Updated PaDEL to cdk-2.9

PaDEL-Descriptor/nbproject/private/private.properties

@@ -1,7 +1,7 @@
-compile.on.save=false
-do.depend=false
-do.jar=true
-javac.debug=false
-javadoc.preview=true
-jaxbwiz.endorsed.dirs=C:\\Program Files\\NetBeans 6.8\\ide12\\modules\\ext\\jaxb\\api
-user.properties.file=C:\\Users\\phayapc\\.netbeans\\7.0\\build.properties
+compile.on.save=false
+do.depend=false
+do.jar=true
+javac.debug=false
+javadoc.preview=true
+jaxbwiz.endorsed.dirs=C:\\Program Files\\NetBeans 6.8\\ide12\\modules\\ext\\jaxb\\api
+user.properties.file=/Users/rvdploeg_hu/Library/Application Support/NetBeans/22/build.properties

PaDEL-Descriptor/nbproject/project.properties

@@ -1,119 +1,130 @@
-annotation.processing.enabled=true
-annotation.processing.enabled.in.editor=false
-annotation.processing.run.all.processors=true
-ant.customtasks.libs=JWSAntTasks
-application.desc=A software to calculate molecular descriptors and fingerprints
-application.homepage=http://padel.nus.edu.sg
-application.splash=D:\\My Documents\\Programming Projects\\Java Projects\\PaDEL-Descriptor\\src\\padeldescriptor\\resources\\PaDELlogoSplash.jpg
-application.title=PaDEL-Descriptor
-application.vendor=Pharmaceutical Data Exploration Laboratory
-build.classes.dir=${build.dir}/classes
-build.classes.excludes=**/*.java,**/*.form
-# This directory is removed when the project is cleaned:
-build.dir=build
-build.generated.dir=${build.dir}/generated
-build.generated.sources.dir=${build.dir}/generated-sources
-# Only compile against the classpath explicitly listed here:
-build.sysclasspath=ignore
-build.test.classes.dir=${build.dir}/test/classes
-build.test.results.dir=${build.dir}/test/results
-debug.classpath=\
-    ${run.classpath}
-debug.test.classpath=\
-    ${run.test.classpath}
-# This directory is removed when the project is cleaned:
-dist.dir=dist
-dist.jar=${dist.dir}/PaDEL-Descriptor.jar
-dist.javadoc.dir=${dist.dir}/javadoc
-endorsed.classpath=\
-    ${file.reference.javaws.jar-1}
-excludes=
-file.reference.ambit2-base-2.4.7-SNAPSHOT.jar=../lib/ambit2-base-2.4.7-SNAPSHOT.jar
-file.reference.ambit2-core-2.4.7-SNAPSHOT.jar=../lib/ambit2-core-2.4.7-SNAPSHOT.jar
-file.reference.ambit2-smarts-2.4.7-SNAPSHOT.jar=../lib/ambit2-smarts-2.4.7-SNAPSHOT.jar
-file.reference.cdk-1.4.15.jar=../lib/cdk-1.4.15.jar
-file.reference.commons-cli-1.2.jar=../lib/commons-cli-1.2.jar
-file.reference.guava-17.0.jar=../lib/guava-17.0.jar
-file.reference.jama.jar=../lib/jama.jar
-file.reference.javaws.jar=C:\\Program Files (x86)\\Java\\jdk1.6.0_18\\jre\\lib\\javaws.jar
-file.reference.javaws.jar-1=C:\\Program Files\\Java\\jdk1.6.0_43\\jre\\lib\\javaws.jar
-file.reference.jgrapht-0.6.0.jar=../lib/jgrapht-0.6.0.jar
-file.reference.l2fprod-common-all.jar=../lib/l2fprod-common-all.jar
-file.reference.libPaDEL-Descriptor.jar=../libPaDEL-Descriptor/dist/libPaDEL-Descriptor.jar
-file.reference.libPaDEL-Jobs.jar=../libPaDEL-Jobs/dist/libPaDEL-Jobs.jar
-file.reference.libPaDEL.jar=../libPaDEL/dist/libPaDEL.jar
-file.reference.rapidminer.jar=../lib/rapidminer.jar
-file.reference.vecmath1.2-1.14.jar=../lib/vecmath1.2-1.14.jar
-file.reference.xom-1.1.jar=../lib/xom-1.1.jar
-file.reference.jdesktop=../lib/appframework-1.0.3.jar
-libs.swing-app-framework.classpath=../lib/swing-worker-1.1.jar
-includes=**
-jar.compress=true
-javac.classpath=\
-    ${libs.swing-app-framework.classpath}:\
-    ${file.reference.libPaDEL.jar}:\
