResonanceGenerator();
IMoleculeSet resonanceStructures = gRI.getStructures(molecule);
IAtomContainerSet resonanceStructures = gRI.getStructures(molecule);
Assert.assertEquals(2,resonanceStructures.getAtomContainerCount());
}

Expand All @@ -918,7 +917,7 @@ public StructureResonanceGeneratorTest() {
Assert.assertEquals(6, molecule.getAtomCount());

StructureResonanceGenerator gRI = new StructureResonanceGenerator();
IMoleculeSet resonanceStructures = gRI.getStructures(molecule);
IAtomContainerSet resonanceStructures = gRI.getStructures(molecule);

Assert.assertEquals(2,resonanceStructures.getAtomContainerCount());
}
Expand Down Expand Up @@ -959,7 +958,7 @@ public StructureResonanceGeneratorTest() {
Assert.assertEquals(17, molecule.getAtomCount());

StructureResonanceGenerator gRI = new StructureResonanceGenerator(true);
IMoleculeSet resonanceStructures = gRI.getStructures(molecule);
IAtomContainerSet resonanceStructures = gRI.getStructures(molecule);

Assert.assertEquals(4,resonanceStructures.getAtomContainerCount());
}
Expand Down Expand Up @@ -1008,7 +1007,7 @@ public StructureResonanceGeneratorTest() {

gRI.setReactions(newReactionList);

IMoleculeSet resonanceStructures = gRI.getStructures(molecule);
IAtomContainerSet resonanceStructures = gRI.getStructures(molecule);

Assert.assertEquals(2,resonanceStructures.getAtomContainerCount());
}
Expand Down Expand Up @@ -1053,25 +1052,25 @@ public StructureResonanceGeneratorTest() {
Assert.assertTrue("Bond is expected to be marked aromatic!", molecule.getBond(6).getFlag(CDKConstants.ISAROMATIC));

StructureResonanceGenerator gRI = new StructureResonanceGenerator(false);
IMoleculeSet setOfMolecules = gRI.getStructures(molecule);
IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);

Assert.assertEquals(5,setOfMolecules.getAtomContainerCount());

IMolecule prod1 = setOfMolecules.getMolecule(1);
IAtomContainer prod1 = setOfMolecules.getAtomContainer(1);
Assert.assertTrue("Bond is expected to be marked aromatic!", prod1.getBond(1).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod1.getBond(2).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod1.getBond(3).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod1.getBond(4).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod1.getBond(5).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod1.getBond(6).getFlag(CDKConstants.ISAROMATIC));
IMolecule prod2 = setOfMolecules.getMolecule(2);
IAtomContainer prod2 = setOfMolecules.getAtomContainer(2);
Assert.assertTrue("Bond is expected to be marked aromatic!", prod2.getBond(1).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod2.getBond(2).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod2.getBond(3).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod2.getBond(4).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod2.getBond(5).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod2.getBond(6).getFlag(CDKConstants.ISAROMATIC));
IMolecule prod3 = setOfMolecules.getMolecule(3);
IAtomContainer prod3 = setOfMolecules.getAtomContainer(3);
Assert.assertTrue("Bond is expected to be marked aromatic!", prod3.getBond(1).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod3.getBond(2).getFlag(CDKConstants.ISAROMATIC));
Assert.assertTrue("Bond is expected to be marked aromatic!", prod3.getBond(3).getFlag(CDKConstants.ISAROMATIC));
Expand All @@ -1090,7 +1089,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule);

StructureResonanceGenerator gRI = new StructureResonanceGenerator();
IMoleculeSet setOfMolecules = gRI.getStructures(molecule);
IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);

Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());

Expand All @@ -1108,7 +1107,7 @@ public StructureResonanceGeneratorTest() {
lpcheck.saturate(molecule);

StructureResonanceGenerator gRI = new StructureResonanceGenerator();
IMoleculeSet setOfMolecules = gRI.getStructures(molecule);
IAtomContainerSet setOfMolecules = gRI.getStructures(molecule);

Assert.assertEquals(2,setOfMolecules.getAtomContainerCount());
}
Expand Down

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