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[Cdk-commits] SF.net SVN: cdk: [10181] trunk/cdk/src/org/openscience/cdk/test/smiles/ DeduceBondSystemToolTest.java
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From: <eg...@us...> - 2008-02-19 05:57:11
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Revision: 10181
http://cdk.svn.sourceforge.net/cdk/?rev=10181&view=rev
Author: egonw
Date: 2008-02-18 21:57:02 -0800 (Mon, 18 Feb 2008)
Log Message:
-----------
Added a few more unit tests, from DeduceBondOrderTestFromHybridization
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/smiles/DeduceBondSystemToolTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/smiles/DeduceBondSystemToolTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/smiles/DeduceBondSystemToolTest.java 2008-02-19 05:56:43 UTC (rev 10180)
+++ trunk/cdk/src/org/openscience/cdk/test/smiles/DeduceBondSystemToolTest.java 2008-02-19 05:57:02 UTC (rev 10181)
@@ -21,11 +21,18 @@
package org.openscience.cdk.test.smiles;
import org.junit.Assert;
+import org.junit.BeforeClass;
import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.config.Elements;
+import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IAtomType.Hybridization;
+import org.openscience.cdk.nonotify.NNAtom;
+import org.openscience.cdk.nonotify.NNBond;
+import org.openscience.cdk.nonotify.NNMolecule;
import org.openscience.cdk.smiles.DeduceBondSystemTool;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.test.NewCDKTestCase;
@@ -39,12 +46,18 @@
*/
public class DeduceBondSystemToolTest extends NewCDKTestCase {
+ private static DeduceBondSystemTool dbst;
+
+ @BeforeClass public static void setup() {
+ dbst = new DeduceBondSystemTool();
+ }
+
@Test(timeout=1000)
public void testPyrrole() throws Exception {
String smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule molecule = smilesParser.parseSmiles(smiles);
- DeduceBondSystemTool dbst = new DeduceBondSystemTool();
+
molecule = dbst.fixAromaticBondOrders(molecule);
Assert.assertNotNull(molecule);
@@ -54,4 +67,235 @@
Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
}
}
+
+ /**
+ * @cdk.inchi InChI=1/C6H4O2/c7-5-1-2-6(8)4-3-5/h1-4H
+ */
+ @Test public void xtestQuinone() throws Exception {
+ IMolecule enol = new NNMolecule();
+
+ // atom block
+ IAtom atom1 = new NNAtom(Elements.CARBON);
+ atom1.setHybridization(Hybridization.SP2);
+ IAtom atom2 = new NNAtom(Elements.CARBON);
+ atom2.setHybridization(Hybridization.SP2);
+ IAtom atom3 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom4 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom5 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom6 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom7 = new NNAtom(Elements.OXYGEN);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom8 = new NNAtom(Elements.OXYGEN);
+ atom3.setHybridization(Hybridization.SP2);
+
+ // bond block
+ IBond bond1 = new NNBond(atom1, atom2);
+ IBond bond2 = new NNBond(atom2, atom3);
+ IBond bond3 = new NNBond(atom3, atom4);
+ IBond bond4 = new NNBond(atom4, atom5);
+ IBond bond5 = new NNBond(atom5, atom6);
+ IBond bond6 = new NNBond(atom6, atom1);
+ IBond bond7 = new NNBond(atom7, atom1);
+ IBond bond8 = new NNBond(atom8, atom4);
+
+ enol.addAtom(atom1);
+ enol.addAtom(atom2);
+ enol.addAtom(atom3);
+ enol.addAtom(atom4);
+ enol.addAtom(atom5);
+ enol.addAtom(atom6);
+ enol.addAtom(atom7);
+ enol.addAtom(atom8);
+ enol.addBond(bond1);
+ enol.addBond(bond2);
+ enol.addBond(bond3);
+ enol.addBond(bond4);
+ enol.addBond(bond5);
+ enol.addBond(bond6);
+ enol.addBond(bond7);
+ enol.addBond(bond8);
+
+ // now have the algorithm have a go at it
+ enol = dbst.fixAromaticBondOrders(enol);
+ Assert.assertNotNull(enol);
+
+ // now check whether it did the right thing
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, bond1.getOrder());
+ Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, bond2.getOrder());
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, bond3.getOrder());
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, bond4.getOrder());
+ Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, bond5.getOrder());
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, bond6.getOrder());
+ Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, bond7.getOrder());
+ Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, bond8.getOrder());
+ }
+
+ /**
+ * @cdk.inchi InChI=1/C4H5N/c1-2-4-5-3-1/h1-5H
+ */
+ @Test public void xtestPyrrole() throws Exception {
+ IMolecule enol = new NNMolecule();
+
+ // atom block
+ IAtom atom1 = new NNAtom(Elements.CARBON);
+ atom1.setHybridization(Hybridization.SP2);
+ IAtom atom2 = new NNAtom(Elements.CARBON);
+ atom2.setHybridization(Hybridization.SP2);
+ IAtom atom3 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom4 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom5 = new NNAtom(Elements.NITROGEN);
+ atom3.setHybridization(Hybridization.SP2);
+
+ // bond block
+ IBond bond1 = new NNBond(atom1, atom2);
+ IBond bond2 = new NNBond(atom2, atom3);
+ IBond bond3 = new NNBond(atom3, atom4);
+ IBond bond4 = new NNBond(atom4, atom5);
