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[Cdk-commits] SF.net SVN: cdk: [7515] trunk/cdk/src/org/openscience/cdk/test/modeling/ builder3d/ModelBuilder3dTest.java
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From: <sh...@us...> - 2006-12-20 12:31:16
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Revision: 7515
http://svn.sourceforge.net/cdk/?rev=7515&view=rev
Author: shk3
Date: 2006-12-20 04:31:10 -0800 (Wed, 20 Dec 2006)
Log Message:
-----------
added some tests and @cdk.bug comments
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java 2006-12-20 12:06:01 UTC (rev 7514)
+++ trunk/cdk/src/org/openscience/cdk/test/modeling/builder3d/ModelBuilder3dTest.java 2006-12-20 12:31:10 UTC (rev 7515)
@@ -24,6 +24,10 @@
package org.openscience.cdk.test.modeling.builder3d;
import java.io.InputStream;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
import javax.vecmath.Point2d;
@@ -32,19 +36,31 @@
import junit.framework.Test;
import junit.framework.TestSuite;
+import org.openscience.cdk.Atom;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.geometry.GeometryToolsInternalCoordinates;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemFile;
+import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.io.CMLReader;
+import org.openscience.cdk.io.CMLWriter;
+import org.openscience.cdk.io.IChemObjectWriter;
import org.openscience.cdk.io.MDLV2000Reader;
+import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.modeling.builder3d.ModelBuilder3D;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.HydrogenAdder;
+import org.openscience.cdk.tools.IDCreator;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
/**
@@ -59,6 +75,7 @@
boolean standAlone = false;
private LoggingTool logger;
+ private List inputList = null;
/**
* Constructor for the ModelBuilder3dTest
@@ -247,6 +264,10 @@
fail(exc.toString());
}
}
+
+ /*
+ * @cdk.bug 1315823
+ */
public void testModelBuilder3D_232() throws Exception{
if (!this.runSlowTests()) fail("Slow tests turned of");
@@ -264,7 +285,13 @@
mb3d.setMolecule(new Molecule(ac),false);
mb3d.generate3DCoordinates();
assertNotNull(ac.getAtom(0).getPoint3d());
- } catch (Exception exc) {
+ double avlength=GeometryToolsInternalCoordinates.getBondLengthAverage3D(ac);
+ for(int i=0;i<ac.getBondCount();i++){
+ double distance=ac.getBond(i).getAtom(0).getPoint3d().distance(ac.getBond(i).getAtom(1).getPoint3d());
+ assertFalse(distance < avlength/2);
+ assertFalse(distance > avlength*2);
+ }
+ } catch (Exception exc) {
System.out.println("Cannot layout molecule 232");
if (standAlone)
{
@@ -304,6 +331,7 @@
/**
* Test for SF bug #1309731.
+ * @cdk.bug 1309731
*/
public void testModelBuilder3D_keepChemObjectIDs(){
ModelBuilder3D mb3d = new ModelBuilder3D();
@@ -342,4 +370,169 @@
assertEquals("carbon1", carbon1.getID());
assertEquals("oxygen1", oxygen1.getID());
}
+ /*
+ * this is a test contributed by mario baseda / see bug #1610997
+ * @cdk.bug 1610997
+ */
+ public void test_LocalWorkerModel3DBuildersWithMM2ForceField()throws CDKException, Exception{
+ if (!this.runSlowTests()) fail("Slow tests turned of");
+
+ boolean notCalculatedResults = false;
+ inputList = new ArrayList();
+
+ ////////////////////////////////////////////////////////////////////////////////////////////
+ //generate the input molecules. This are molecules without x, y, z coordinats
+
+ String[] smiles = new String[] {"CC", "OCC", "O(C)CCC", "c1ccccc1", "C(=C)=C","OCC=CCc1ccccc1(C=C)", "O(CC=C)CCN", "CCCCCCCCCCCCCCC", "OCC=CCO", "NCCCCN"};
+ SmilesParser sp = new SmilesParser();
+ IAtomContainer[] atomContainer = new IAtomContainer[smiles.length];
+ for (int i = 0; i < smiles.length; i++) {
+ atomContainer[i] = sp.parseSmiles(smiles[i]);
+
+ inputList.add(CMLChemFileWrapper.wrapAtomContainerInChemModel(atomContainer[i]));
+ }
+
+ ///////////////////////////////////////////////////////////////////////////////////////////
+ // Generate 2D coordinats for the input molecules with the Structure Diagram Generator
+
+ StructureDiagramGenerator str;
+ CMLChemFile resultFile = null;
+ List<CMLChemFile> resultList = new ArrayList<CMLChemFile>();
+ for (Iterator iter = inputList.iterator(); iter.hasNext();) {
+ CMLChemFile file = (CMLChemFile) iter.next();
