From 94c6c751998d8c37c4002ac2f971346b2ab37ba5 Mon Sep 17 00:00:00 2001
From: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc>
Date: Thu, 18 Sep 2008 20:22:08 +0000
Subject: [PATCH] Implemented a progressbar that ticks by descr/mol calculation
 and added option to cancel build.

git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@7041 fcb5ba71-d80d-0410-8237-ba3920747fcc
---
 .../META-INF/MANIFEST.MF                      |  5 +-
 .../bioclipse/cdk/qsar/test/TestCDKQsar.java  | 48 +++++++++++++
 .../bioclipse/cdk/qsar/test/testCDKAT.java    | 67 +++++++++++++++++++
 .../src/testFiles/0037.cml                    |  1 +
 4 files changed, 120 insertions(+), 1 deletion(-)
 create mode 100644 plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/testCDKAT.java
 create mode 100644 plugins/net.bioclipse.cdk.qsar.test/src/testFiles/0037.cml

diff --git a/plugins/net.bioclipse.cdk.qsar.test/META-INF/MANIFEST.MF b/plugins/net.bioclipse.cdk.qsar.test/META-INF/MANIFEST.MF
index 732d55d..259a3b2 100644
--- a/plugins/net.bioclipse.cdk.qsar.test/META-INF/MANIFEST.MF
+++ b/plugins/net.bioclipse.cdk.qsar.test/META-INF/MANIFEST.MF
@@ -12,7 +12,10 @@ Require-Bundle: org.eclipse.ui,
  net.bioclipse.core;bundle-version="2.0.0",
  net.bioclipse.qsar;bundle-version="1.0.0",
  org.junit4;bundle-version="4.3.1",
- org.eclipse.emf.ecore.edit;bundle-version="2.4.0"
+ org.eclipse.emf.ecore.edit;bundle-version="2.4.0",
+ net.bioclipse.core.tests;bundle-version="0.1.0",
+ org.eclipse.core.resources;bundle-version="3.4.0",
+ org.openscience.cdk;bundle-version="1.1.0"
 Bundle-RequiredExecutionEnvironment: J2SE-1.5
 Bundle-ActivationPolicy: lazy
 Import-Package: org.apache.log4j;version="1.2.15"
diff --git a/plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/TestCDKQsar.java b/plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/TestCDKQsar.java
index 561982b..1ab57ee 100644
--- a/plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/TestCDKQsar.java
+++ b/plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/TestCDKQsar.java
@@ -2,10 +2,17 @@
 
 import static org.junit.Assert.*;
 
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
+import net.bioclipse.cdk.business.ICDKManager;
+import net.bioclipse.cdk.domain.ICDKMolecule;
+import net.bioclipse.core.MockIFile;
 import net.bioclipse.core.business.BioclipseException;
 import net.bioclipse.core.domain.IMolecule;
 import net.bioclipse.core.domain.SmilesMolecule;
@@ -20,9 +27,15 @@
 import net.bioclipse.qsar.descriptor.model.DescriptorProvider;
 import net.bioclipse.qsar.init.Activator;
 
+import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.FileLocator;
+import org.eclipse.core.runtime.Path;
+import org.eclipse.core.runtime.Platform;
 import org.eclipse.core.runtime.preferences.DefaultScope;
 import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.junit.Test;
+import org.osgi.framework.Bundle;
 
 public class TestCDKQsar {
 
@@ -225,6 +238,41 @@ public void testCalculateXlogPFromSmiles() throws BioclipseException{
 		
 		
 	}
+	
+	@Test
+	public void testCalculateXlogPFromCML() throws BioclipseException, FileNotFoundException, IOException, CoreException{
+
+		ICDKManager cdk=net.bioclipse.cdk.business.Activator.getDefault().getCDKManager();
+		
+		Bundle bun=Platform.getBundle(net.bioclipse.cdk.qsar.test.Activator.PLUGIN_ID);
+		System.out.println("wee bun: " + bun);
+
+		URL url=FileLocator.find(bun, new Path("src/testFiles/0037.cml"), null);
+		System.out.println("wee url: " + url);
+		
+		String str=FileLocator.toFileURL(url).getFile();
+		System.out.println("wee File: " + str);
+		
+        ICDKMolecule mol = cdk.loadMolecule( new MockIFile(str), null );
+		
+		IDescriptorResult dres1=qsar.calculate(mol, xlogpID);
+		assertNotNull(dres1);
+		assertNull(dres1.getErrorMessage(),dres1.getErrorMessage());
+		assertEquals(xlogpID, dres1.getDescriptorId());
+
+		System.out.println("Mol: " + mol.getSmiles() + 
+				" ; Desc: " + dres1.getDescriptorId() +": ");
+		for (int i=0; i<dres1.getValues().length;i++){
+			System.out.println("    " + dres1.getLabels()[i] 
+			                                     + "=" + dres1.getValues()[i] ); 
+		}
+		
+		assertEquals("XLogP", dres1.getLabels()[0]);
+		assertEquals(0.184, dres1.getValues()[0]);
+		
+		
+	}
+
 
