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[Cdk-commits] SF.net SVN: cdk: [10175] branches/miguelrojasch/reaction/src/org/ openscience/cdk/test/tools/StructureResonanceGeneratorTest.java
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From: <mig...@us...> - 2008-02-18 15:00:37
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Revision: 10175
http://cdk.svn.sourceforge.net/cdk/?rev=10175&view=rev
Author: miguelrojasch
Date: 2008-02-18 06:59:55 -0800 (Mon, 18 Feb 2008)
Log Message:
-----------
added new tests
Modified Paths:
--------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/tools/StructureResonanceGeneratorTest.java
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/tools/StructureResonanceGeneratorTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/tools/StructureResonanceGeneratorTest.java 2008-02-18 14:36:39 UTC (rev 10174)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/tools/StructureResonanceGeneratorTest.java 2008-02-18 14:59:55 UTC (rev 10175)
@@ -454,69 +454,50 @@
QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getMolecule(1),qAC));
}
-// /**
-// * A unit test suite for JUnit: Resonance Formic acid C(=O)O <=> [C-](-[O+])O <=> [C+](-[O-])O <=> C([O-])=[O+]
-// *
-// * InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)/f/h2H
-// *
-// * @return The test suite
-// */
-// @Test public void testFormicAcid() throws Exception {
-//// IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C(=O)O");
-// IMolecule molecule = builder.newMolecule();
-// molecule.addAtom(builder.newAtom("C"));
-// molecule.addAtom(builder.newAtom("O"));
-// molecule.addBond(0, 1, IBond.Order.DOUBLE);
-// molecule.addAtom(builder.newAtom("O"));
-// molecule.addBond(0, 2, IBond.Order.SINGLE);
-// addExplicitHydrogens(molecule);
-// AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-// LonePairElectronChecker lpcheck = new LonePairElectronChecker();
-// lpcheck.saturate(molecule);
-// makeSureAtomTypesAreRecognized(molecule);
-//
-// StructureResonanceGenerator gR = new StructureResonanceGenerator(false,true,false,true,false,false,100);
-// IAtomContainerSet setOfMolecules = gR.getAllStructures(molecule);
-//
-// Assert.assertEquals(3,setOfMolecules.getAtomContainerCount());
-//
-//// IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+](-[O-])O");
-// IMolecule molecule2 = builder.newMolecule();
-// molecule2.addAtom(builder.newAtom("C"));
-// molecule2.getAtom(0).setFormalCharge(1);
-// molecule2.addAtom(builder.newAtom("O"));
-// molecule2.getAtom(1).setFormalCharge(-1);
-// molecule2.addBond(0, 1, IBond.Order.SINGLE);
-// molecule2.addAtom(builder.newAtom("O"));
-// molecule2.addBond(0, 2, IBond.Order.SINGLE);
-// addExplicitHydrogens(molecule2);
-// AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule2);
-// lpcheck.saturate(molecule2);
-// makeSureAtomTypesAreRecognized(molecule2);
-//
-// Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(1),molecule2));
-//
-//// IMolecule molecule3 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C([O-])=[O+]");
-// IMolecule molecule3 = builder.newMolecule();
-// molecule3.addAtom(builder.newAtom("C"));
-// molecule3.addAtom(builder.newAtom("O"));
-// molecule3.getAtom(1).setFormalCharge(-1);
-// molecule3.addBond(0, 1, IBond.Order.SINGLE);
-// molecule3.addAtom(builder.newAtom("O"));
