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[Cdk-commits] SF.net SVN: cdk: [8470] trunk/cdk/src/org/openscience/cdk/test/atomtype/ MMFF94AtomTypeMatcherTest.java
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From: <eg...@us...> - 2007-07-01 18:03:51
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Revision: 8470
http://svn.sourceforge.net/cdk/?rev=8470&view=rev
Author: egonw
Date: 2007-07-01 11:03:46 -0700 (Sun, 01 Jul 2007)
Log Message:
-----------
Now uses AbstractAtomTypeTest too
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/atomtype/MMFF94AtomTypeMatcherTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/atomtype/MMFF94AtomTypeMatcherTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/atomtype/MMFF94AtomTypeMatcherTest.java 2007-07-01 17:48:17 UTC (rev 8469)
+++ trunk/cdk/src/org/openscience/cdk/test/atomtype/MMFF94AtomTypeMatcherTest.java 2007-07-01 18:03:46 UTC (rev 8470)
@@ -1,7 +1,4 @@
-/* $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
+/* $Revision$ $Author$ $Date$
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
*
@@ -20,31 +17,30 @@
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
*/
-
package org.openscience.cdk.test.atomtype;
import java.io.InputStream;
import java.io.InputStreamReader;
-import junit.framework.Test;
-import junit.framework.TestSuite;
+import junit.framework.JUnit4TestAdapter;
+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.Molecule;
import org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher;
+import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.config.Elements;
-import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.io.MDLReader;
+import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.nonotify.NNMolecule;
-import org.openscience.cdk.test.CDKTestCase;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.tools.AtomTypeTools;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.LoggingTool;
@@ -53,40 +49,33 @@
/**
* Checks the functionality of the AtomType-MMFF94AtomTypeMatcher.
*
- * @cdk.module test-extra
+ * @cdk.module test-experimental
*
* @see org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher
*/
-public class MMFF94AtomTypeMatcherTest extends CDKTestCase {
+public class MMFF94AtomTypeMatcherTest extends AbstractAtomTypeTest {
- private LoggingTool logger;
+ private static LoggingTool logger;
private final IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
- private HydrogenAdder haad=new HydrogenAdder();
+ private static HydrogenAdder haad=new HydrogenAdder();
private static IMolecule testMolecule = null;
- public MMFF94AtomTypeMatcherTest(String name) {
- super(name);
- }
-
- public void setUp() throws Exception {
- logger = new LoggingTool(this);
- }
+ @BeforeClass public static void setUpTestMolecule() throws Exception {
+ logger = new LoggingTool(MMFF94AtomTypeMatcherTest.class);
- public void setUpTestMolecule() throws Exception {
if (testMolecule == null) {
//logger.debug("**** START ATOMTYPE TEST ******");
AtomTypeTools att=new AtomTypeTools();
MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
- InputStream ins=this.getClass().getClassLoader().getResourceAsStream("data/mdl/mmff94AtomTypeTest_molecule.mol");
- MDLReader mdl=new MDLReader(new InputStreamReader(ins));
- testMolecule=(Molecule)mdl.read(new NNMolecule());
+ InputStream ins = MMFF94AtomTypeMatcherTest.class.getClassLoader().getResourceAsStream("data/mdl/mmff94AtomTypeTest_molecule.mol");
+ MDLV2000Reader mdl=new MDLV2000Reader(new InputStreamReader(ins));
+ testMolecule = (IMolecule)mdl.read(new NNMolecule());
att.assignAtomTypePropertiesToAtom(testMolecule);
for (int i=0;i<testMolecule.getAtomCount();i++){
logger.debug("atomNr:" + testMolecule.getAtom(i).toString());
IAtomType matched = atm.findMatchingAtomType(testMolecule, testMolecule.getAtom(i));
- assertNotNull(matched);
AtomTypeManipulator.configure(testMolecule.getAtom(i), matched);
}
@@ -94,58 +83,58 @@
}
}
- public static Test suite() {
- return new TestSuite(MMFF94AtomTypeMatcherTest.class);
+ public static junit.framework.Test suite() {
+ return new JUnit4TestAdapter(MMFF94AtomTypeMatcherTest.class);
}
- public void testMMFF94AtomTypeMatcher() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testMMFF94AtomTypeMatcher() throws Exception {
MMFF94AtomTypeMatcher matcher = new MMFF94AtomTypeMatcher();
- assertNotNull(matcher);
+ Assert.assertNotNull(matcher);
}
- public void testFindMatchingAtomType_IAtomContainer_IAtom() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testFindMatchingAtomType_IAtomContainer_IAtom() throws Exception {
setUpTestMolecule();
for (int i=0;i<testMolecule.getAtomCount();i++) {