-    ${file.reference.libPaDEL-Descriptor.jar}:\
-    ${file.reference.libPaDEL-Jobs.jar}:\
-    ${file.reference.l2fprod-common-all.jar}:\
-    ${file.reference.commons-cli-1.2.jar}:\
-    ${file.reference.jgrapht-0.6.0.jar}:\
-    ${file.reference.vecmath1.2-1.14.jar}:\
-    ${file.reference.xom-1.1.jar}:\
-    ${file.reference.jama.jar}:\
-    ${file.reference.rapidminer.jar}:\
-    ${file.reference.cdk-1.4.15.jar}:\
-    ${file.reference.ambit2-base-2.4.7-SNAPSHOT.jar}:\
-    ${file.reference.ambit2-core-2.4.7-SNAPSHOT.jar}:\
-    ${file.reference.ambit2-smarts-2.4.7-SNAPSHOT.jar}:\
-    ${file.reference.guava-17.0.jar}:\
-    ${file.reference.jdesktop}
-# Space-separated list of extra javac options
-javac.compilerargs=
-javac.deprecation=false
-javac.processorpath=\
-    ${javac.classpath}
-javac.source=1.8
-javac.target=1.8
-javac.test.classpath=\
-    ${javac.classpath}:\
-    ${build.classes.dir}:\
-    ${libs.junit.classpath}:\
-    ${libs.junit_4.classpath}
-javadoc.additionalparam=
-javadoc.author=false
-javadoc.encoding=${source.encoding}
-javadoc.noindex=false
-javadoc.nonavbar=false
-javadoc.notree=false
-javadoc.private=false
-javadoc.splitindex=true
-javadoc.use=true
-javadoc.version=false
-javadoc.windowtitle=
-jaxbwiz.endorsed.dirs="${netbeans.home}/../ide12/modules/ext/jaxb/api"
-jnlp.codebase.type=user
-jnlp.codebase.url=D:\\My Documents\\Programming Projects\\Java Projects\\PaDEL-Descriptor\\dist
-jnlp.codebase.user=http://padel.nus.edu.sg/software/padeldescriptor/
-jnlp.descriptor=application
-jnlp.enabled=true
-jnlp.icon=D:\\My Documents\\Programming Projects\\Java Projects\\PaDEL-Descriptor\\src\\padeldescriptor\\resources\\PaDELlogoSplash.jpg
-jnlp.offline-allowed=true
-jnlp.signed=true
-main.class=padeldescriptor.PaDELDescriptorApp
-manifest.file=manifest.mf
-meta.inf.dir=${src.dir}/META-INF
-mkdist.disabled=false
-platform.active=default_platform
-run.classpath=\
-    ${javac.classpath}:\
-    ${build.classes.dir}
-# Space-separated list of JVM arguments used when running the project
-# (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value
-# or test-sys-prop.name=value to set system properties for unit tests):
-run.jvmargs=-Xmx512m
-run.test.classpath=\
-    ${javac.test.classpath}:\
-    ${build.test.classes.dir}
-source.encoding=UTF-8
-src.dir=src
-test.src.dir=test
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.run.all.processors=true
+ant.customtasks.libs=JWSAntTasks
+application.desc=A software to calculate molecular descriptors and fingerprints
+application.homepage=http://padel.nus.edu.sg
+application.splash=D:\\My Documents\\Programming Projects\\Java Projects\\PaDEL-Descriptor\\src\\padeldescriptor\\resources\\PaDELlogoSplash.jpg
+application.title=PaDEL-Descriptor
+application.vendor=Pharmaceutical Data Exploration Laboratory
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+debug.classpath=\
+    ${run.classpath}
+debug.modulepath=\
+    ${run.modulepath}
+debug.test.classpath=\
+    ${run.test.classpath}
+debug.test.modulepath=\
+    ${run.test.modulepath}
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/PaDEL-Descriptor.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+endorsed.classpath=
+excludes=
+file.reference.ambit2-base-2.4.7-SNAPSHOT.jar=../lib/ambit2-base-2.4.7-SNAPSHOT.jar
+file.reference.ambit2-core-2.4.7-SNAPSHOT.jar=../lib/ambit2-core-2.4.7-SNAPSHOT.jar
+file.reference.ambit2-smarts-2.4.7-SNAPSHOT.jar=../lib/ambit2-smarts-2.4.7-SNAPSHOT.jar