-// molecule3.getAtom(2).setFormalCharge(1);
-// molecule3.addBond(0, 2, IBond.Order.DOUBLE);
-// addExplicitHydrogens(molecule3);
-// AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule3);
-// lpcheck.saturate(molecule3);
-// makeSureAtomTypesAreRecognized(molecule3);
-//
-// Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getAtomContainer(2),molecule3));
-// }
-//
/**
+ * A unit test suite for JUnit: Resonance Formic acid C(=O)O <=> [C-](-[O+])O <=> [C+](-[O-])O <=> C([O-])=[O+]
+ *
+ * @cdk.inchi InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)/f/h2H
+ *
+ * @return The test suite
+ */
+ @Test public void testFormicAcid() throws Exception {
+ IMolecule molecule = builder.newMolecule();
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addAtom(builder.newAtom("O"));
+ molecule.addBond(0, 1, IBond.Order.DOUBLE);
+ molecule.addAtom(builder.newAtom("O"));
+ molecule.addBond(0, 2, IBond.Order.SINGLE);
+ addExplicitHydrogens(molecule);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+ lpcheck.saturate(molecule);
+
+ StructureResonanceGenerator gR = new StructureResonanceGenerator();
+ IMoleculeSet setOfMolecules = gR.getStructures(molecule);
+
+ Assert.assertEquals(2,setOfMolecules.getMoleculeCount());
+
+ IMolecule molecule2 = builder.newMolecule();
+ molecule2.addAtom(builder.newAtom("C"));
+ molecule2.addAtom(builder.newAtom("O"));
+ molecule2.getAtom(1).setFormalCharge(-1);
+ molecule2.addBond(0, 1, IBond.Order.SINGLE);
+ molecule2.addAtom(builder.newAtom("O"));
+ molecule2.getAtom(2).setFormalCharge(1);
+ molecule2.addBond(0, 2, IBond.Order.DOUBLE);
+ addExplicitHydrogens(molecule2);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule2);
+ lpcheck.saturate(molecule2);
+
+ QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(molecule2);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(setOfMolecules.getMolecule(1),qAC));
+
+ }
+
+ /**
* A unit test suite for JUnit: Resonance Formic acid F-C=C <=> [F+]=C-[C-]
*
- * InChI=1/C2H3F/c1-2-3/h2H,1H2
+ * @cdk.inchi InChI=1/C2H3F/c1-2-3/h2H,1H2
*
* @return The test suite
*/
@@ -554,7 +535,7 @@
/**
* A unit test suite for JUnit: Resonance Fluorobenzene Fc1ccccc1 <=> ...
*
- * InChI=1/C6H5F/c7-6-4-2-1-3-5-6/h1-5H
+ * @cdk.inchi InChI=1/C6H5F/c7-6-4-2-1-3-5-6/h1-5H
*
* @return The test suite
*/
@@ -638,7 +619,7 @@
/**
* A unit test suite for JUnit: Resonance n1ccccc1 <=> ...
*
- * InChI=1/C6H7N/c7-6-4-2-1-3-5-6/h1-5H,7H2
+ * @cdk.inchi InChI=1/C6H7N/c7-6-4-2-1-3-5-6/h1-5H,7H2
*
* @return The test suite
*/
@@ -726,7 +707,7 @@
* A unit test suite for JUnit.
* [H]C([H])=C([H])[O-] => O=C([H])[C-]([H])[H]
*
- * InChI=1/C2H4O/c1-2-3/h2-3H,1H2/p-1/fC2H3O/h3h/q-1
+ * @cdk.inchi InChI=1/C2H4O/c1-2-3/h2-3H,1H2/p-1/fC2H3O/h3h/q-1
*
* @throws Exception
*/
@@ -756,7 +737,7 @@
* + [H]C1=C([H])[C-]([H])C([H])=C(C1=[N+]([H])[H])C([H])([H])[H]
* + [H]C=1C([H])=C([H])[C-](C(C=1([H]))=[N+]([H])[H])C([H])([H])[H]
*
- * InChI=1/C7H9N/c1-6-4-2-3-5-7(6)8/h2-5H,8H2,1H3
+ * @cdk.inchi InChI=1/C7H9N/c1-6-4-2-3-5-7(6)8/h2-5H,8H2,1H3
*
* @throws Exception
*/
@@ -793,7 +774,7 @@
*
* A unit test suite for JUnit.
*
- * InChI=1/C8H10/c1-7-5-3-4-6-8(7)2/h3-6H,1-2H3
+ * @cdk.inchi InChI=1/C8H10/c1-7-5-3-4-6-8(7)2/h3-6H,1-2H3
*
* @see #testIsomphrXilene()
*
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