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[Cdk-commits] SF.net SVN: cdk: [10085] branches/miguelrojasch/reaction/src/org/ openscience/cdk/test/reaction/type/TautomerizationReactionTest.java
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From: <mig...@us...> - 2008-02-13 12:21:41
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Revision: 10085
http://cdk.svn.sourceforge.net/cdk/?rev=10085&view=rev
Author: miguelrojasch
Date: 2008-02-13 04:21:18 -0800 (Wed, 13 Feb 2008)
Log Message:
-----------
added reverse process of the tautomerization in the test
Modified Paths:
--------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/TautomerizationReactionTest.java
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/TautomerizationReactionTest.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/TautomerizationReactionTest.java 2008-02-13 10:41:47 UTC (rev 10084)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/test/reaction/type/TautomerizationReactionTest.java 2008-02-13 12:21:18 UTC (rev 10085)
@@ -29,6 +29,7 @@
import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
@@ -74,23 +75,9 @@
@Test public void testAutomaticCentreActive() throws Exception {
IReactionProcess type = new TautomerizationReaction();
+
+ IMolecule molecule = getAcetaldehyde();
- IMolecule molecule = builder.newMolecule();
- molecule.addAtom(builder.newAtom("O"));
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(0, 1, IBond.Order.DOUBLE);
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(1, 2, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(1, 3, IBond.Order.SINGLE);
- molecule.addBond(2, 4, IBond.Order.SINGLE);
- molecule.addBond(2, 5, IBond.Order.SINGLE);
- molecule.addBond(2, 6, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
setOfReactants.addMolecule(molecule);
@@ -104,27 +91,25 @@
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
- IMolecule molecule2 = builder.newMolecule();
- molecule2.addAtom(builder.newAtom("O"));
- molecule2.addAtom(builder.newAtom("C"));
- molecule2.addBond(0, 1, IBond.Order.SINGLE);
- molecule2.addAtom(builder.newAtom("C"));
- molecule2.addBond(1, 2, IBond.Order.DOUBLE);
- molecule2.addAtom(builder.newAtom("H"));
- molecule2.addAtom(builder.newAtom("H"));
- molecule2.addAtom(builder.newAtom("H"));
- molecule2.addAtom(builder.newAtom("H"));
- molecule2.addBond(1, 3, IBond.Order.SINGLE);
- molecule2.addBond(2, 4, IBond.Order.SINGLE);
- molecule2.addBond(2, 5, IBond.Order.SINGLE);
- molecule2.addBond(0, 6, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule2);
+ IMolecule molecule2 = getEthenol();
IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,queryAtom));
+
+ // reverse process
+ IMoleculeSet setOfReactants2 = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ setOfReactants2.addMolecule(molecule2);
+
+ IReactionSet setOfReactions2 = type.initiate(setOfReactants2, null);
+
+ Assert.assertEquals(1, setOfReactions2.getReactionCount());
+ Assert.assertEquals(1, setOfReactions2.getReaction(0).getProductCount());
+
+ IMolecule product2 = setOfReactions2.getReaction(0).getProducts().getMolecule(0);
+
+ queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product2);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule,queryAtom));
}
-
-
/**
* A unit test suite for JUnit for acetaldehyde.
* Reaction: O=C-C-H => O(H)-C=C.
@@ -136,22 +121,7 @@
*/
@Test public void testManuallyCentreActive() throws Exception {
IReactionProcess type = new TautomerizationReaction();
-
- IMolecule molecule = builder.newMolecule();
- molecule.addAtom(builder.newAtom("O"));
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(0, 1, IBond.Order.DOUBLE);
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(1, 2, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(1, 3, IBond.Order.SINGLE);
- molecule.addBond(2, 4, IBond.Order.SINGLE);
- molecule.addBond(2, 5, IBond.Order.SINGLE);
- molecule.addBond(2, 6, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+ IMolecule molecule = getAcetaldehyde();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
setOfReactants.addMolecule(molecule);
@@ -174,25 +144,33 @@
Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
+
+ IMolecule molecule2 = getEthenol();
- IMolecule molecule2 = builder.newMolecule();
- molecule2.addAtom(builder.newAtom("O"));
- molecule2.addAtom(builder.newAtom("C"));
- molecule2.addBond(0, 1, IBond.Order.SINGLE);
- molecule2.addAtom(builder.newAtom("C"));
- molecule2.addBond(1, 2, IBond.Order.DOUBLE);
- molecule2.addAtom(builder.newAtom("H"));
- molecule2.addAtom(builder.newAtom("H"));
- molecule2.addAtom(builder.newAtom("H"));
- molecule2.addAtom(builder.newAtom("H"));
- molecule2.addBond(1, 3, IBond.Order.SINGLE);
- molecule2.addBond(2, 4, IBond.Order.SINGLE);
