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[Cdk-commits] SF.net SVN: cdk: [10023] branches/miguelrojasch/reaction/src/org/ openscience/cdk/test/reaction/type/CleavageBondReactionTest.java
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From: <mig...@us...> - 2008-02-04 16:29:49
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Revision: 10023
http://cdk.svn.sourceforge.net/cdk/?rev=10023&view=rev
Author: miguelrojasch
Date: 2008-02-04 08:29:03 -0800 (Mon, 04 Feb 2008)
Log Message:
-----------
Added test mapping
Modified Paths:
--------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/CleavageBondReactionTest.java
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/CleavageBondReactionTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/CleavageBondReactionTest.java 2008-02-04 16:13:07 UTC (rev 10022)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/CleavageBondReactionTest.java 2008-02-04 16:29:03 UTC (rev 10023)
@@ -47,6 +47,7 @@
import org.openscience.cdk.test.reaction.ReactionProcessTest;
import org.openscience.cdk.tools.LonePairElectronChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.ReactionManipulator;
/**
* TestSuite that runs a test for the CleavageBondReactionTest.
@@ -64,21 +65,22 @@
@BeforeClass public static void setUp() throws Exception {
setReaction(CleavageBondReaction.class);
}
-
+
/**
- * A unit test suite for JUnit. Reaction:
+ * A unit test suite for JUnit. Reaction: Ethylbenzaldehyde.
* CCc1ccc(C=O)cc1 => C+ Cc1ccc(C=O)cc1
* CCc1ccc(C=O)cc1 => CC + c1ccc(C=O)cc1
* Automatic looking for active center.
+ *
+ * @cdk.inchi InChI=1/C9H10O/c1-2-8-3-5-9(7-10)6-4-8/h3-7H,2H2,1H3
*
* @return The test suite
*/
- @Test public void test1() throws Exception {
+ @Test public void testEthylbenzaldehydeManual() throws Exception {
IReactionProcess type = new CleavageBondReaction();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
-// IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("CCc1ccc(C=O)cc1");
- // Ethylbenzaldehyde. InChI=1/C9H10O/c1-2-8-3-5-9(7-10)6-4-8/h3-7H,2H2,1H3, smiles CCc1ccc(C=O)cc1
+ //smiles("CCc1ccc(C=O)cc1")
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("C"));
molecule.addAtom(builder.newAtom("C"));
@@ -126,7 +128,6 @@
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
/*C*/
-// IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C");
IMolecule molecule2 = builder.newMolecule();
molecule2.addAtom(builder.newAtom("C"));
molecule2.addAtom(builder.newAtom("H"));
@@ -141,7 +142,6 @@
product = setOfReactions.getReaction(0).getProducts().getMolecule(1);
/*Cc1ccc(C=O)cc1*/
-// IMolecule molecule3 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("Cc1ccc(C=O)cc1");
IMolecule molecule3 = builder.newMolecule();
molecule3.addAtom(builder.newAtom("C"));
molecule3.getAtom(0).setFormalCharge(1);
@@ -171,7 +171,6 @@
product = setOfReactions.getReaction(1).getProducts().getMolecule(0);
/*CC*/
-// molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("CC");
molecule2 = builder.newMolecule();
molecule2.addAtom(builder.newAtom("C"));
molecule2.addAtom(builder.newAtom("C"));
@@ -186,7 +185,6 @@
product = setOfReactions.getReaction(1).getProducts().getMolecule(1);
/*c1ccc(C=O)cc1*/
-// molecule3 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("c1ccc(C=O)cc1");
molecule3 = builder.newMolecule();
molecule3.addAtom(builder.newAtom("C"));
molecule3.addAtom(builder.newAtom("C"));
@@ -218,6 +216,82 @@
}
/**
+ * A unit test suite for JUnit. Reaction: Ethylbenzaldehyde.
+ * CCc1ccc(C=O)cc1 => C+ Cc1ccc(C=O)cc1
+ * CCc1ccc(C=O)cc1 => CC + c1ccc(C=O)cc1
+ * Automatic looking for active center.
+ *
+ * @cdk.inchi InChI=1/C9H10O/c1-2-8-3-5-9(7-10)6-4-8/h3-7H,2H2,1H3
+ *
+ * @see #testEthylbenzaldehydeManual()
+ * @return The test suite
+ */
+ @Test public void testEthylbenzaldehydeMapping() throws Exception {
+ IReactionProcess type = new CleavageBondReaction();
+ IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+
+ //smiles("CCc1ccc(C=O)cc1")
+ IMolecule molecule = builder.newMolecule();
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(0, 1, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(1, 2, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(2, 3, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(3, 4, IBond.Order.DOUBLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(4, 5, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(5, 6, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("O"));
+ molecule.addBond(6, 7, IBond.Order.DOUBLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(5, 8, IBond.Order.DOUBLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(8, 9, IBond.Order.SINGLE);
+ molecule.addBond(9, 2, IBond.Order.DOUBLE);
+ addExplicitHydrogens(molecule);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+
+ LonePairElectronChecker lpcheck = new LonePairElectronChecker();
+ lpcheck.saturate(molecule);
+
+ molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule.getBond(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
+
+ setOfReactants.addMolecule(molecule);
+
+ /*has active center*/
+ Object[] params = {Boolean.TRUE};
+ type.setParameters(params);
+
+ /* initiate */
+ makeSureAtomTypesAreRecognized(molecule);
+
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+
+ IMolecule product11 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
+ IMolecule product12 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
+
+ Assert.assertEquals(2,setOfReactions.getReaction(0).getMappingCount());
+ IAtom mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(0));
+ Assert.assertEquals(mappedProductA1, product11.getAtom(0));
+ IAtom mappedProductA2 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(1));
+ Assert.assertEquals(mappedProductA2, product12.getAtom(0));
+
+ IMolecule product21 = setOfReactions.getReaction(1).getProducts().getMolecule(0);
+ IMolecule product22 = setOfReactions.getReaction(1).getProducts().getMolecule(1);
+
+ Assert.assertEquals(2,setOfReactions.getReaction(0).getMappingCount());
+ mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(1), molecule.getAtom(1));
+ Assert.assertEquals(mappedProductA1, product21.getAtom(1));
+ mappedProductA2 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(1), molecule.getAtom(2));
+ Assert.assertEquals(mappedProductA2, product22.getAtom(0));
+
+ }
+ /**
* Test to recognize if a IMolecule matcher correctly the CDKAtomTypes.
*
* @param molecule The IMolecule to analyze
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