Merged master into 2.5.x

bioclipse · Jan 9, 2012 · ed4eaed · ed4eaed
2 parents ff14ecd + 004996c
commit ed4eaed
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Showing 9 changed files with 2,898 additions and 1,936 deletions.
diff --git a/features/net.bioclipse.qsar.test_feature/feature.xml.orig b/features/net.bioclipse.qsar.test_feature/feature.xml.orig
@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<feature
+      id="net.bioclipse.qsar.test_feature"
+      label="QSAR Test Feature"
+      version="2.5.0.qualifier"
+      provider-name="The Bioclipse Project"
+      plugin="net.bioclipse.qsar.test">
+
+   <description>
+      QSAR (Quantitative Structure-Activity Relationship) functionality
+for Bioclipse.
+   </description>
+
+   <copyright>
+      (C) 2006-2009 The Bioclipse Project contributors and others.
+   </copyright>
+
+   <license url="http://www.eclipse.org/org/documents/epl-v10.php">
+      This feature and the accompanying materials are made available
+under the terms of the Eclipse Public License v1.0 + exception,
+putting no constraints on choice of backend and/or license for
+creating plugins for Bioclipse; it is totally open for both open
+source plugins as well as commercial. The exception allows GPL
+plugins to be written and run in any combination with EPL licensed
+plugins, addressing incompatibility between the EPL and the GPL
+v.2.
+The Eclipse Public License accompanies this distribution, and
+is available at http://www.eclipse.org/legal/epl-v10.html
+   </license>
+
+   <requires>
+<<<<<<< HEAD
+      <import feature="net.bioclipse.rdf_feature" version="2.5.0.qualifier" match="greaterOrEqual"/>
+      <import feature="net.bioclipse.chemoinformatics_feature" version="2.5.0.qualifier" match="greaterOrEqual"/>
+=======
+      <import feature="net.bioclipse.rdf_feature" version="2.4.0" match="greaterOrEqual"/>
+      <import feature="net.bioclipse.chemoinformatics_feature" version="2.4.0" match="greaterOrEqual"/>
+>>>>>>> master
+      <import feature="net.bioclipse.qsar_feature" version="2.5.0.qualifier"/>
+   </requires>
+
+   <plugin
+         id="net.bioclipse.cdk.qsar.test"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
+   <plugin
+         id="net.bioclipse.qsar.test"
+         download-size="0"
+         install-size="0"
+         version="0.0.0"
+         unpack="false"/>
+
+</feature>
diff --git a/plugins/net.bioclipse.cdk.qsar/src/net/bioclipse/cdk/qsar/impl/CDKDescriptorCalculator.java b/plugins/net.bioclipse.cdk.qsar/src/net/bioclipse/cdk/qsar/impl/CDKDescriptorCalculator.java
@@ -24,6 +24,7 @@
 import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.exception.NoSuchAtomException;
+import org.openscience.cdk.geometry.GeometryTools;
 import org.openscience.cdk.graph.SpanningTree;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -188,22 +189,22 @@ public Map<? extends IMolecule, List<IDescriptorResult>> calculateDescriptor(
     private List<IDescriptorResult> doCalculate(ICDKMolecule cdkmol, 
                                                 List<DescriptorType> descriptorTypes, 
                                                 IProgressMonitor monitor)  throws OperationCanceledException{
-
+    	
         //Get atomcontainer from IMolecule
         IAtomContainer container=cdkmol.getAtomContainer();
 
         //Make sure e have a Molecule, otherwise create it
         if (!(container instanceof org.openscience.cdk.interfaces.IMolecule))
             container = container.getBuilder().newInstance(
                      org.openscience.cdk.interfaces.IMolecule.class, container);
-
+        
         //Store results here
         List<IDescriptorResult> results = new ArrayList<IDescriptorResult>();
 
         //Preprocess atomcontainer. Return null if all is well, else String with error
         //========================
         String atomcontainerError=doCDKPreprocessing(container);
-
+        
         //Loop over all descriptors
         //=========================
         for (DescriptorType descType : descriptorTypes){
@@ -339,6 +340,7 @@ else if (obj instanceof String) {
                 String[] resultLabels = null;
 //                logger.debug("# result values: " + resultVals.length);
 
+
                 //Calculate descriptor
                 try {
                     DescriptorValue value = ((IMolecularDescriptor) cdkDescriptor).calculate(container);
@@ -416,7 +418,6 @@ else if (resultLabels.length != resultVals.length) {
      */
     private String doCDKPreprocessing(IAtomContainer container) {
 
-
         //Add hydrogens
         try {
 
@@ -432,7 +433,7 @@ private String doCDKPreprocessing(IAtomContainer container) {
 
             CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(container.getBuilder());
             hAdder.addImplicitHydrogens(container);
-            AtomContainerManipulator.convertImplicitToExplicitHydrogens(container);
+//            AtomContainerManipulator.convertImplicitToExplicitHydrogens(container);
         } catch (Exception e1) {
             String emsg="Error addding hydrogens : " + e1.getMessage();
             logger.error(emsg);

diff --git a/plugins/net.bioclipse.qsar.test/META-INF/MANIFEST.MF.orig b/plugins/net.bioclipse.qsar.test/META-INF/MANIFEST.MF.orig
@@ -0,0 +1,30 @@
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: Test Plug-in
+Bundle-SymbolicName: net.bioclipse.qsar.test;singleton:=true
+Bundle-Version: 2.5.0.qualifier
+Bundle-Activator: net.bioclipse.qsar.test.Activator
+Require-Bundle: org.eclipse.ui,
+ org.eclipse.core.runtime,
+ net.bioclipse.qsar,
+ net.bioclipse.core,
+<<<<<<< HEAD
+ net.bioclipse.qsar.model,
+ net.bioclipse.qsar.model.edit,
+ net.bioclipse.qsar.ui,
+ net.bioclipse.core.tests
+=======
+ net.bioclipse.qsar.model;bundle-version="1.0.0",
+ net.bioclipse.qsar.model.edit;bundle-version="1.0.0",
+ net.bioclipse.qsar.ui;bundle-version="2.0.0",
+ net.bioclipse.core.tests;bundle-version="2.5.0"
+>>>>>>> master
+Bundle-ActivationPolicy: lazy
+Bundle-RequiredExecutionEnvironment: J2SE-1.5
+Import-Package: org.apache.log4j,
+ org.junit,
+ org.junit.runner,
+ org.junit.runners
+Export-Package: net.bioclipse.qsar.test,
+ net.bioclipse.qsar.test.business
+Bundle-ClassPath: .