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[Cdk-commits] SF.net SVN: cdk: [10798] cdk/branches/cdk-egonw-originalstructgen/src/org/ openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest .java
Revision: 10798
http://cdk.svn.sourceforge.net/cdk/?rev=10798&view=rev
Author: egonw
Date: 2008-05-03 16:07:03 -0700 (Sat, 03 May 2008)
Log Message:
-----------
Backported a number of tests from trunk
Modified Paths:
--------------
cdk/branches/cdk-egonw-originalstructgen/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java
Modified: cdk/branches/cdk-egonw-originalstructgen/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java
===================================================================
--- cdk/branches/cdk-egonw-originalstructgen/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java 2008-05-03 22:48:41 UTC (rev 10797)
+++ cdk/branches/cdk-egonw-originalstructgen/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java 2008-05-03 23:07:03 UTC (rev 10798)
@@ -25,6 +25,9 @@
*/
package org.openscience.cdk.test.structgen.deterministic;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
import java.util.Vector;
import javax.vecmath.Vector2d;
@@ -33,17 +36,15 @@
import junit.framework.TestCase;
import junit.framework.TestSuite;
-import org.openscience.cdk.*;
-import org.openscience.cdk.structgen.deterministic.*;
-import org.openscience.cdk.applications.swing.*;
-import org.openscience.cdk.Bond;
import org.openscience.cdk.Molecule;
+import org.openscience.cdk.SetOfMolecules;
import org.openscience.cdk.applications.swing.MoleculeListViewer;
import org.openscience.cdk.applications.swing.MoleculeViewer2D;
import org.openscience.cdk.layout.StructureDiagramGenerator;
-import org.openscience.cdk.structgen.RandomGenerator;
-import org.openscience.cdk.templates.MoleculeFactory;
+import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.structgen.deterministic.GENMDeterministicGenerator;
+import org.openscience.cdk.tools.ConnectivityChecker;
/**
* @cdk.module test
@@ -54,7 +55,8 @@
boolean standAlone = false;
public MoleculeListViewer moleculeListViewer = null;
-
+ private SmilesGenerator smilesGenerator = new SmilesGenerator();
+
public GENMDeterministicGeneratorTest(String name) {
super(name);
}
@@ -81,9 +83,12 @@
{
try
{
- GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C8H10O1");
- Vector structures=gdg.getStructures();
- everythingOk(structures);
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C6H10O1");
+ Vector smiles=gdg.getSMILES();
+ assertEquals(747, smiles.size());
+ for(int i=0;i<smiles.size();i++)
+ System.out.println(smiles.get(i));
+// everythingOk(structures);
}
catch(Exception e)
{
@@ -91,8 +96,122 @@
}
}
+ public void testEthane() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C2H6");
+ List structures = gdg.getStructures();
+ assertEquals(1, structures.size());
+ assertUnique(structures);
+ assertOK(structures);
+ }
+ public void testEthanol() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C2H6O");
+ List structures = gdg.getStructures();
+ assertEquals(2, structures.size());
+ assertUnique(structures);
+ assertOK(structures);
+ }
+ public void testPropene() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C3H6");
+ List structures = gdg.getStructures();
+ assertEquals(2, structures.size());
+ assertOK(structures);
+ List uniqueSMILES = assertUnique(structures);
+ assertTrue(uniqueSMILES.contains("C1CC1"));
+ assertTrue(uniqueSMILES.contains("C=CC"));
+ }
+
+ public void testButene() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C4H10");
+ List structures = gdg.getStructures();
+ assertEquals(2, structures.size());
+ assertOK(structures);
+ List uniqueSMILES = assertUnique(structures);
+ assertTrue(uniqueSMILES.contains("CCCC"));
+ assertTrue(uniqueSMILES.contains("CC(C)C"));
+ }
+
+ /**
+ * @cdk.bug 1678346
+ */
+ public void testPhosphate() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("H2P1O4");
+ List structures = gdg.getStructures();
+ assertEquals(2, structures.size());
+ assertOK(structures);
+ List uniqueSMILES = assertUnique(structures);
+// System.out.println("List: " + uniqueSMILES);
+ assertTrue(uniqueSMILES.contains("OP(=O)(=O)O"));
+ }
+
+ public void testDichloroEthane() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C2H4F2");
+ List structures = gdg.getStructures();
+ assertEquals(2, structures.size());
+ assertOK(structures);
+ List uniqueSMILES = assertUnique(structures);
+ System.out.println("List: " + uniqueSMILES);
+ assertTrue(uniqueSMILES.contains("FCCF"));
+ }
+
+ public void testTMS() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C4H12Si1");
+ List structures = gdg.getStructures();
+ assertEquals(1, structures.size());
+ assertOK(structures);
+ List uniqueSMILES = assertUnique(structures);
+ System.out.println("List: " + uniqueSMILES);
+ assertTrue(uniqueSMILES.contains("C[Si](C)(C)C"));
+ }
+
+ public void testMMS() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C1H6Si1");
+ List structures = gdg.getStructures();
+ assertEquals(1, structures.size());
+ assertOK(structures);
+ List uniqueSMILES = assertUnique(structures);
+ System.out.println("List: " + uniqueSMILES);
+ assertTrue(uniqueSMILES.contains("C[Si](C)(C)C"));
+ }
+
+ public void testDMS() throws Exception {
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C2H8Si1");
+ List structures = gdg.getStructures();
+ assertEquals(1, structures.size());
+ assertOK(structures);
+ List uniqueSMILES = assertUnique(structures);
+ System.out.println("List: " + uniqueSMILES);
+ assertTrue(uniqueSMILES.contains("C[Si](C)(C)C"));
+ }
+
+ private List assertUnique(List structures) {
+ List uniques = new ArrayList();
+ Iterator structs = structures.iterator();
+ while (structs.hasNext()) {
+ Molecule mol = (Molecule)structs.next();
+ String SMILES = smilesGenerator.createSMILES(mol);
+ if (uniques.contains(SMILES)) {
+ fail("Duplicate structure generated: " + SMILES);
+ }
+ uniques.add(SMILES);
+ }
+ return uniques;
+ }
+
+ private void assertOK(List structures) throws Exception {
+ Molecule mol = null;
+ for (int f = 0; f<structures.size(); f++) {
+ mol = (Molecule)structures.get(f);
+ assertNotNull(mol);
+ assertTrue(mol.getAtomCount() > 0);
+ assertTrue(mol.getBondCount() > 0);
+ // make sure the thing is connected
+ SetOfMolecules molSet = ConnectivityChecker.partitionIntoMolecules(mol);
+ assertEquals(1, molSet.getAtomContainerCount());
+ }
+ }
+
/**
* For SMILES test
@@ -101,12 +220,12 @@
{
try
{
- GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C8H12");
+ GENMDeterministicGenerator gdg = new GENMDeterministicGenerator("C6H6");
Vector smiles=gdg.getSMILES();
- //for(int i=0;i<smiles.size();i++)
- // System.out.println(smiles.get(i));
- //everythingOk(structures);
- displaySMILES(smiles);
+ for(int i=0;i<smiles.size();i++)
+ System.out.println(smiles.get(i));
+// everythingOk(structures);
+// displaySMILES(smiles);
}
catch(Exception e)
{
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