- assertNotNull(testMolecule.getAtom(i).getAtomTypeName());
- assertTrue(testMolecule.getAtom(i).getAtomTypeName().length() > 0);
+ Assert.assertNotNull(testMolecule.getAtom(i).getAtomTypeName());
+ Assert.assertTrue(testMolecule.getAtom(i).getAtomTypeName().length() > 0);
}
}
// FIXME: Below should be tests for *all* atom types in the MM2 atom type specificiation
- public void testSthi() throws Exception {
+ @Test public void testSthi() throws Exception {
setUpTestMolecule();
- assertEquals("Sthi",testMolecule.getAtom(0).getAtomTypeName());
+ assertAtomType("Sthi",testMolecule.getAtom(0));
}
- public void testCsp2() throws Exception {
+ @Test public void testCsp2() throws Exception {
setUpTestMolecule();
- assertEquals("Csp2",testMolecule.getAtom(7).getAtomTypeName());
+ assertAtomType("Csp2",testMolecule.getAtom(7));
}
- public void testCsp() throws Exception {
+ @Test public void testCsp() throws Exception {
setUpTestMolecule();
- assertEquals("Csp",testMolecule.getAtom(51).getAtomTypeName());
+ assertAtomType("Csp",testMolecule.getAtom(51));
}
- public void testNdbO() throws Exception {
+ @Test public void testNdbO() throws Exception {
setUpTestMolecule();
- assertEquals("N=O",testMolecule.getAtom(148).getAtomTypeName());
+ assertAtomType("N=O",testMolecule.getAtom(148));
}
- public void testOar() throws Exception {
+ @Test public void testOar() throws Exception {
setUpTestMolecule();
- assertEquals("Oar",testMolecule.getAtom(198).getAtomTypeName());
+ assertAtomType("Oar",testMolecule.getAtom(198));
}
- public void testN2OX() throws Exception {
+ @Test public void testN2OX() throws Exception {
setUpTestMolecule();
- assertEquals("N2OX",testMolecule.getAtom(233).getAtomTypeName());
+ assertAtomType("N2OX",testMolecule.getAtom(233));
}
- public void testNAZT() throws Exception {
+ @Test public void testNAZT() throws Exception {
setUpTestMolecule();
- assertEquals("NAZT",testMolecule.getAtom(256).getAtomTypeName());
+ assertAtomType("NAZT",testMolecule.getAtom(256));
}
// Other tests
- public void testFindMatchingAtomType_IAtomContainer_IAtom_Methanol() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testFindMatchingAtomType_IAtomContainer_IAtom_Methanol() throws Exception {
// logger.debug("**** START ATOMTYPE Methanol TEST ******");
//System.out.println("**** START ATOMTYPE Methanol TEST ******");
@@ -166,11 +155,11 @@
for (int i=0;i<mol.getAtomCount();i++){
logger.debug("atomNr:" + mol.getAtom(i).toString());
IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
- assertNotNull(matched);
+ Assert.assertNotNull(matched);
AtomTypeManipulator.configure(mol.getAtom(i), matched);
}
for (int i=0; i<testResult.length;i++){
- assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
+ assertAtomType(testResult[i],mol.getAtom(i));
}
//System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
@@ -178,7 +167,7 @@
/**
* A unit test for JUnit with Methylamine
*/
- public void testFindMatchingAtomType_IAtomContainer_IAtom_Methylamine() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testFindMatchingAtomType_IAtomContainer_IAtom_Methylamine() throws Exception {
//System.out.println("**** START ATOMTYPE Methylamine TEST ******");
IMolecule mol = builder.newMolecule();
IAtom carbon = builder.newAtom(Elements.CARBON);
@@ -197,18 +186,18 @@
for (int i=0;i<mol.getAtomCount();i++){
logger.debug("atomNr:" + mol.getAtom(i).toString());
IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
- assertNotNull(matched);
+ Assert.assertNotNull(matched);
AtomTypeManipulator.configure(mol.getAtom(i), matched);
}
for (int i=0; i<testResult.length;i++){
- assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
+ assertAtomType(testResult[i],mol.getAtom(i));
}
//System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
}
/**
* A unit test for JUnit with ethoxyethane
*/
- public void testFindMatchingAtomType_IAtomContainer_IAtom_Ethoxyethane() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testFindMatchingAtomType_IAtomContainer_IAtom_Ethoxyethane() throws Exception {
//System.out.println("**** START ATOMTYPE Ethoxyethane TEST ******");
IMolecule mol = builder.newMolecule();
IAtom carbon = builder.newAtom(Elements.CARBON);
@@ -230,18 +219,18 @@
for (int i=0;i<mol.getAtomCount();i++){
logger.debug("atomNr:" + mol.getAtom(i).toString());
IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
- assertNotNull(matched);
+ Assert.assertNotNull(matched);
AtomTypeManipulator.configure(mol.getAtom(i), matched);
}
for (int i=0; i<testResult.length;i++){
- assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
+ assertAtomType(testResult[i],mol.getAtom(i));
}
//System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
}