+file.reference.cdk-2.9.jar=../lib/cdk-2.9.jar
+file.reference.commons-cli-1.2.jar=../lib/commons-cli-1.2.jar
+file.reference.guava-17.0.jar=../lib/guava-17.0.jar
+file.reference.jama.jar=../lib/jama-1.0.3.jar
+file.reference.javaws.jar=C:\\Program Files (x86)\\Java\\jdk1.6.0_18\\jre\\lib\\javaws.jar
+file.reference.javaws.jar-1=C:\\Program Files\\Java\\jdk1.6.0_43\\jre\\lib\\javaws.jar
+file.reference.jgrapht-0.6.0.jar=../lib/jgrapht-0.6.0.jar
+file.reference.l2fprod-common-all.jar=../lib/l2fprod-common-all.jar
+file.reference.libPaDEL-Descriptor.jar=../libPaDEL-Descriptor/dist/libPaDEL-Descriptor.jar
+file.reference.libPaDEL-Jobs.jar=../libPaDEL-Jobs/dist/libPaDEL-Jobs.jar
+file.reference.libPaDEL.jar=../libPaDEL/dist/libPaDEL.jar
+file.reference.rapidminer.jar=../lib/rapidminer.jar
+file.reference.vecmath1.2-1.14.jar=../lib/vecmath1.2-1.14.jar
+file.reference.xom-1.1.jar=../lib/xom-1.1.jar
+file.reference.jdesktop=../lib/appframework-1.0.3.jar
+javac.modulepath=
+javac.processormodulepath=
+javac.test.modulepath=\
+    ${javac.modulepath}
+libs.swing-app-framework.classpath=../lib/swing-worker-1.1.jar
+includes=**
+jar.compress=true
+javac.classpath=\
+    ${libs.swing-app-framework.classpath}:\
+    ${file.reference.libPaDEL.jar}:\
+    ${file.reference.libPaDEL-Descriptor.jar}:\
+    ${file.reference.libPaDEL-Jobs.jar}:\
+    ${file.reference.l2fprod-common-all.jar}:\
+    ${file.reference.commons-cli-1.2.jar}:\
+    ${file.reference.jgrapht-0.6.0.jar}:\
+    ${file.reference.vecmath1.2-1.14.jar}:\
+    ${file.reference.xom-1.1.jar}:\
+    ${file.reference.jama.jar}:\
+    ${file.reference.rapidminer.jar}:\
+    ${file.reference.cdk-2.9.jar}:\
+    ${file.reference.ambit2-base-2.4.7-SNAPSHOT.jar}:\
+    ${file.reference.ambit2-core-2.4.7-SNAPSHOT.jar}:\
+    ${file.reference.ambit2-smarts-2.4.7-SNAPSHOT.jar}:\
+    ${file.reference.guava-17.0.jar}:\
+    ${file.reference.jdesktop}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.processorpath=\
+    ${javac.classpath}
+javac.source=1.8
+javac.target=1.8
+javac.test.classpath=\
+    ${javac.classpath}:\
+    ${build.classes.dir}:\
+    ${libs.junit.classpath}:\
+    ${libs.junit_4.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+jaxbwiz.endorsed.dirs="${netbeans.home}/../ide12/modules/ext/jaxb/api"
+jnlp.codebase.type=user
+jnlp.codebase.url=D:\\My Documents\\Programming Projects\\Java Projects\\PaDEL-Descriptor\\dist
+jnlp.codebase.user=http://padel.nus.edu.sg/software/padeldescriptor/
+jnlp.descriptor=application
+jnlp.enabled=false
+jnlp.icon=D:\\My Documents\\Programming Projects\\Java Projects\\PaDEL-Descriptor\\src\\padeldescriptor\\resources\\PaDELlogoSplash.jpg
+jnlp.offline-allowed=true
+jnlp.signed=true
+main.class=padeldescriptor.PaDELDescriptorApp
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+mkdist.disabled=false
+platform.active=default_platform
+run.classpath=\
+    ${javac.classpath}:\
+    ${build.classes.dir}
+# Space-separated list of JVM arguments used when running the project
+# (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value
+# or test-sys-prop.name=value to set system properties for unit tests):
+run.jvmargs=-Xmx512m
+run.modulepath=\
+    ${javac.modulepath}
+run.test.classpath=\
+    ${javac.test.classpath}:\
+    ${build.test.classes.dir}
+run.test.modulepath=\
+    ${javac.test.modulepath}
+source.encoding=UTF-8
+src.dir=src
+test.src.dir=test

