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[Cdk-commits] SF.net SVN: cdk: [8283] trunk/cdk/src/org/openscience/cdk/test/atomtype
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From: <eg...@us...> - 2007-05-01 12:48:32
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Revision: 8283
http://svn.sourceforge.net/cdk/?rev=8283&view=rev
Author: egonw
Date: 2007-05-01 05:48:26 -0700 (Tue, 01 May 2007)
Log Message:
-----------
More unit like tests
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/atomtype/MM2AtomTypeMatcherTest.java
trunk/cdk/src/org/openscience/cdk/test/atomtype/MMFF94AtomTypeMatcherTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/atomtype/MM2AtomTypeMatcherTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/atomtype/MM2AtomTypeMatcherTest.java 2007-05-01 10:47:34 UTC (rev 8282)
+++ trunk/cdk/src/org/openscience/cdk/test/atomtype/MM2AtomTypeMatcherTest.java 2007-05-01 12:48:26 UTC (rev 8283)
@@ -25,21 +25,21 @@
package org.openscience.cdk.test.atomtype;
-import java.io.BufferedReader;
-//import java.io.FileReader;
-import java.io.InputStreamReader;
import java.io.InputStream;
import junit.framework.Test;
import junit.framework.TestSuite;
+
+import org.openscience.cdk.atomtype.MM2AtomTypeMatcher;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.io.IChemObjectReader;
+import org.openscience.cdk.io.MDLV2000Reader;
+import org.openscience.cdk.nonotify.NNMolecule;
import org.openscience.cdk.test.CDKTestCase;
-import org.openscience.cdk.io.MDLReader;
-import org.openscience.cdk.interfaces.IAtomType;
-import org.openscience.cdk.atomtype.MM2AtomTypeMatcher;
-import org.openscience.cdk.Molecule;
-import org.openscience.cdk.tools.manipulator.*;
import org.openscience.cdk.tools.AtomTypeTools;
import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
/**
* Checks the functionality of the AtomType-MMFF94AtomTypeMatcher.
@@ -52,12 +52,35 @@
private LoggingTool logger;
+ private static IMolecule testMolecule = null;
+
public MM2AtomTypeMatcherTest(String name) {
super(name);
}
- public void setUp() {
+ public void setUp() throws Exception {
logger = new LoggingTool(this);
+
+ if (testMolecule == null) {
+ // read the test file and percieve atom types
+ AtomTypeTools att=new AtomTypeTools();
+ MM2AtomTypeMatcher atm= new MM2AtomTypeMatcher();
+ logger.debug("**** reading MOL file ******");
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream("data/mdl/mmff94AtomTypeTest_molecule.mol");
+ IChemObjectReader mdl = new MDLV2000Reader(ins);
+ testMolecule=(IMolecule)mdl.read(new NNMolecule());
+ assertTrue(testMolecule.getAtomCount() > 0);
+ logger.debug("Molecule load:"+testMolecule.getAtomCount());
+ att.assignAtomTypePropertiesToAtom(testMolecule);
+ for (int i=0;i<testMolecule.getAtomCount();i++){
+ logger.debug("atomNr:"+i);
+ IAtomType matched = null;
+ matched = atm.findMatchingAtomType(testMolecule, testMolecule.getAtom(i));
+ logger.debug("Found AtomType: ", matched);
+ assertNotNull(matched);
+ AtomTypeManipulator.configure(testMolecule.getAtom(i), matched);
+ }
+ }
}
public static Test suite() {
@@ -70,40 +93,33 @@
}
public void testFindMatchingAtomType_IAtomContainer_IAtom() throws Exception {
- if (!this.runSlowTests()) fail("Slow tests turned of");
-
- logger.debug("**** START MM2 ATOMTYPE TEST ******");
- AtomTypeTools att=new AtomTypeTools();
- Molecule mol=null;
- MM2AtomTypeMatcher atm= new MM2AtomTypeMatcher();
- BufferedReader fin =null;
- InputStream ins=null;
- logger.debug("**** reading MOL file ******");
- ins = this.getClass().getClassLoader().getResourceAsStream("data/mdl/mmff94AtomTypeTest_molecule.mol");
- fin = new BufferedReader(new InputStreamReader(ins));
- MDLReader mdl=new MDLReader(fin);
- mol=(Molecule)mdl.read(new Molecule());
- assertTrue(mol.getAtomCount() > 0);
- logger.debug("Molecule load:"+mol.getAtomCount());
- att.assignAtomTypePropertiesToAtom(mol);
- for (int i=0;i<mol.getAtomCount();i++){
- logger.debug("atomNr:"+i);
- IAtomType matched = null;
- matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
- logger.debug("Found AtomType: ", matched);
- assertNotNull(matched);
- AtomTypeManipulator.configure(mol.getAtom(i), matched);
- }
-
- logger.debug("MM2 Atom 0:"+mol.getAtom(0).getAtomTypeName());
-
- assertEquals("Sthi",mol.getAtom(0).getAtomTypeName());
- assertEquals("Csp2",mol.getAtom(7).getAtomTypeName());
- assertEquals("Csp",mol.getAtom(51).getAtomTypeName());
- assertEquals("N=C",mol.getAtom(148).getAtomTypeName());
- assertEquals("Oar",mol.getAtom(198).getAtomTypeName());
- assertEquals("N2OX",mol.getAtom(233).getAtomTypeName());
- assertEquals("Nsp2",mol.getAtom(256).getAtomTypeName());
- logger.debug("**** END OF ATOMTYPE TEST ******");
+ for (int i=0;i<testMolecule.getAtomCount();i++) {
+ assertNotNull(testMolecule.getAtom(i).getAtomTypeName());
+ 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() {
+ assertEquals("Sthi",testMolecule.getAtom(0).getAtomTypeName());
+ }