/**
* A unit test for JUnit with Methanethiol
*/
- public void testFindMatchingAtomType_IAtomContainer_IAtom_Methanethiol() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testFindMatchingAtomType_IAtomContainer_IAtom_Methanethiol() throws Exception {
//System.out.println("**** START ATOMTYPE Methanethiol TEST ******");
IMolecule mol = builder.newMolecule();
IAtom carbon = builder.newAtom(Elements.CARBON);
@@ -260,18 +249,18 @@
for (int i=0;i<mol.getAtomCount();i++){
logger.debug("atomNr:" + mol.getAtom(i).toString());
IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
- assertNotNull(matched);
+ Assert.assertNotNull(matched);
AtomTypeManipulator.configure(mol.getAtom(i), matched);
}
for (int i=0; i<testResult.length;i++){
- assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
+ assertAtomType(testResult[i],mol.getAtom(i));
}
//System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
}
/**
* A unit test for JUnit with Chloromethane
*/
- public void testFindMatchingAtomType_IAtomContainer_IAtom_Chloromethane() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testFindMatchingAtomType_IAtomContainer_IAtom_Chloromethane() throws Exception {
//System.out.println("**** START ATOMTYPE Chlormethane TEST ******");
IMolecule mol = builder.newMolecule();
IAtom carbon = builder.newAtom(Elements.CARBON);
@@ -290,18 +279,18 @@
for (int i=0;i<mol.getAtomCount();i++){
logger.debug("atomNr:" + mol.getAtom(i).toString());
IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
- assertNotNull(matched);
+ Assert.assertNotNull(matched);
AtomTypeManipulator.configure(mol.getAtom(i), matched);
}
for (int i=0; i<testResult.length;i++){
- assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
+ assertAtomType(testResult[i],mol.getAtom(i));
}
//System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
}
/**
* A unit test for JUnit with Benzene
*/
- public void testFindMatchingAtomType_IAtomContainer_IAtom_Benzene() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testFindMatchingAtomType_IAtomContainer_IAtom_Benzene() throws Exception {
//System.out.println("**** START ATOMTYPE Benzene TEST ******");
IMolecule mol = builder.newMolecule();
for (int i=0; i<6; i++) {
@@ -338,12 +327,12 @@
for (int i=0;i<mol.getAtomCount();i++){
logger.debug("atomNr:" + mol.getAtom(i).toString());
IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
- assertNotNull(matched);
+ Assert.assertNotNull(matched);
//System.out.println("MatchedTypeID:"+matched.getID()+" "+matched.getSymbol()+" "+matched.getAtomTypeName());
AtomTypeManipulator.configure(mol.getAtom(i), matched);
}
for (int i=0; i<testResult.length;i++){
- assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
+ assertAtomType(testResult[i],mol.getAtom(i));
}
//System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
@@ -352,7 +341,7 @@
/**
* A unit test for JUnit with Water
*/
- public void testFindMatchingAtomType_IAtomContainer_IAtom_Water() throws ClassNotFoundException, CDKException, java.lang.Exception {
+ @Test public void testFindMatchingAtomType_IAtomContainer_IAtom_Water() throws Exception {
//System.out.println("**** START ATOMTYPE Water TEST ******");
IMolecule mol = builder.newMolecule();
IAtom oxygen = builder.newAtom(Elements.OXYGEN);
@@ -367,12 +356,38 @@
for (int i=0;i<mol.getAtomCount();i++){
logger.debug("atomNr:" + mol.getAtom(i).toString());
IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
- assertNotNull(matched);
+ Assert.assertNotNull(matched);
AtomTypeManipulator.configure(mol.getAtom(i), matched);
}
for (int i=0; i<testResult.length;i++){
- assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
+ assertAtomType(testResult[i],mol.getAtom(i));
}
//System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
}
+
+ /**
+ * The test seems to be run by JUnit in order in which they found
+ * in the source. Ugly, but @AfterClass does not work because that
+ * methods does cannot Assert.assert anything.
+ */
+ @Test public void countTestedAtomTypes() {
+ AtomTypeFactory factory = AtomTypeFactory.getInstance(
+ "org/openscience/cdk/config/data/mmff94_atomtypes.xml",
+ NoNotificationChemObjectBuilder.getInstance()
+ );
+
+ IAtomType[] expectedTypes = factory.getAllAtomTypes();
+ if (expectedTypes.length != testedAtomTypes.size()) {
+ String errorMessage = "Atom types not tested:";
+ for (int i=0; i<expectedTypes.length; i++) {
+ if (!testedAtomTypes.containsKey(expectedTypes[i].getAtomTypeName()))
+ errorMessage += " " + expectedTypes[i].getAtomTypeName();
+ }
+ Assert.assertEquals(errorMessage,
+ factory.getAllAtomTypes().length,
+ testedAtomTypes.size()
+ );
+ }
+ }
+
}
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