- molecule2.addBond(2, 5, IBond.Order.SINGLE);
- molecule2.addBond(0, 6, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule2);
-
IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,queryAtom));
+
+ // reverse process
+ /*manually putting the active center*/
+ molecule2.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule2.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule2.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule2.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule2.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule2.getBond(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ molecule2.getBond(5).setFlag(CDKConstants.REACTIVE_CENTER,true);
+ IMoleculeSet setOfReactants2 = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
+ setOfReactants2.addMolecule(molecule2);
+
+ IReactionSet setOfReactions2 = type.initiate(setOfReactants2, null);
+
+ Assert.assertEquals(1, setOfReactions2.getReactionCount());
+ Assert.assertEquals(1, setOfReactions2.getReaction(0).getProductCount());
+
+ IMolecule product2 = setOfReactions2.getReaction(0).getProducts().getMolecule(0);
+
+ queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product2);
+ Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule,queryAtom));
}
/**
@@ -221,23 +199,8 @@
@Test public void testCDKConstants_REACTIVE_CENTER() throws Exception {
IReactionProcess type = new TautomerizationReaction();
IMoleculeSet setOfReactants = builder.newMoleculeSet();
+ IMolecule molecule = getAcetaldehyde();
- IMolecule molecule = builder.newMolecule();
- molecule.addAtom(builder.newAtom("O"));
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(0, 1, IBond.Order.DOUBLE);
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(1, 2, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(1, 3, IBond.Order.SINGLE);
- molecule.addBond(2, 4, IBond.Order.SINGLE);
- molecule.addBond(2, 5, IBond.Order.SINGLE);
- molecule.addBond(2, 6, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
-
/*manually putting the active center*/
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
@@ -282,22 +245,7 @@
IReactionProcess type = new TautomerizationReaction();
IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
-
- IMolecule molecule = builder.newMolecule();
- molecule.addAtom(builder.newAtom("O"));
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(0, 1, IBond.Order.DOUBLE);
- molecule.addAtom(builder.newAtom("C"));
- molecule.addBond(1, 2, IBond.Order.SINGLE);
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addAtom(builder.newAtom("H"));
- molecule.addBond(1, 3, IBond.Order.SINGLE);
- molecule.addBond(2, 4, IBond.Order.SINGLE);
- molecule.addBond(2, 5, IBond.Order.SINGLE);
- molecule.addBond(2, 6, IBond.Order.SINGLE);
- AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+ IMolecule molecule = getAcetaldehyde();
setOfReactants.addMolecule(molecule);
@@ -329,4 +277,57 @@
Assert.assertEquals(mappedProductB1, product.getBond(5));
}
+ /**
+ * Get the Acetaldehyde structure.
+ *
+ * @cdk.inchi InChI=1/C2H4O/c1-2-3/h2H,1H3
+ *
+ * @return The IMolecule
+ * @throws CDKException
+ */
+ private IMolecule getAcetaldehyde() throws CDKException {
+ IMolecule molecule = builder.newMolecule();
+ molecule.addAtom(builder.newAtom("O"));
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(0, 1, IBond.Order.DOUBLE);
+ molecule.addAtom(builder.newAtom("C"));
+ molecule.addBond(1, 2, IBond.Order.SINGLE);
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addAtom(builder.newAtom("H"));
+ molecule.addBond(1, 3, IBond.Order.SINGLE);
+ molecule.addBond(2, 4, IBond.Order.SINGLE);
+ molecule.addBond(2, 5, IBond.Order.SINGLE);
+ molecule.addBond(2, 6, IBond.Order.SINGLE);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
+ return molecule;
+ }
+
+ /**
+ * Get the Ethenol structure.
+ *
+ * @cdk.inchi InChI=1/C2H4O/c1-2-3/h2-3H,1H2
+ *
+ * @return The IMolecule
+ * @throws CDKException
+ */
+ private IMolecule getEthenol() throws CDKException {
+ IMolecule molecule2 = builder.newMolecule();
+ molecule2.addAtom(builder.newAtom("O"));
+ molecule2.addAtom(builder.newAtom("C"));
+ molecule2.addBond(0, 1, IBond.Order.SINGLE);
+ molecule2.addAtom(builder.newAtom("C"));
+ molecule2.addBond(1, 2, IBond.Order.DOUBLE);
+ molecule2.addAtom(builder.newAtom("H"));
+ molecule2.addAtom(builder.newAtom("H"));
+ molecule2.addAtom(builder.newAtom("H"));
+ molecule2.addAtom(builder.newAtom("H"));
+ molecule2.addBond(1, 3, IBond.Order.SINGLE);
+ molecule2.addBond(2, 4, IBond.Order.SINGLE);
+ molecule2.addBond(2, 5, IBond.Order.SINGLE);
+ molecule2.addBond(0, 6, IBond.Order.SINGLE);
+ AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule2);
+ return molecule2;
+ }
}
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