+ public void testCsp2() {
+ assertEquals("Csp2",testMolecule.getAtom(7).getAtomTypeName());
+ }
+ public void testCsp() {
+ assertEquals("Csp",testMolecule.getAtom(51).getAtomTypeName());
+ }
+ public void testNdbC() {
+ assertEquals("N=C",testMolecule.getAtom(148).getAtomTypeName());
+ }
+ public void testOar() {
+ assertEquals("Oar",testMolecule.getAtom(198).getAtomTypeName());
+ }
+ public void testN2OX() {
+ assertEquals("N2OX",testMolecule.getAtom(233).getAtomTypeName());
+ }
+ public void testNsp2() {
+ assertEquals("Nsp2",testMolecule.getAtom(256).getAtomTypeName());
+ }
}
Modified: trunk/cdk/src/org/openscience/cdk/test/atomtype/MMFF94AtomTypeMatcherTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/atomtype/MMFF94AtomTypeMatcherTest.java 2007-05-01 10:47:34 UTC (rev 8282)
+++ trunk/cdk/src/org/openscience/cdk/test/atomtype/MMFF94AtomTypeMatcherTest.java 2007-05-01 12:48:26 UTC (rev 8283)
@@ -25,7 +25,6 @@
package org.openscience.cdk.test.atomtype;
-import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
@@ -44,6 +43,7 @@
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.MDLReader;
+import org.openscience.cdk.nonotify.NNMolecule;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.AtomTypeTools;
import org.openscience.cdk.tools.HydrogenAdder;
@@ -62,13 +62,37 @@
private LoggingTool logger;
private final IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
private HydrogenAdder haad=new HydrogenAdder();
+
+ private static IMolecule testMolecule = null;
+
public MMFF94AtomTypeMatcherTest(String name) {
super(name);
}
- public void setUp() {
+ public void setUp() throws Exception {
logger = new LoggingTool(this);
}
+
+ 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());
+
+ 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);
+ }
+
+ logger.debug("MMFF94 Atom 0:"+testMolecule.getAtom(0).getAtomTypeName());
+ }
+ }
public static Test suite() {
return new TestSuite(MMFF94AtomTypeMatcherTest.class);
@@ -81,42 +105,46 @@
}
public void testFindMatchingAtomType_IAtomContainer_IAtom() throws ClassNotFoundException, CDKException, java.lang.Exception {
- if (!this.runSlowTests()) fail("Slow tests turned of");
-
- //logger.debug("**** START ATOMTYPE TEST ******");
- AtomTypeTools att=new AtomTypeTools();
- //SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
- Molecule mol=null;
- //HydrogenAdder hAdder = new HydrogenAdder();
- MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
- BufferedReader fin =null;
- InputStream ins=this.getClass().getClassLoader().getResourceAsStream("data/mdl/mmff94AtomTypeTest_molecule.mol");
- fin = new BufferedReader(new InputStreamReader(ins));
- //fin=new BufferedReader(new FileReader("data/mmff94AtomTypeTest_molecule.mol"));
- MDLReader mdl=new MDLReader(fin);
- mol=(Molecule)mdl.read(new Molecule());
-
- att.assignAtomTypePropertiesToAtom(mol);
- 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);
- AtomTypeManipulator.configure(mol.getAtom(i), matched);
- }
-
- logger.debug("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());
- //logger.debug("Atom 0:"+mol.getAtomAt(256).getAtomTypeName());
-
- assertEquals("Sthi",mol.getAtom(0).getAtomTypeName());
- assertEquals("Csp2",mol.getAtom(7).getAtomTypeName());
- assertEquals("Csp",mol.getAtom(51).getAtomTypeName());
- assertEquals("N=O",mol.getAtom(148).getAtomTypeName());
- assertEquals("Oar",mol.getAtom(198).getAtomTypeName());
- assertEquals("N2OX",mol.getAtom(233).getAtomTypeName());
- assertEquals("NAZT",mol.getAtom(256).getAtomTypeName());
- //logger.debug("**** END OF ATOMTYPE TEST ******");
+ setUpTestMolecule();
+ for (int i=0;i<testMolecule.getAtomCount();i++) {
+ assertNotNull(testMolecule.getAtom(i).getAtomTypeName());
+ 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 {
+ setUpTestMolecule();
+ assertEquals("Sthi",testMolecule.getAtom(0).getAtomTypeName());
+ }
+ public void testCsp2() throws Exception {
+ setUpTestMolecule();
+ assertEquals("Csp2",testMolecule.getAtom(7).getAtomTypeName());
+ }
+ public void testCsp() throws Exception {
+ setUpTestMolecule();
+ assertEquals("Csp",testMolecule.getAtom(51).getAtomTypeName());
+ }
+ public void testNdbO() throws Exception {
+ setUpTestMolecule();
+ assertEquals("N=O",testMolecule.getAtom(148).getAtomTypeName());
+ }
+ public void testOar() throws Exception {
+ setUpTestMolecule();
+ assertEquals("Oar",testMolecule.getAtom(198).getAtomTypeName());
+ }
+ public void testN2OX() throws Exception {
+ setUpTestMolecule();
+ assertEquals("N2OX",testMolecule.getAtom(233).getAtomTypeName());
+ }
+ public void testNAZT() throws Exception {
+ setUpTestMolecule();
+ assertEquals("NAZT",testMolecule.getAtom(256).getAtomTypeName());
+ }
+
+ // Other tests
+
public void testFindMatchingAtomType_IAtomContainer_IAtom_Methanol() throws ClassNotFoundException, CDKException, java.lang.Exception {
// logger.debug("**** START ATOMTYPE Methanol TEST ******");
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