 	@Test
 	public void testCalculateBCUTFromSmiles() throws BioclipseException{
diff --git a/plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/testCDKAT.java b/plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/testCDKAT.java
new file mode 100644
index 0000000..17fc884
--- /dev/null
+++ b/plugins/net.bioclipse.cdk.qsar.test/src/net/bioclipse/cdk/qsar/test/testCDKAT.java
@@ -0,0 +1,67 @@
+package net.bioclipse.cdk.qsar.test;
+
+import java.io.InputStream;
+
+import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IChemFile;
+import org.openscience.cdk.io.CMLReader;
+import org.openscience.cdk.io.ReaderFactory;
+import org.openscience.cdk.io.formats.CMLFormat;
+import org.openscience.cdk.io.formats.IChemFormatMatcher;
+import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
+import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
+import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
+
+public class testCDKAT {
+
+	/**
+	 * @param args
+	 */
+	public static void main(String[] args) {
+
+        InputStream ins = testCDKAT.class.getResourceAsStream("/testFiles/0037.cml");
+        
+        CMLReader reader=new CMLReader(ins);
+        
+        IChemFile chemFile = new org.openscience.cdk.ChemFile();
+
+
+        //Read file
+        try {
+            chemFile=(IChemFile)reader.read(chemFile);
+        } catch (CDKException e) {
+        	e.printStackTrace();
+        }
+        
+        IAtomContainer container = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
+        
+		try {
+
+			CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(container.getBuilder());
+	        for (IAtom atom : container.atoms()) {
+	            IAtomType matched = matcher.findMatchingAtomType(container, atom);
+	            if (matched != null){
+	            	AtomTypeManipulator.configure(atom, matched);
+	            }else{
+	            	System.out.println("Could not find matching atom type for atom: " + atom);
+	            }
+	        }
+	        
+			CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(container.getBuilder());
+			hAdder.addImplicitHydrogens(container);
+			AtomContainerManipulator.convertImplicitToExplicitHydrogens(container);
+
+		} catch (Exception e1) {
+			System.out.println("Error addding hydrogens : " + e1.getMessage());
+		}
+
+
+
+	}
+
+}
diff --git a/plugins/net.bioclipse.cdk.qsar.test/src/testFiles/0037.cml b/plugins/net.bioclipse.cdk.qsar.test/src/testFiles/0037.cml
new file mode 100644
index 0000000..d9e4bc4
--- /dev/null
+++ b/plugins/net.bioclipse.cdk.qsar.test/src/testFiles/0037.cml
@@ -0,0 +1 @@
+<cml xmlns="http://www.xml-cml.org/schema"><molecule title="" id="nmrshiftdb20110444"><atomArray><atom id="a1" elementType="C" x2="2.89" y2="-1.25" formalCharge="0" hydrogenCount="0" /><atom id="a2" elementType="C" x2="2.89" y2="-0.42" formalCharge="0" hydrogenCount="0" /><atom id="a3" elementType="C" x2="2.17" y2="0.0" formalCharge="0" hydrogenCount="0" /><atom id="a4" elementType="C" x2="1.44" y2="-0.42" formalCharge="0" hydrogenCount="0" /><atom id="a5" elementType="C" x2="1.44" y2="-1.25" formalCharge="0" hydrogenCount="0" /><atom id="a6" elementType="C" x2="0.72" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a7" elementType="C" x2="3.61" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a8" elementType="C" x2="2.17" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a9" elementType="C" x2="2.89" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a10" elementType="C" x2="1.44" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a11" elementType="C" x2="0.0" y2="-4.58" formalCharge="0" hydrogenCount="0" /><atom id="a12" elementType="C" x2="0.72" y2="-5.0" formalCharge="0" hydrogenCount="0" /><atom id="a13" elementType="C" x2="0.0" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a14" elementType="C" x2="2.89" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a15" elementType="C" x2="3.61" y2="-4.17" formalCharge="0" hydrogenCount="0" /><atom id="a16" elementType="C" x2="4.33" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a17" elementType="C" x2="4.33" y2="-2.92" formalCharge="0" hydrogenCount="0" /><atom id="a18" elementType="C" x2="3.61" y2="-2.5" formalCharge="0" hydrogenCount="0" /><atom id="a19" elementType="O" x2="1.44" y2="-3.75" formalCharge="0" hydrogenCount="0" /><atom id="a20" elementType="N" x2="2.17" y2="-1.67" formalCharge="0" hydrogenCount="0" /><atom id="a21" elementType="N" x2="0.0" y2="-2.08" formalCharge="0" hydrogenCount="0" /><atom id="a22" elementType="Si" x2="0.72" y2="-4.17" formalCharge="0" hydrogenCount="0" /></atomArray><bondArray><bond id="b1" atomRefs2="a1 a20" order="S" /><bond id="b2" atomRefs2="a1 a2" order="S" /><bond id="b3" atomRefs2="a1 a7" order="S" /><bond id="b4" atomRefs2="a2 a3" order="S" /><bond id="b5" atomRefs2="a3 a4" order="S" /><bond id="b6" atomRefs2="a4 a5" order="S" /><bond id="b7" atomRefs2="a5 a20" order="S" /><bond id="b8" atomRefs2="a5 a6" order="S" /><bond id="b9" atomRefs2="a6 a21" order="T" /><bond id="b10" atomRefs2="a8 a20" order="S" /><bond id="b11" atomRefs2="a8 a9" order="S" /><bond id="b12" atomRefs2="a8 a10" order="S" /><bond id="b13" atomRefs2="a9 a14" order="D" /><bond id="b14" atomRefs2="a9 a18" order="S" /><bond id="b15" atomRefs2="a10 a19" order="S" /><bond id="b16" atomRefs2="a11 a22" order="S" /><bond id="b17" atomRefs2="a12 a22" order="S" /><bond id="b18" atomRefs2="a13 a22" order="S" /><bond id="b19" atomRefs2="a14 a15" order="S" /><bond id="b20" atomRefs2="a15 a16" order="D" /><bond id="b21" atomRefs2="a16 a17" order="S" /><bond id="b22" atomRefs2="a17 a18" order="D" /><bond id="b23" atomRefs2="a19 a22" order="S" /></bondArray></molecule></cml>