+ List moleculeList = ChemFileManipulator.getAllAtomContainers(file);
+ IAtomContainer molecules;
+ for (Iterator iterator = moleculeList.iterator(); iterator.hasNext();){
+ molecules = (IAtomContainer)iterator.next();
+ str = new StructureDiagramGenerator();
+ str.setMolecule((IMolecule)molecules);
+ str.generateCoordinates();
+ resultFile = CMLChemFileWrapper.wrapAtomContainerInChemModel(str.getMolecule());
+ resultList.add(resultFile);
+ }
+ }
+ inputList = resultList;
+
+ /////////////////////////////////////////////////////////////////////////////////////////////
+ // Delete x and y coordinats
+
+ for (Iterator iter = inputList.iterator(); iter.hasNext();) {
+ IChemFile element = (IChemFile) iter.next();
+ List MoleculeList = ChemFileManipulator.getAllAtomContainers(element);
+ IAtomContainer molecules;
+ for (Iterator iterator = MoleculeList.iterator(); iterator.hasNext();){
+ molecules = (IAtomContainer)iterator.next();
+ for (Iterator atom = molecules.atoms(); atom.hasNext();){
+ Atom last = (Atom) atom.next();
+ last.setPoint2d(null);
+ }
+ }
+ }
+
+ ////////////////////////////////////////////////////////////////////////////////////////////////////
+ // Test for the method Model3DBuildersWithMM2ForceField
+
+ try {
+ ModelBuilder3D mb3d=new ModelBuilder3D();
+ mb3d.setTemplateHandler();
+ for (Iterator iter = inputList.iterator(); iter.hasNext();) {
+ CMLChemFile file = (CMLChemFile) iter.next();
+ List moleculeList = ChemFileManipulator.getAllAtomContainers(file);
+ IAtomContainer molecules;
+ for (Iterator iterator = moleculeList.iterator(); iterator.hasNext();){
+ molecules = (IAtomContainer)iterator.next();
+ try {
+ IMolecule mol = file.getBuilder().newMolecule(molecules);
+ /*for(int i=0;i<mol.getAtomCount();i++){
+ mol.getAtom(i).setFlag(CDKConstants.ISPLACED,false);
+ mol.getAtom(i).setFlag(CDKConstants.VISITED,false);
+ } */
+ mb3d.setMolecule(mol,false);
+ mb3d.generate3DCoordinates();
+ System.out.println("Calculation done");
+ } catch (Exception e) {
+ e.printStackTrace();
+ notCalculatedResults = true;
+ System.err.println("Calculation error "+e);
+ }
+ }
+ }
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw new Exception(exception);
+ }
+ assertEquals(false, notCalculatedResults);
+ }
+
}
+
+class CMLChemFile extends ChemFile {
+
+ /**
+ * Constructs an empty ChemFile.
+ */
+ public CMLChemFile() {
+ super();
+ }
+
+ /**
+ * Constructs a ChemFile from a CML String.
+ *
+ * @param CMLString to deserialize the ChemFile from.
+ * @throws Exception
+ */
+ public CMLChemFile(String CMLString) throws Exception {
+ CMLReader reader = new CMLReader(
+ new StringReader(CMLString)
+ );
+ reader.read(this);
+ }
+
+ /**
+ * Serializes this ChemFile into a CML String.
+ *
+ * @return The CML String serialization.
+ * @throws Exception
+ */
+ public String toCML() throws Exception {
+ IDCreator idCreator = new IDCreator();
+ idCreator.createIDs(this);
+
+ StringWriter stringWriter = new StringWriter();
+ IChemObjectWriter writer = new CMLWriter(stringWriter);
+ writer.write(this);
+
+ return stringWriter.toString();
+ }
+
+ private static final long serialVersionUID = -5664142472726700883L;
+
+}
+
+
+class CMLChemFileWrapper {
+ /**
+ * Method which converts an atomContainer to a CMLChemFile
+ * @param atomContainer
+ * @return CMLChemFile which contains the information of the atomContainer
+ */
+ public static CMLChemFile wrapAtomContainerInChemModel(IAtomContainer atomContainer) {
+ CMLChemFile file = new CMLChemFile();
+ IChemModel model = atomContainer.getBuilder().newChemModel();
+ IChemSequence sequence = atomContainer.getBuilder().newChemSequence();
+ IMoleculeSet moleculeSet = atomContainer.getBuilder().newMoleculeSet();
+ moleculeSet.addAtomContainer(atomContainer);
+ model.setMoleculeSet(moleculeSet);
+ sequence.addChemModel(model);
+ file.addChemSequence(sequence);
+
+ return file;
+ }
+ public static CMLChemFile[] wrapAtomContainerArrayInChemModel(IAtomContainer[] atomContainer) {
+ CMLChemFile[] cmlChemfile = new CMLChemFile[atomContainer.length];
+ for (int i = 0; i < atomContainer.length; i++) {
+ cmlChemfile[i] = wrapAtomContainerInChemModel(atomContainer[i]);
+ }
+ return cmlChemfile;
+ }
+}
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