From db9a31139cea58d379a474e74fbc8b97b734e02b Mon Sep 17 00:00:00 2001 From: rajarshi Date: Wed, 21 Nov 2007 22:48:51 +0000 Subject: [PATCH] Cleaned up test code for the ALOGP descriptor. Still missing a value git-svn-id: https://cdk.svn.sourceforge.net/svnroot/cdk/trunk/cdk@9474 eb4e18e3-b210-0410-a6ab-dec725e4b171 --- .../molecular/ALOGPDescriptorTest.java | 56 ++++++++++++------- 1 file changed, 36 insertions(+), 20 deletions(-) diff --git a/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java b/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java index 24290c458db..4fb4683f0cb 100644 --- a/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java +++ b/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java @@ -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); + } }