PaDEL-Descriptor/src/com/rapidminer/operator/chemistry/CompoundAddHydrogens.java

@@ -50,11 +50,11 @@ public void doWork() throws OperatorException
 
         for (int i=0, endi=mols.size(); i<endi; ++i)
         {
-            IAtomContainer molecule = mols.getMolecule(i);
+            IAtomContainer molecule = mols.getAtomContainer(i);
 
             try
             {
-                ori.addMolecule((IAtomContainer)molecule.clone());
+                ori.addAtomContainer((IAtomContainer)molecule.clone());
                 AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
                 CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
                 adder.addImplicitHydrogens(molecule);

PaDEL-Descriptor/src/com/rapidminer/operator/chemistry/CompoundConvert3D.java

@@ -35,9 +35,11 @@
 import java.util.logging.Logger;
 import libpadeldescriptor.libPaDELDescriptorJob;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.modeling.builder3d.ModelBuilder3D;
 import org.openscience.cdk.modeling.builder3d.TemplateHandler3D;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 /*
@@ -91,7 +93,7 @@ public void doWork() throws OperatorException
         {
             for (int i=0, endi=mols.size(); i<endi; ++i)
             {
-                ori.addMolecule((IAtomContainer)mols.getMolecule(i).clone());
+                ori.addAtomContainer((IAtomContainer)mols.getAtomContainer(i).clone());
             }
         }
         catch (Exception ex)
@@ -104,13 +106,13 @@ public void doWork() throws OperatorException
         {
             for (int i=0, endi=mols.size(); i<endi; ++i)
             {
-                mols.setMolecule(i, Convert3D(mols.getMolecule(i), forcefield));
+                mols.setAtomContainer(i, Convert3D(mols.getAtomContainer(i), forcefield));
             }
         }
         else
         {
             int cpdIndex = getParameterAsInt(PARAMETER_CPD_INDEX);            
-            mols.setMolecule(cpdIndex-1, Convert3D(mols.getMolecule(cpdIndex-1), forcefield));
+            mols.setAtomContainer(cpdIndex-1, Convert3D(mols.getAtomContainer(cpdIndex-1), forcefield));
         }
 
         mols.recalculateStatistics();
@@ -125,9 +127,10 @@ private IAtomContainer Convert3D(IAtomContainer molecule, String forcefield)
         {
             AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
             // Calculate 3D coordinates.
+            IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
             TemplateHandler3D template = TemplateHandler3D.getInstance();
-            ModelBuilder3D mb3d = ModelBuilder3D.getInstance(template,forcefield);
-            return (IAtomContainer) mb3d.generate3DCoordinates((IMolecule) molecule, true);
+            ModelBuilder3D mb3d = ModelBuilder3D.getInstance(template, forcefield, builder);
+            return (IAtomContainer) mb3d.generate3DCoordinates((IAtomContainer) molecule, true);
         }
         catch (Exception ex)
         {

PaDEL-Descriptor/src/com/rapidminer/operator/chemistry/CompoundCountSubstructure.java

@@ -32,6 +32,8 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
 
 /*
@@ -72,13 +74,14 @@ public void doWork() throws OperatorException
         ArrayList<String> counts = new ArrayList<String>(mols.size());
         for (int i=0, endi=mols.size(); i<endi; ++i)
         {
-            IAtomContainer molecule = mols.getMolecule(i);
+            IAtomContainer molecule = mols.getAtomContainer(i);
 
             try
             {
-                ori.addMolecule((IAtomContainer)molecule.clone());
+                ori.addAtomContainer((IAtomContainer)molecule.clone());
 
-                SMARTSQueryTool sqt = new SMARTSQueryTool(smart);
+                IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
+                SMARTSQueryTool sqt = new SMARTSQueryTool(smart, builder);
                 if (sqt.matches(molecule))
                 {
                     counts.add(String.valueOf(sqt.getUniqueMatchingAtoms().size()));

PaDEL-Descriptor/src/com/rapidminer/operator/chemistry/CompoundDescriptors.java

@@ -336,7 +336,7 @@ public void doWork() throws OperatorException
             List<String> descriptorValues = results.get(i);
             int maxDescriptors = descriptorValues.size() + 1;
             double[] data = new double[maxDescriptors];
-            data[0] = exampleTable.findAttribute("Compound").getMapping().mapString(mols.getMoleculeName(i-1));
+            data[0] = exampleTable.findAttribute("Compound").getMapping().mapString(mols.getAtomContainerName(i-1));
             for (int j=0, endj=descriptorValues.size(); j<endj; ++j)
             {
                 if (!descriptorValues.get(j).equals(""))

PaDEL-Descriptor/src/com/rapidminer/operator/chemistry/CompoundDetectDimensionality.java

@@ -58,11 +58,11 @@ public void doWork() throws OperatorException
         DecimalFormat df = new DecimalFormat("#0.0000");
         for (int i=0, endi=mols.size(); i<endi; ++i)
         {
-            IAtomContainer molecule = mols.getMolecule(i);
+            IAtomContainer molecule = mols.getAtomContainer(i);
 
             try
             {
-                ori.addMolecule((IAtomContainer)molecule.clone());                
+                ori.addAtomContainer((IAtomContainer)molecule.clone());                
             }
             catch (Exception ex)
             {