+ IBond bond5 = new NNBond(atom5, atom1);
+
+ enol.addAtom(atom1);
+ enol.addAtom(atom2);
+ enol.addAtom(atom3);
+ enol.addAtom(atom4);
+ enol.addAtom(atom5);
+ enol.addBond(bond1);
+ enol.addBond(bond2);
+ enol.addBond(bond3);
+ enol.addBond(bond4);
+ enol.addBond(bond5);
+
+ // now have the algorithm have a go at it
+ enol = dbst.fixAromaticBondOrders(enol);
+ Assert.assertNotNull(enol);
+
+ // now check whether it did the right thing
+ Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, bond1.getOrder());;
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, bond2.getOrder());;
+ Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, bond3.getOrder());;
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, bond4.getOrder());;
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, bond5.getOrder());;
+ }
+
+ @Test public void xtestPyridine() throws Exception {
+ IMolecule enol = new NNMolecule();
+
+ // atom block
+ IAtom atom1 = new NNAtom(Elements.CARBON);
+ atom1.setHybridization(Hybridization.SP2);
+ IAtom atom2 = new NNAtom(Elements.CARBON);
+ atom2.setHybridization(Hybridization.SP2);
+ IAtom atom3 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom4 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom5 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom6 = new NNAtom(Elements.NITROGEN);
+ atom3.setHybridization(Hybridization.SP2);
+
+ // bond block
+ IBond bond1 = new NNBond(atom1, atom2);
+ IBond bond2 = new NNBond(atom2, atom3);
+ IBond bond3 = new NNBond(atom3, atom4);
+ IBond bond4 = new NNBond(atom4, atom5);
+ IBond bond5 = new NNBond(atom5, atom6);
+ IBond bond6 = new NNBond(atom6, atom1);
+
+ enol.addAtom(atom1);
+ enol.addAtom(atom2);
+ enol.addAtom(atom3);
+ enol.addAtom(atom4);
+ enol.addAtom(atom5);
+ enol.addAtom(atom6);
+ enol.addBond(bond1);
+ enol.addBond(bond2);
+ enol.addBond(bond3);
+ enol.addBond(bond4);
+ enol.addBond(bond5);
+ enol.addBond(bond6);
+
+ // now have the algorithm have a go at it
+ enol = dbst.fixAromaticBondOrders(enol);
+ Assert.assertNotNull(enol);
+
+ // now check whether it did the right thing
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond1.getOrder().ordinal() + bond6.getOrder().ordinal()); // around atom1
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond1.getOrder().ordinal() + bond2.getOrder().ordinal()); // around atom2
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond2.getOrder().ordinal() + bond3.getOrder().ordinal()); // around atom3
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond3.getOrder().ordinal() + bond4.getOrder().ordinal()); // around atom4
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond4.getOrder().ordinal() + bond5.getOrder().ordinal()); // around atom5
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond5.getOrder().ordinal() + bond6.getOrder().ordinal()); // around atom6
+ }
+
+ /**
+ * @cdk.inchi InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H
+ */
+ @Test public void xtestBenzene() throws Exception {
+ IMolecule enol = new NNMolecule();
+
+ // atom block
+ IAtom atom1 = new NNAtom(Elements.CARBON);
+ atom1.setHybridization(Hybridization.SP2);
+ IAtom atom2 = new NNAtom(Elements.CARBON);
+ atom2.setHybridization(Hybridization.SP2);
+ IAtom atom3 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom4 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom5 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+ IAtom atom6 = new NNAtom(Elements.CARBON);
+ atom3.setHybridization(Hybridization.SP2);
+
+ // bond block
+ IBond bond1 = new NNBond(atom1, atom2);
+ IBond bond2 = new NNBond(atom2, atom3);
+ IBond bond3 = new NNBond(atom3, atom4);
+ IBond bond4 = new NNBond(atom4, atom5);
+ IBond bond5 = new NNBond(atom5, atom6);
+ IBond bond6 = new NNBond(atom6, atom1);
+
+ enol.addAtom(atom1);
+ enol.addAtom(atom2);
+ enol.addAtom(atom3);
+ enol.addAtom(atom4);
+ enol.addAtom(atom5);
+ enol.addAtom(atom6);
+ enol.addBond(bond1);
+ enol.addBond(bond2);
+ enol.addBond(bond3);
+ enol.addBond(bond4);
+ enol.addBond(bond5);
+ enol.addBond(bond6);
+
+ // now have the algorithm have a go at it
+ enol = dbst.fixAromaticBondOrders(enol);
+ Assert.assertNotNull(enol);
+
+ // now check whether it did the right thing
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond1.getOrder().ordinal() + bond6.getOrder().ordinal()); // around atom1
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond1.getOrder().ordinal() + bond2.getOrder().ordinal()); // around atom2
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond2.getOrder().ordinal() + bond3.getOrder().ordinal()); // around atom3
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond3.getOrder().ordinal() + bond4.getOrder().ordinal()); // around atom4
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond4.getOrder().ordinal() + bond5.getOrder().ordinal()); // around atom5
+ Assert.assertEquals(CDKConstants.BONDORDER_SINGLE.ordinal() + CDKConstants.BONDORDER_DOUBLE.ordinal(),
+ bond5.getOrder().ordinal() + bond6.getOrder().ordinal()); // around atom6
+ }
}
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