From: <raj...@us...> - 2007-11-21 22:49:10
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Revision: 9474 http://cdk.svn.sourceforge.net/cdk/?rev=9474&view=rev Author: rajarshi Date: 2007-11-21 14:48:51 -0800 (Wed, 21 Nov 2007) Log Message: ----------- Cleaned up test code for the ALOGP descriptor. Still missing a value Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java Modified: trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java 2007-11-21 14:08:57 UTC (rev 9473) +++ trunk/cdk/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java 2007-11-21 22:48:51 UTC (rev 9474) @@ -2,14 +2,18 @@ import junit.framework.Test; import junit.framework.TestSuite; +import org.openscience.cdk.Bond; import org.openscience.cdk.DefaultChemObjectBuilder; -import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.qsar.DescriptorValue; +import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.descriptors.molecular.ALOGP; import org.openscience.cdk.qsar.result.DoubleArrayResult; -import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.test.CDKTestCase; -import org.openscience.cdk.tools.HydrogenAdder; +import org.openscience.cdk.tools.CDKHydrogenAdder; +import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** * Test suite for the alogp descriptor @@ -18,31 +22,43 @@ */ public class ALOGPDescriptorTest extends CDKTestCase { + private IMolecularDescriptor alogp; + private CDKHydrogenAdder hydrogenAdder; + public static Test suite() { return new TestSuite(ALOGPDescriptorTest.class); } - public void test1() { - try { - DescriptorValue v = getALOGP("CCCCl"); - assertEquals(0.5192, ((DoubleArrayResult) v.getValue()).get(0), 1E-10); - assertEquals(19.1381, ((DoubleArrayResult) v.getValue()).get(2), 1E-10); - } catch (Exception x) { - fail(x.getMessage()); - } + protected void setUp() throws CDKException { + alogp = new ALOGP(); + hydrogenAdder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance()); } - private DescriptorValue getALOGP(String smiles) throws Exception { - IMolecule mol = null; - SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); - mol = sp.parseSmiles(smiles); - HydrogenAdder ha = new HydrogenAdder(); - ha.addExplicitHydrogensToSatisfyValency(mol); + public void testChloroButane() throws Exception { + IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newAtomContainer(); + IAtom c1 = DefaultChemObjectBuilder.getInstance().newAtom("C"); + IAtom c2 = DefaultChemObjectBuilder.getInstance().newAtom("C"); + IAtom c3 = DefaultChemObjectBuilder.getInstance().newAtom("C"); + IAtom c4 = DefaultChemObjectBuilder.getInstance().newAtom("C"); + IAtom cl = DefaultChemObjectBuilder.getInstance().newAtom("Cl"); + mol.addAtom(c1); + mol.addAtom(c2); + mol.addAtom(c3); + mol.addAtom(c4); + mol.addAtom(cl); - ALOGP descr = new ALOGP(); - return descr.calculate(mol); + mol.addBond(new Bond(c1, c2)); + mol.addBond(new Bond(c2, c3)); + mol.addBond(new Bond(c3, c4)); + mol.addBond(new Bond(c4, cl)); + // add explicit hydrogens here + hydrogenAdder.addImplicitHydrogens(mol); + AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol); + + DescriptorValue v = alogp.calculate(mol); + assertEquals(0.5192, ((DoubleArrayResult) v.getValue()).get(0), 0.0001); + assertEquals(19.1381, ((DoubleArrayResult) v.getValue()).get(2), 0.0001); } - } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |