diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..aa9e151 Binary files /dev/null and b/.DS_Store differ diff --git a/PaDEL-Descriptor/.DS_Store b/PaDEL-Descriptor/.DS_Store new file mode 100644 index 0000000..5008ddf Binary files /dev/null and b/PaDEL-Descriptor/.DS_Store differ diff --git a/PaDEL-Descriptor/nbproject/jnlp-impl.xml b/PaDEL-Descriptor/nbproject/jnlp-impl.xml index cf1c99a..96d4bfd 100644 --- a/PaDEL-Descriptor/nbproject/jnlp-impl.xml +++ b/PaDEL-Descriptor/nbproject/jnlp-impl.xml @@ -1,262 +1,700 @@ - + - - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + - - - - - - - - - - - $${APPLICATION.TITLE} - $${APPLICATION.VENDOR} - - $${APPLICATION.DESC} - $${APPLICATION.DESC.SHORT} - - - - - - - - - - - - - -]]> + + + + + + + + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - + + + + + + + + + + + + + + + + - - + + - - - - + + + + + + - + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + To run this application from the command line without Ant, try: + + javaws "${jnlp.file.resolved}" + + + + + + + - + - - + + - - - + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + - - + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - - - - - - + - + - - - + + + - + + + + + + + + + + + - @@ -278,184 +716,172 @@ made subject to such option by the copyright holder. + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + - + + + + + + + + + + + + + + + + + + - - - - + + - - - - - - - + + + + + - - + + + + + + + + + + - - + + + + + + - - + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - - - - - - + + + - - + + - + - - - - - - - - - - - - - + + - + - - - + + + + + - - - - + + + + + + + + + + + + + + + + - - + + + + - - - - - - - - - - - - - - - Test page for launching the application via JNLP - - -

Test page for launching the application via JNLP

- Launch the application - - - -]]> + + + + + + + + + + + + + + diff --git a/PaDEL-Descriptor/nbproject/jnlp-impl_backup.xml b/PaDEL-Descriptor/nbproject/jnlp-impl_backup.xml new file mode 100644 index 0000000..cf1c99a --- /dev/null +++ b/PaDEL-Descriptor/nbproject/jnlp-impl_backup.xml @@ -0,0 +1,461 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $${APPLICATION.TITLE} + $${APPLICATION.VENDOR} + + $${APPLICATION.DESC} + $${APPLICATION.DESC.SHORT} + + + + + + + + + + + + + +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Test page for launching the application via JNLP + + +

Test page for launching the application via JNLP

+ Launch the application + + + +]]> + + + diff --git a/PaDEL-Descriptor/nbproject/private/private.properties b/PaDEL-Descriptor/nbproject/private/private.properties index d3e3e6c..a558da4 100644 --- a/PaDEL-Descriptor/nbproject/private/private.properties +++ b/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 diff --git a/PaDEL-Descriptor/nbproject/project.properties b/PaDEL-Descriptor/nbproject/project.properties index cd94e5a..9d79e98 100644 --- a/PaDEL-Descriptor/nbproject/project.properties +++ b/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 diff --git a/PaDEL-Descriptor/src/com/rapidminer/operator/chemistry/CompoundAddHydrogens.java b/PaDEL-Descriptor/src/com/rapidminer/operator/chemistry/CompoundAddHydrogens.java index c86c6ae..63fa10b 100644 --- a/PaDEL-Descriptor/src/com/rapidminer/operator/chemistry/CompoundAddHydrogens.java +++ b/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 counts = new ArrayList(mols.size()); for (int i=0, endi=mols.size(); i 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 smiles = new ArrayList(mols.size()); for (int i=0, endi=mols.size(); i getMolecules() return temp; } - public IAtomContainer getMolecule(int index) + public IAtomContainer getAtomContainer(int index) { return mols.get(index); } - public void setMolecule(int index, IAtomContainer mol) + public void setAtomContainer(int index, IAtomContainer mol) { mols.set(index, mol); calculateStatistics(mol, index); } - public String getMoleculeName(int index) + public String getAtomContainerName(int index) { return (String)mols.get(index).getProperty("cdk:Title"); } diff --git a/jama-1.0.3.jar b/jama-1.0.3.jar new file mode 100644 index 0000000..c800759 Binary files /dev/null and b/jama-1.0.3.jar differ diff --git a/lib/cdk-2.9.jar b/lib/cdk-2.9.jar new file mode 100644 index 0000000..311f731 Binary files /dev/null and b/lib/cdk-2.9.jar differ diff --git a/lib/jama-1.0.3.jar b/lib/jama-1.0.3.jar new file mode 100644 index 0000000..c800759 Binary files /dev/null and b/lib/jama-1.0.3.jar differ diff --git a/libPaDEL-Descriptor/grep b/libPaDEL-Descriptor/grep deleted file mode 100644 index e69de29..0000000 diff --git a/libPaDEL-Descriptor/nbproject/project.properties b/libPaDEL-Descriptor/nbproject/project.properties index 6178d1a..c200944 100644 --- a/libPaDEL-Descriptor/nbproject/project.properties +++ b/libPaDEL-Descriptor/nbproject/project.properties @@ -26,18 +26,18 @@ dist.javadoc.dir=${dist.dir}/javadoc endorsed.classpath= excludes= 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.cdk-2.9.jar=../lib/cdk-2.9.jar file.reference.guava-17.0.jar=../lib/guava-17.0.jar file.reference.jgrapht-0.6.0.jar=../lib/jgrapht-0.6.0.jar file.reference.libPaDEL-Jobs.jar=../libPaDEL-Jobs/dist/libPaDEL-Jobs.jar file.reference.vecmath1.2-1.14.jar=../lib/vecmath1.2-1.14.jar -file.reference.cdk=../lib/cdk-1.4.15.jar +file.reference.cdk=../lib/cdk-2.9.jar includes=** jar.compress=true javac.classpath=\ ${file.reference.jgrapht-0.6.0.jar}:\ ${file.reference.vecmath1.2-1.14.jar}:\ - ${file.reference.cdk-1.4.15.jar}:\ + ${file.reference.cdk-2.9.jar}:\ ${file.reference.libPaDEL-Jobs.jar}:\ ${file.reference.ambit2-smarts-2.4.7-SNAPSHOT.jar}:\ ${file.reference.guava-17.0.jar}:\ diff --git a/libPaDEL-Descriptor/reply3 b/libPaDEL-Descriptor/reply3 deleted file mode 100644 index 2e4621e..0000000 --- a/libPaDEL-Descriptor/reply3 +++ /dev/null @@ -1,137 +0,0 @@ -Buildfile: /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/build.xml - --pre-init: - --init-private: - --init-user: - --init-project: - --init-macrodef-property: - --do-init: - --post-init: - --init-check: - --init-ap-cmdline-properties: - --init-macrodef-javac-with-processors: - --init-macrodef-javac-without-processors: - --init-macrodef-javac: - --init-macrodef-junit: - --init-debug-args: - --init-macrodef-nbjpda: - --init-macrodef-debug: - --init-macrodef-java: - --init-presetdef-jar: - --init-ap-cmdline-supported: - --init-ap-cmdline: - -init: - --deps-jar-init: - [delete] Deleting: /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/build/built-jar.properties - -deps-jar: - --warn-already-built-jar: -[propertyfile] Updating property file: /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/build/built-jar.properties - --check-automatic-build: - --clean-after-automatic-build: - --verify-automatic-build: - --pre-pre-compile: - --pre-compile: - --copy-persistence-xml: - --compile-depend: - --do-compile: - [javac] Compiling 1 source file to /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/build/classes - [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 - [javac] warning: [options] source value 8 is obsolete and will be removed in a future release - [javac] warning: [options] target value 8 is obsolete and will be removed in a future release - [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:165: error: > expected - [javac] * for(int v = 0; v/* */< h.length; v++) { - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:165: error: expected - [javac] * for(int v = 0; v/* */< h.length; v++) { - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:165: error: expected - [javac] * for(int v = 0; v/* */< h.length; v++) { - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:166: error: illegal start of expression - [javac] * // vs[v] is 'v' in 'g' - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:167: error: illegal start of expression - [javac] * } - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:167: error: illegal start of expression - [javac] * } - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:168: error: illegal start of type - [javac] * - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:168: error: expected - [javac] * - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:168: error: expected - [javac] * - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:168: error: expected - [javac] * - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:168: error: expected - [javac] * - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:170: error: ';' expected - [javac] * @param graph adjacency list graph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:170: error: ';' expected - [javac] * @param graph adjacency list graph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:171: error: ';' expected - [javac] * @param include the vertices of he graph to include in the subgraph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:171: error: ';' expected - [javac] * @param include the vertices of he graph to include in the subgraph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:171: error: ';' expected - [javac] * @param include the vertices of he graph to include in the subgraph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:171: error: ';' expected - [javac] * @param include the vertices of he graph to include in the subgraph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:171: error: ';' expected - [javac] * @param include the vertices of he graph to include in the subgraph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:171: error: expected - [javac] * @param include the vertices of he graph to include in the subgraph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:172: error: expected - [javac] * @return the subgraph - [javac] ^ - [javac] /Users/rvdploeg_hu/Software/PaDEL/PaDEL-Descriptor/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java:172: error: ';' expected - [javac] * @return the subgraph - [javac] ^ - [javac] 21 errors - [javac] 4 warnings diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/AtomPairs2DFingerprintCount.java b/libPaDEL-Descriptor/src/libpadeldescriptor/AtomPairs2DFingerprintCount.java index 2f64b49..9e4fd2f 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/AtomPairs2DFingerprintCount.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/AtomPairs2DFingerprintCount.java @@ -30,6 +30,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.matrix.TopologicalMatrix; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -121,6 +122,10 @@ public AtomPairs2DFingerprintCount() } } + @Override + public void initialise(IChemObjectBuilder builder) { + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/AtomPairs2DFingerprinter.java b/libPaDEL-Descriptor/src/libpadeldescriptor/AtomPairs2DFingerprinter.java index 74a561f..1458872 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/AtomPairs2DFingerprinter.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/AtomPairs2DFingerprinter.java @@ -28,7 +28,14 @@ import java.util.ArrayList; import java.util.BitSet; +import java.util.Map; + +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.fingerprint.BitSetFingerprint; +import org.openscience.cdk.fingerprint.IBitFingerprint; +import org.openscience.cdk.fingerprint.ICountFingerprint; import org.openscience.cdk.fingerprint.IFingerprinter; +import org.openscience.cdk.fingerprint.IntArrayCountFingerprint; import org.openscience.cdk.graph.matrix.TopologicalMatrix; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; @@ -166,5 +173,29 @@ public BitSet getFingerprint(IAtomContainer container) return fp; } + + @Override + public String getVersionDescription() { + // Method not needed in this PaDEL version, so return an empty string or null + return ""; // or you can return null, depending on the use case + } + + @Override + public IBitFingerprint getBitFingerprint(IAtomContainer container) throws CDKException { + // Since the method isn't needed, just return null + return null; + } + + @Override + public ICountFingerprint getCountFingerprint(IAtomContainer container) throws CDKException { + // Method not needed in this PaDEL version, so return an empty string or null + return null; + } + + @Override + public Map getRawFingerprint(IAtomContainer container) throws CDKException { + // Method not needed in this PaDEL version, so return an empty string or null + return null; + } } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/AtomTypeAwareSaturationChecker.java b/libPaDEL-Descriptor/src/libpadeldescriptor/AtomTypeAwareSaturationChecker.java index 0aa24d1..1db7fa6 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/AtomTypeAwareSaturationChecker.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/AtomTypeAwareSaturationChecker.java @@ -26,7 +26,6 @@ package libpadeldescriptor; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; @@ -57,7 +56,6 @@ * @cdk.keyword bond order * @cdk.module valencycheck */ -@TestClass( "org.openscience.cdk.tools.ATASaturationCheckerTest" ) public class AtomTypeAwareSaturationChecker implements IValencyChecker, IDeduceBondOrderTool { diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/Autocorrelation3DDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/Autocorrelation3DDescriptor.java index bc05091..d8233c2 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/Autocorrelation3DDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/Autocorrelation3DDescriptor.java @@ -31,6 +31,7 @@ import org.openscience.cdk.graph.matrix.TopologicalMatrix; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -57,6 +58,8 @@ public class Autocorrelation3DDescriptor implements IMolecularDescriptor { public String[] names; private static final String[] wtypes = {"u", "m", "v", "e", "p", "i", "s", "r"}; + private IChemObjectBuilder builder; + public Autocorrelation3DDescriptor() { names = new String[wtypes.length*maxLag]; @@ -71,6 +74,11 @@ public Autocorrelation3DDescriptor() } } + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/AutocorrelationDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/AutocorrelationDescriptor.java index 0976a7e..41e5a39 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/AutocorrelationDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/AutocorrelationDescriptor.java @@ -26,12 +26,12 @@ package libpadeldescriptor; -import org.openscience.cdk.Molecule; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.matrix.TopologicalMatrix; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -106,6 +106,13 @@ public AutocorrelationDescriptor() } } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( @@ -154,7 +161,7 @@ public DescriptorValue calculate(IAtomContainer container) double[] s = new double[natom]; try { - Molecule mol = new Molecule((IAtomContainer)container.clone()); + IAtomContainer mol = (IAtomContainer) container.clone(); GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges(); peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true); IntrinsicStateDescriptor isd = new IntrinsicStateDescriptor(); diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/BaryszMatrixDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/BaryszMatrixDescriptor.java index d2124ea..71aefd5 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/BaryszMatrixDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/BaryszMatrixDescriptor.java @@ -34,6 +34,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IBond.Order; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -84,6 +85,13 @@ public DescriptorSpecification getSpecification() { "PaDEL"); } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public String[] getParameterNames() { return null; //To change body of implemented methods use File | Settings | File Templates. diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/BurdenModifiedEigenvaluesDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/BurdenModifiedEigenvaluesDescriptor.java index d1e2f88..3833896 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/BurdenModifiedEigenvaluesDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/BurdenModifiedEigenvaluesDescriptor.java @@ -34,6 +34,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IBond.Order; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -79,6 +80,13 @@ public BurdenModifiedEigenvaluesDescriptor() } } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_AcidicGroupCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_AcidicGroupCountDescriptor.java index ccb5862..e6f06dd 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_AcidicGroupCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_AcidicGroupCountDescriptor.java @@ -20,9 +20,8 @@ public CDK_AcidicGroupCountDescriptor() cdkDescriptor_ = new AcidicGroupCountDescriptor(); initDescriptorsValues(); } - catch (CDKException ex) + finally { - Logger.getLogger(CDK_AcidicGroupCountDescriptor.class.getName()).log(Level.SEVERE, null, ex); } } } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_BasicGroupCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_BasicGroupCountDescriptor.java index 73cb2b1..6dac731 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_BasicGroupCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_BasicGroupCountDescriptor.java @@ -20,9 +20,8 @@ public CDK_BasicGroupCountDescriptor() cdkDescriptor_ = new BasicGroupCountDescriptor(); initDescriptorsValues(); } - catch (CDKException ex) + finally { - Logger.getLogger(CDK_BasicGroupCountDescriptor.class.getName()).log(Level.SEVERE, null, ex); } } } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_Descriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_Descriptor.java index 59a06c6..8b31248 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_Descriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_Descriptor.java @@ -98,7 +98,7 @@ public String[] getDescriptorValues() * * @param molecule Molecule for calculating descriptors. */ - public void setMolecule(IAtomContainer molecule) + public void setAtomContainer(IAtomContainer molecule) { this.molecule_ = molecule; initDescriptorsValues(); diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_Fingerprint.java b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_Fingerprint.java index 4defe21..0c5a8e8 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_Fingerprint.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_Fingerprint.java @@ -104,7 +104,7 @@ public String[] getDescriptorNames() * * @param molecule Molecule for calculating descriptors. */ - public void setMolecule(IAtomContainer molecule) + public void setAtomContainer(IAtomContainer molecule) { this.molecule_ = molecule; initDescriptorsValues(); diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_PubchemFingerprinter.java b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_PubchemFingerprinter.java index 9b2ddab..e721d9a 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_PubchemFingerprinter.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/CDK_PubchemFingerprinter.java @@ -1,6 +1,8 @@ package libpadeldescriptor; import org.openscience.cdk.fingerprint.PubchemFingerprinter; +import org.openscience.cdk.interfaces.IChemObjectBuilder; +import org.openscience.cdk.DefaultChemObjectBuilder; /** * Make PubchemFingerprinter in CDK runnable in a separate thread. @@ -12,7 +14,9 @@ public class CDK_PubchemFingerprinter extends CDK_Fingerprint public CDK_PubchemFingerprinter() { super(); - cdkFingerprinter_ = new PubchemFingerprinter(); + IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance(); + boolean someBooleanValue = true; + cdkFingerprinter_ = new PubchemFingerprinter(builder, someBooleanValue); initDescriptorsValues(); this.setPrefix("PubchemFP"); } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/ConstitutionalDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/ConstitutionalDescriptor.java index f9b072c..b1e2020 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/ConstitutionalDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/ConstitutionalDescriptor.java @@ -28,6 +28,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -69,6 +70,13 @@ public ConstitutionalDescriptor() } } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/DetourMatrixDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/DetourMatrixDescriptor.java index aa12b91..d5964cb 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/DetourMatrixDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/DetourMatrixDescriptor.java @@ -33,6 +33,7 @@ import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -71,6 +72,13 @@ public DetourMatrixDescriptor() } } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/EStateAtomTypeDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/EStateAtomTypeDescriptor.java index 2343d2b..71b87c2 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/EStateAtomTypeDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/EStateAtomTypeDescriptor.java @@ -34,6 +34,7 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -484,6 +485,13 @@ public EStateAtomTypeDescriptor() { } } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/ElectrotopologicalStateDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/ElectrotopologicalStateDescriptor.java index fe12757..8b620fa 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/ElectrotopologicalStateDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/ElectrotopologicalStateDescriptor.java @@ -27,12 +27,11 @@ import java.util.Iterator; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -88,7 +87,6 @@ *@cdk.set qsar-descriptors * @cdk.dictref qsar-descriptors:electrotopologicalState */ -@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.electrotopologicalStateDescriptorTest") public class ElectrotopologicalStateDescriptor implements IAtomicDescriptor { private static final String[] names = {"ElectrotopologicalState"}; @@ -100,14 +98,19 @@ public class ElectrotopologicalStateDescriptor implements IAtomicDescriptor { public ElectrotopologicalStateDescriptor() { } + private IChemObjectBuilder builder; - /** + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + + /** * Gets the specification attribute of the ElectrotopologicalStateDescriptor * object * *@return The specification value */ - @TestMethod(value="testGetSpecification") @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( @@ -121,7 +124,6 @@ public DescriptorSpecification getSpecification() { /** * This descriptor does have any parameter. */ - @TestMethod(value="testSetParameters_arrayObject") @Override public void setParameters(Object[] params) throws CDKException { } @@ -134,7 +136,6 @@ public void setParameters(Object[] params) throws CDKException { * @return The parameters value * @see #setParameters */ - @TestMethod(value="testGetParameters") @Override public Object[] getParameters() { return null; @@ -145,7 +146,6 @@ public Object[] getParameters() { * * @return Names of descriptors */ - @TestMethod(value="testNamesConsistency") @Override public String[] getDescriptorNames() { return names; @@ -172,7 +172,6 @@ private DescriptorValue getDummyDescriptorValue(Exception e) { *@param ac AtomContainer *@return a double with electrotopological state of the heavy atom */ - @TestMethod(value="testCalculate_IAtomContainer") @Override public DescriptorValue calculate(IAtom atom, IAtomContainer ac) { try @@ -256,7 +255,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer ac, int[] pathLength * * @return The parameterNames value */ - @TestMethod(value="testGetParameterNames") @Override public String[] getParameterNames() { return new String[0]; @@ -269,7 +267,6 @@ public String[] getParameterNames() { * @param name Description of the Parameter * @return An Object of class equal to that of the parameter being requested */ - @TestMethod(value="testGetParameterType_String") @Override public Object getParameterType(String name) { return null; diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/ExtendedTopochemicalAtomDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/ExtendedTopochemicalAtomDescriptor.java index 168d7a0..9b57c95 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/ExtendedTopochemicalAtomDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/ExtendedTopochemicalAtomDescriptor.java @@ -22,7 +22,6 @@ import java.util.List; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.matrix.TopologicalMatrix; import org.openscience.cdk.interfaces.IAtom; @@ -30,6 +29,7 @@ import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IBond.Order; import org.openscience.cdk.interfaces.IRingSet; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.AtomValenceTool; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -100,13 +100,18 @@ public class ExtendedTopochemicalAtomDescriptor implements IMolecularDescriptor */ public ExtendedTopochemicalAtomDescriptor() {} + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } /** * Gets the specification attribute of the ExtendedTopochemicalAtomDescriptor object * *@return The specification value */ - @TestMethod("testGetSpecification") @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( @@ -173,7 +178,6 @@ private DescriptorValue getDummyDescriptorValue(Exception e) { *@param container AtomContainer *@return Extended Topochemical Atom (ETA) descriptors. */ - @TestMethod("testCalculate_IAtomContainer") @Override public DescriptorValue calculate(IAtomContainer container) { diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java b/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java index 8dd3d5f..e7b13ea 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/GraphUtil.java @@ -25,8 +25,6 @@ package libpadeldescriptor; import com.google.common.collect.Maps; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; @@ -45,7 +43,6 @@ * @see ShortestPaths * {@code org.openscience.cdk.ringsearch.RingSearch} */ -@TestClass("org.openscience.cdk.graph.GraphUtilTest") public class GraphUtil { private static final int DEFAULT_DEGREE = 4; @@ -62,8 +59,6 @@ private GraphUtil() { * @throws IllegalArgumentException a bond was found which contained atoms * not in the molecule */ - @TestMethod("testToAdjList,testToAdjList_resize,testToAdjList_missingAtom," + - "testToAdjList_Empty,testToAdjList_Null") public static int[][] toAdjList(IAtomContainer container) { if (container == null) @@ -112,7 +107,6 @@ public static int[][] toAdjList(IAtomContainer container) { * @throws IllegalArgumentException a bond was found which contained atoms * not in the molecule */ - @TestMethod("testToAdjList_withMap") public static int[][] toAdjList(IAtomContainer container, EdgeToBondMap bondMap) { if (container == null) @@ -172,7 +166,6 @@ public static int[][] toAdjList(IAtomContainer container, EdgeToBondMap bondMap) * @param include the vertices of he graph to include in the subgraph * @return the subgraph */ - @TestMethod("sequentialSubgraph,intermittentSubgraph,resizeSubgraph") public static int[][] subgraph(int[][] graph, int[] include) { // number of vertices in the graph and the subgraph @@ -225,9 +218,8 @@ public static int[][] subgraph(int[][] graph, int[] include) { * same) * @throws IllegalArgumentException thrown if the vertices do not form a * cycle -* {@code org.openscience.cdk.ringsearch.RingSearch#isolated()} +* {@see org.openscience.cdk.ringsearch.RingSearch#isolated()} */ - @TestMethod("testCycle,testAcyclic,testAcyclic2") public static int[] cycle(int[][] graph, int[] vertices) { int n = graph.length; @@ -269,7 +261,6 @@ public static int[] cycle(int[][] graph, int[] vertices) { * @param marked marked values * @return first marked value, -1 if none found */ - @TestMethod("firstMarked") static int firstMarked(int[] xs, boolean[] marked) { for (int x : xs) if (marked[x]) return x; diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/HalogenCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/HalogenCountDescriptor.java index 5080126..559dc94 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/HalogenCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/HalogenCountDescriptor.java @@ -28,6 +28,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -65,6 +66,13 @@ public HalogenCountDescriptor() { } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/HeavyAtomCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/HeavyAtomCountDescriptor.java index 0217a7c..0e14fbd 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/HeavyAtomCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/HeavyAtomCountDescriptor.java @@ -25,9 +25,9 @@ package libpadeldescriptor; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -60,6 +60,13 @@ public HeavyAtomCountDescriptor() { elementName = "*"; } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + /** * Returns a Map which specifies which descriptor * is implemented by this class. @@ -75,7 +82,6 @@ public HeavyAtomCountDescriptor() { * * @return An object containing the descriptor specification */ - @TestMethod("testGetSpecification") @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( @@ -93,7 +99,6 @@ public DescriptorSpecification getSpecification() { *or else the parameter is not of type String *@see #getParameters */ - @TestMethod("testSetParameters_arrayObject") @Override public void setParameters(Object[] params) throws CDKException { if (params.length > 1) { @@ -112,7 +117,6 @@ public void setParameters(Object[] params) throws CDKException { *@return The parameters value *@see #setParameters */ - @TestMethod("testGetParameters") @Override public Object[] getParameters() { // return the parameters as used for the descriptor calculation @@ -121,7 +125,6 @@ public Object[] getParameters() { return params; } - @TestMethod(value="testNamesConsistency") @Override public String[] getDescriptorNames() { return names; @@ -137,7 +140,6 @@ public String[] getDescriptorNames() { // it could be interesting to accept as elementName a SMARTS atom, to get the frequency of this atom // this could be useful for other descriptors like polar surface area... - @TestMethod("testCalculate_IAtomContainer") @Override public DescriptorValue calculate(IAtomContainer container) { elementName = "*"; @@ -224,7 +226,6 @@ private int CountAtoms(IAtomContainer container) * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ - @TestMethod("testGetDescriptorResultType") @Override public IDescriptorResult getDescriptorResultType() { return new IntegerResult(1); @@ -236,7 +237,6 @@ public IDescriptorResult getDescriptorResultType() { * *@return The parameterNames value */ - @TestMethod("testGetParameterNames") @Override public String[] getParameterNames() { String[] params = new String[1]; @@ -251,7 +251,6 @@ public String[] getParameterNames() { *@param name Description of the Parameter *@return An Object whose class is that of the parameter requested */ - @TestMethod("testGetParameterType_String") @Override public Object getParameterType(String name) { return ""; diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/HydrogenEStateDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/HydrogenEStateDescriptor.java index eb0338c..c151c7d 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/HydrogenEStateDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/HydrogenEStateDescriptor.java @@ -27,12 +27,11 @@ import java.io.IOException; import java.util.Iterator; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -89,7 +88,6 @@ *@cdk.set qsar-descriptors *@cdk.dictref qsar-descriptors:hydrogenEStateDescriptor */ -@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.hydrogenEStateDescriptorTest") public class HydrogenEStateDescriptor implements IAtomicDescriptor { private static final String[] names = {"HydrogenEState"}; @@ -101,6 +99,12 @@ public class HydrogenEStateDescriptor implements IAtomicDescriptor { public HydrogenEStateDescriptor() { } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } /** * Gets the specification attribute of the HydrogenEStateDescriptor @@ -108,7 +112,6 @@ public HydrogenEStateDescriptor() { * *@return The specification value */ - @TestMethod(value="testGetSpecification") @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( @@ -122,7 +125,6 @@ public DescriptorSpecification getSpecification() { /** * This descriptor does have any parameter. */ - @TestMethod(value="testSetParameters_arrayObject") @Override public void setParameters(Object[] params) throws CDKException { } @@ -135,7 +137,6 @@ public void setParameters(Object[] params) throws CDKException { * @return The parameters value * @see #setParameters */ - @TestMethod(value="testGetParameters") @Override public Object[] getParameters() { return null; @@ -146,7 +147,6 @@ public Object[] getParameters() { * * @return Names of descriptors */ - @TestMethod(value="testNamesConsistency") @Override public String[] getDescriptorNames() { return names; @@ -173,7 +173,6 @@ private DescriptorValue getDummyDescriptorValue(Exception e) { *@param ac AtomContainer *@return a double with hydrogen eletrotopological state of the heavy atom */ - @TestMethod(value="testCalculate_IAtomContainer") @Override public DescriptorValue calculate(IAtom atom, IAtomContainer ac) { try @@ -268,7 +267,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer ac, int[] pathLength * * @return The parameterNames value */ - @TestMethod(value="testGetParameterNames") @Override public String[] getParameterNames() { return new String[0]; @@ -281,7 +279,6 @@ public String[] getParameterNames() { * @param name Description of the Parameter * @return An Object of class equal to that of the parameter being requested */ - @TestMethod(value="testGetParameterType_String") @Override public Object getParameterType(String name) { return null; diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/InformationContentDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/InformationContentDescriptor.java index 616064b..6db7d87 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/InformationContentDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/InformationContentDescriptor.java @@ -35,12 +35,14 @@ import java.util.logging.Logger; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.config.Isotopes; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IBond.Order; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -117,6 +119,13 @@ public class InformationContentDescriptor implements IMolecularDescriptor { public InformationContentDescriptor() { } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( @@ -370,6 +379,16 @@ private double evalModInfoContent(HashMap,Integer> classes { int maxAtoms = atomContainer.getAtomCount(); double sum = 0; + + Isotopes isofac; + + try { + isofac = Isotopes.getInstance(); // Move the getInstance() inside try-catch + } catch (IOException ex) { + Logger.getLogger(InformationContentDescriptor.class.getName()).log(Level.SEVERE, "Error getting Isotopes instance", ex); + return 0; // Return 0 or handle this error as needed if instance creation fails + } + for (ArrayList coordinates : classes.keySet()) { Integer n = classes.get(coordinates); @@ -377,8 +396,10 @@ private double evalModInfoContent(HashMap,Integer> classes double m = 0.0; try { - m = IsotopeFactory.getInstance(atomContainer.getBuilder()).getMajorIsotope(coordinates.get(0).a).getExactMass(); - } + m = Isotopes.getInstance() + .getMajorIsotope(coordinates.get(0).a) + .getExactMass(); + } catch (IOException ex) { Logger.getLogger(InformationContentDescriptor.class.getName()).log(Level.SEVERE, null, ex); diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/IntrinsicStateDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/IntrinsicStateDescriptor.java index df687a7..9cf1c68 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/IntrinsicStateDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/IntrinsicStateDescriptor.java @@ -26,11 +26,10 @@ -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.AtomValenceTool; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -88,7 +87,6 @@ *@cdk.set qsar-descriptors * @cdk.dictref qsar-descriptors:intrinsicState */ -@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.IntrinsicStateDescriptorTest") public class IntrinsicStateDescriptor implements IAtomicDescriptor { private static final String[] names = {"IntrinsicState", "IntrinsicState2"}; @@ -100,14 +98,19 @@ public class IntrinsicStateDescriptor implements IAtomicDescriptor { public IntrinsicStateDescriptor() { } + private IChemObjectBuilder builder; - /** + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + + /** * Gets the specification attribute of the IntrinsicStateDescriptor * object * *@return The specification value */ - @TestMethod(value="testGetSpecification") @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( @@ -121,7 +124,6 @@ public DescriptorSpecification getSpecification() { /** * This descriptor does have any parameter. */ - @TestMethod(value="testSetParameters_arrayObject") @Override public void setParameters(Object[] params) throws CDKException { } @@ -134,7 +136,6 @@ public void setParameters(Object[] params) throws CDKException { * @return The parameters value * @see #setParameters */ - @TestMethod(value="testGetParameters") @Override public Object[] getParameters() { return null; @@ -145,7 +146,6 @@ public Object[] getParameters() { * * @return Names of descriptors */ - @TestMethod(value="testNamesConsistency") @Override public String[] getDescriptorNames() { return names; @@ -172,7 +172,6 @@ private DescriptorValue getDummyDescriptorValue(Exception e) { *@param ac AtomContainer *@return a double with intrinsic state of the heavy atom */ - @TestMethod(value="testCalculate_IAtomContainer") @Override public DescriptorValue calculate(IAtom atom, IAtomContainer ac) { try @@ -209,7 +208,6 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer ac) { * * @return The parameterNames value */ - @TestMethod(value="testGetParameterNames") @Override public String[] getParameterNames() { return new String[0]; @@ -222,7 +220,6 @@ public String[] getParameterNames() { * @param name Description of the Parameter * @return An Object of class equal to that of the parameter being requested */ - @TestMethod(value="testGetParameterType_String") @Override public Object getParameterType(String name) { return null; diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/IteratingPaDELReader.java b/libPaDEL-Descriptor/src/libpadeldescriptor/IteratingPaDELReader.java index 7816918..9da1872 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/IteratingPaDELReader.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/IteratingPaDELReader.java @@ -43,11 +43,11 @@ import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.ISimpleChemObjectReader; import org.openscience.cdk.io.ReaderFactory; import org.openscience.cdk.io.formats.HINFormat; @@ -61,7 +61,8 @@ import org.openscience.cdk.io.formats.PubChemSubstancesXMLFormat; import org.openscience.cdk.io.formats.SMILESFormat; import org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader; -import org.openscience.cdk.io.iterator.IteratingMDLReader; +import org.openscience.cdk.io.iterator.IteratingSDFReader; +import org.openscience.cdk.io.MDLReader; import org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader; import org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader; import org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader; @@ -88,7 +89,7 @@ public class IteratingPaDELReader extends DefaultIteratingChemObjectReader { private File molecule; private PaDELIteratingSMILESReader iteratingSMILESReader; - private IteratingMDLReader iteratingMDLReader; + private IteratingSDFReader iteratingSDFReader; private IteratingPCCompoundASNReader iteratingPCCompoundASNReader; private IteratingPCCompoundXMLReader iteratingPCCompoundXMLReader; private IteratingPCSubstancesXMLReader iteratingPCSubstancesXMLReader; @@ -101,7 +102,7 @@ public class IteratingPaDELReader extends DefaultIteratingChemObjectReader { * * @param molecule * @see org.openscience.cdk.DefaultChemObjectBuilder - * @see org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder + * {@see org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder} */ public IteratingPaDELReader(File molecule) throws FileNotFoundException { this.builder = DefaultChemObjectBuilder.getInstance(); @@ -115,7 +116,7 @@ public IteratingPaDELReader(File molecule) throws FileNotFoundException { * @param in The Reader to read from * @param builder The builder to use * @see org.openscience.cdk.DefaultChemObjectBuilder - * @see org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder + * {@see org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder} */ public IteratingPaDELReader(Reader in, IChemObjectBuilder builder) { this.builder = builder; @@ -179,9 +180,9 @@ public boolean hasNext() { } else if (currentFormat instanceof MDLFormat || currentFormat instanceof MDLV2000Format || currentFormat instanceof MDLV3000Format) { - if (iteratingMDLReader.hasNext()) + if (iteratingSDFReader.hasNext()) { - nextMolecule = (IAtomContainer)iteratingMDLReader.next(); + nextMolecule = (IAtomContainer)iteratingSDFReader.next(); ++curLigIndex; hasNext = true; } @@ -273,7 +274,7 @@ public IChemObject next() { public void close() throws IOException { input.close(); if (iteratingSMILESReader!=null) iteratingSMILESReader.close(); - if (iteratingMDLReader!=null) iteratingMDLReader.close(); + if (iteratingSDFReader!=null) iteratingSDFReader.close(); if (iteratingPCCompoundASNReader!=null) iteratingPCCompoundASNReader.close(); if (iteratingPCCompoundXMLReader!=null) iteratingPCCompoundXMLReader.close(); if (iteratingPCSubstancesXMLReader!=null) iteratingPCSubstancesXMLReader.close(); @@ -320,7 +321,7 @@ else if (molecule.getName().endsWith(".hin")) } else if (currentFormat instanceof MDLFormat || currentFormat instanceof MDLV2000Format || currentFormat instanceof MDLV3000Format) { - iteratingMDLReader = new IteratingMDLReader(input, builder); + iteratingSDFReader = new IteratingSDFReader(input, builder); } else if (currentFormat instanceof PubChemSubstancesASNFormat) { @@ -348,10 +349,10 @@ else if (currentFormat instanceof PDBFormat) IChemSequence cs = cf.getChemSequence(i); for (int j=0, endj=cs.getChemModelCount(); j> getFragments(IAtomContainer atomContainer, QueryAtomContainer[] queries) { List> uniqueSubgraphs = new ArrayList>(); + + UniversalIsomorphismTester tester = new UniversalIsomorphismTester(); + for (QueryAtomContainer query : queries) { List subgraphMaps = null; try { // we get the list of bond mappings - subgraphMaps = UniversalIsomorphismTester.getSubgraphMaps(atomContainer, query); + subgraphMaps = tester.getSubgraphMaps(atomContainer, query); } catch (CDKException e) { e.printStackTrace(); } @@ -133,8 +134,8 @@ public static double evalSimpleIndex(IAtomContainer atomContainer, List> order7(IAtomContainer atomContainer) { return PaDELChiIndexUtils.getFragments(atomContainer, queries); } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELFragmentComplexityDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELFragmentComplexityDescriptor.java index 408debc..a8dcacf 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELFragmentComplexityDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELFragmentComplexityDescriptor.java @@ -21,9 +21,9 @@ package libpadeldescriptor; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -72,7 +72,6 @@ public PaDELFragmentComplexityDescriptor() { } * * @return An object containing the descriptor specification */ - @TestMethod("testGetSpecification") public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#NilaComplexity", @@ -91,7 +90,6 @@ public DescriptorSpecification getSpecification() { * @exception CDKException if more than one parameter or a non-Boolean parameter is specified * @see #getParameters */ - @TestMethod("testSetParameters_arrayObject") public void setParameters(Object[] params) throws CDKException { if (params.length > 0) { throw new CDKException("FragmentComplexityDescriptor expects no parameter"); @@ -105,13 +103,11 @@ public void setParameters(Object[] params) throws CDKException { * @return The parameters value * @see #setParameters */ - @TestMethod("testGetParameters") public Object[] getParameters() { return null; // return the parameters as used for the descriptor calculation } - @TestMethod(value="testNamesConsistency") public String[] getDescriptorNames() { return names; } @@ -123,7 +119,6 @@ public String[] getDescriptorNames() { *@return the complexity *@see #setParameters */ - @TestMethod("testCalculate_IAtomContainer") public DescriptorValue calculate(IAtomContainer container) { //System.out.println("FragmentComplexityDescriptor"); IAtomContainer molecule = AtomContainerManipulator.removeHydrogens(container); @@ -153,7 +148,6 @@ public DescriptorValue calculate(IAtomContainer container) { * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ - @TestMethod("testGetDescriptorResultType") public IDescriptorResult getDescriptorResultType() { return new DoubleResult(0.0); } @@ -164,7 +158,6 @@ public IDescriptorResult getDescriptorResultType() { * *@return The parameterNames value */ - @TestMethod("testGetParameterNames") public String[] getParameterNames() { return null; } @@ -177,10 +170,17 @@ public String[] getParameterNames() { *@param name Description of the Parameter *@return An Object of class equal to that of the parameter being requested */ - @TestMethod("testGetParameterType_String") public Object getParameterType(String name) { return null; } + + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHBondAcceptorCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHBondAcceptorCountDescriptor.java index 6ffbb7a..ac65ee2 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHBondAcceptorCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHBondAcceptorCountDescriptor.java @@ -26,12 +26,12 @@ package libpadeldescriptor; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond.Order; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -136,7 +136,6 @@ public PaDELHBondAcceptorCountDescriptor() { } * * @return The specification value */ - @TestMethod("testGetSpecification") public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "PaDELHBondAcceptorCountDescriptor", @@ -151,7 +150,6 @@ public DescriptorSpecification getSpecification() { * @param params a boolean true means that aromaticity has to be checked * @exception CDKException Description of the Exception */ - @TestMethod("testSetParameters_arrayObject") public void setParameters(Object[] params) throws CDKException { if (params.length != 1) { throw new CDKException("PaDELHBondAcceptorCountDescriptor expects a single parameter"); @@ -168,7 +166,6 @@ public void setParameters(Object[] params) throws CDKException { * * @return The parameters value */ - @TestMethod("testGetParameters") public Object[] getParameters() { // return the parameters as used for the descriptor calculation Object[] params = new Object[1]; @@ -176,7 +173,6 @@ public Object[] getParameters() { return params; } - @TestMethod(value="testNamesConsistency") public String[] getDescriptorNames() { return names; } @@ -193,7 +189,6 @@ private DescriptorValue getDummyDescriptorValue(Exception e) { * @param atomContainer AtomContainer * @return number of H bond acceptors */ - @TestMethod("testCalculate_IAtomContainer") public DescriptorValue calculate(IAtomContainer atomContainer) { int nHBAcc_CDK = 0; int nHBAcc_2 = 0; @@ -405,7 +400,6 @@ public DescriptorValue calculate(IAtomContainer atomContainer) { * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ - @TestMethod("testGetDescriptorResultType") public IDescriptorResult getDescriptorResultType() { return new IntegerArrayResult(names.length); } @@ -415,7 +409,6 @@ public IDescriptorResult getDescriptorResultType() { * * @return The parameterNames value */ - @TestMethod("testGetParameterNames") public String[] getParameterNames() { String[] params = new String[1]; params[0] = "checkAromaticity"; @@ -428,9 +421,16 @@ public String[] getParameterNames() { * @param name Description of the Parameter * @return The parameterType value */ - @TestMethod("testGetParameterType_String") public Object getParameterType(String name) { return false; } + + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHBondDonorCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHBondDonorCountDescriptor.java index 79783c8..d48b9bb 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHBondDonorCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHBondDonorCountDescriptor.java @@ -25,10 +25,10 @@ package libpadeldescriptor; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -91,7 +91,6 @@ public PaDELHBondDonorCountDescriptor() { } * * @return The specification value */ - @TestMethod("testGetSpecification") public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "PaDELHBondDonorCountDescriptor", @@ -107,7 +106,6 @@ public DescriptorSpecification getSpecification() { * @param params this descriptor does not have any parameters * @exception CDKException Description of the Exception */ - @TestMethod("testSetParameters_arrayObject") public void setParameters(Object[] params) throws CDKException { // this descriptor has no parameters; nothing has to be done here } @@ -118,13 +116,11 @@ public void setParameters(Object[] params) throws CDKException { * * @return null as this descriptor does not have any parameters */ - @TestMethod("testGetParameters") public Object[] getParameters() { // no parameters; thus we return null return null; } - @TestMethod(value="testNamesConsistency") public String[] getDescriptorNames() { return names; } @@ -141,7 +137,6 @@ private DescriptorValue getDummyDescriptorValue(Exception e) { * @param atomContainer AtomContainer * @return number of H bond donors */ - @TestMethod("testCalculate_IAtomContainer") public DescriptorValue calculate(IAtomContainer atomContainer) { int nHBDon_CDK = 0; int nHBDon_Lipinski = 0; @@ -217,7 +212,6 @@ public DescriptorValue calculate(IAtomContainer atomContainer) { * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ - @TestMethod("testGetDescriptorResultType") public IDescriptorResult getDescriptorResultType() { return new IntegerArrayResult(names.length); } @@ -228,7 +222,6 @@ public IDescriptorResult getDescriptorResultType() { * * @return null as this descriptor does not have any parameters */ - @TestMethod("testGetParameterNames") public String[] getParameterNames() { // no parameters; thus we return null return null; @@ -242,10 +235,17 @@ public String[] getParameterNames() { * @param name Description of the Parameter * @return null as this descriptor does not have any parameters */ - @TestMethod("testGetParameterType_String") public Object getParameterType(String name) { // no parameters; thus we return null return null; } + + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHINReader.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHINReader.java index b0ac085..f5f5b84 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHINReader.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELHINReader.java @@ -21,17 +21,16 @@ package libpadeldescriptor; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.interfaces.IMoleculeSet; +import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.io.formats.HINFormat; import org.openscience.cdk.io.formats.IResourceFormat; @@ -79,17 +78,14 @@ public PaDELHINReader() { this(new StringReader("")); } - @TestMethod("testGetFormat") public IResourceFormat getFormat() { return HINFormat.getInstance(); } - @TestMethod("testClose") public void close() throws IOException { input.close(); } - @TestMethod("testSetReader_Reader") public void setReader(Reader input) throws CDKException { if (input instanceof BufferedReader) { this.input = (BufferedReader)input; @@ -98,12 +94,10 @@ public void setReader(Reader input) throws CDKException { } } - @TestMethod("testSetReader_InputStream") public void setReader(InputStream input) throws CDKException { setReader(new InputStreamReader(input)); } - @TestMethod("testAccepts") public boolean accepts(Class classObject) { Class[] interfaces = classObject.getInterfaces(); for (Class anInterface : interfaces) { @@ -155,12 +149,12 @@ private String getMolName( String line) { private IChemFile readChemFile(IChemFile file) { IChemSequence chemSequence = file.getBuilder().newInstance(IChemSequence.class); IChemModel chemModel = file.getBuilder().newInstance(IChemModel.class); - IMoleculeSet setOfMolecules = file.getBuilder().newInstance(IMoleculeSet.class); + IAtomContainerSet setOfMolecules = file.getBuilder().newInstance(IAtomContainerSet.class); String info; StringTokenizer tokenizer; List aroringText = new ArrayList(); - List mols = new ArrayList(); + List mols = new ArrayList(); try { String line; @@ -185,7 +179,7 @@ private IChemFile readChemFile(IChemFile file) { info = getMolName(line); line = input.readLine(); } - IMolecule m = file.getBuilder().newInstance(IMolecule.class); + IAtomContainer m = file.getBuilder().newInstance(IAtomContainer.class); m.setProperty(CDKConstants.TITLE ,info); // Each element of cons is an ArrayList of length 3 which stores @@ -302,7 +296,7 @@ private IChemFile readChemFile(IChemFile file) { } } - for (IMolecule mol : mols) setOfMolecules.addMolecule(mol); + for (IAtomContainer mol : mols) setOfMolecules.addAtomContainer(mol); chemModel.setMoleculeSet(setOfMolecules); chemSequence.addChemModel(chemModel); file.addChemSequence(chemSequence); diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELIteratingSMILESReader.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELIteratingSMILESReader.java index 51fb827..1a9ede3 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELIteratingSMILESReader.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELIteratingSMILESReader.java @@ -36,10 +36,8 @@ import org.openscience.cdk.CDKConstants; import org.openscience.cdk.DefaultChemObjectBuilder; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; +import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IChemObject; -import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.SMILESFormat; @@ -66,7 +64,6 @@ * * @cdk.keyword file format, SMILES */ -@TestClass("org.openscience.cdk.io.iterator.IteratingSMILESReaderTest") public class PaDELIteratingSMILESReader extends DefaultIteratingChemObjectReader { private BufferedReader input; @@ -77,17 +74,15 @@ public class PaDELIteratingSMILESReader extends DefaultIteratingChemObjectReader private boolean nextAvailableIsKnown; private boolean hasNext; - private IMolecule nextMolecule; - + private IAtomContainer nextMolecule; /** * Constructs a new PaDELIteratingSMILESReader that can read Molecule from a given Reader. * * @param in The Reader to read from * @param builder The builder to use * @see org.openscience.cdk.DefaultChemObjectBuilder - * @see org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder + * {@see org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder} */ - @TestMethod("testSMILESFileWithNames") public PaDELIteratingSMILESReader(Reader in, IChemObjectBuilder builder) { sp = new SmilesParser(builder); sp.setPreservingAromaticity(true); // PaDEL: Change to true to make sure that aromaticity is not automatically detected in SMILES files. @@ -101,7 +96,6 @@ public PaDELIteratingSMILESReader(Reader in, IChemObjectBuilder builder) { * * @param in The InputStream to read from */ - @TestMethod("testSMILESFileWithNames") public PaDELIteratingSMILESReader(InputStream in) { this(new InputStreamReader(in), DefaultChemObjectBuilder.getInstance()); } @@ -121,7 +115,6 @@ public PaDELIteratingSMILESReader(InputStream in, IChemObjectBuilder builder) { * * @return An instance of {@link org.openscience.cdk.io.formats.SMILESFormat} */ - @TestMethod("testGetFormat") public IResourceFormat getFormat() { return SMILESFormat.getInstance(); } @@ -131,7 +124,6 @@ public IResourceFormat getFormat() { * * @return true if there are molecules to read, false otherwise */ - @TestMethod("testSMILESFileWithNames,testSMILESFileWithSpacesAndTabs,testSMILESTitles,testSMILESFile") public boolean hasNext() { if (!nextAvailableIsKnown) { hasNext = false; @@ -185,7 +177,6 @@ public boolean hasNext() { * * @return The next molecule */ - @TestMethod("testSMILESFileWithNames,testSMILESFileWithSpacesAndTabs,testSMILESTitles,testSMILESFile") public IChemObject next() { if (!nextAvailableIsKnown) { hasNext(); @@ -202,17 +193,14 @@ public IChemObject next() { * * @throws IOException if there is an error during closing */ - @TestMethod("testSMILESFileWithNames,testSMILESFileWithSpacesAndTabs,testClose") public void close() throws IOException { input.close(); } - @TestMethod("testRemove") public void remove() { throw new UnsupportedOperationException(); } - @TestMethod("testSetReader_Reader") public void setReader(Reader reader) { if (reader instanceof BufferedReader) { input = (BufferedReader)reader; @@ -224,7 +212,6 @@ public void setReader(Reader reader) { hasNext = false; } - @TestMethod("testSetReader1,testSetReader_InputStream") public void setReader(InputStream reader) { setReader(new InputStreamReader(reader)); } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELPDBReader.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELPDBReader.java index e7599a0..d17ccd2 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELPDBReader.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELPDBReader.java @@ -37,12 +37,12 @@ import javax.vecmath.Point3d; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.AtomTypeFactory; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.exception.NoSuchAtomTypeException; import org.openscience.cdk.graph.rebond.RebondTool; import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBioPolymer; import org.openscience.cdk.interfaces.IBond; @@ -50,10 +50,9 @@ import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IMonomer; import org.openscience.cdk.interfaces.IStrand; +import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.io.DefaultChemObjectReader; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.PDBFormat; @@ -211,13 +210,13 @@ private IChemFile readChemFile(IChemFile oFile) { // initialize all containers IChemSequence oSeq = oFile.getBuilder().newInstance(IChemSequence.class); IChemModel oModel = oFile.getBuilder().newInstance(IChemModel.class); - IMoleculeSet oSet = oFile.getBuilder().newInstance(IMoleculeSet.class); + IAtomContainerSet oSet = oFile.getBuilder().newInstance(IAtomContainerSet.class); // some variables needed String cCol; PDBAtom oAtom; PDBPolymer oBP = new PDBPolymer(); - IMolecule molecularStructure = oFile.getBuilder().newInstance(IMolecule.class); + IAtomContainer molecularStructure = oFile.getBuilder().newInstance(IAtomContainer.class); StringBuffer cResidue; String oObj; IMonomer oMonomer; @@ -300,7 +299,7 @@ private IChemFile readChemFile(IChemFile oFile) { // add the atom oBP.addAtom(oAtom, oMonomer, oStrand); - if (readConnect.isSet() && atomNumberMap.put(new Integer(oAtom.getSerial()), oAtom) != null) { + if (readConnect.isSet() && atomNumberMap.put(Integer.valueOf(oAtom.getSerial()), oAtom) != null) { logger.warn("Duplicate serial ID found for atom: ", oAtom); } molecularStructure.addAtom(oAtom); // PaDEL @@ -316,7 +315,7 @@ private IChemFile readChemFile(IChemFile oFile) { oAtom = readAtom(cRead, lineLength); oAtom.setHetAtom(true); oBP.addAtom(oAtom); - if (atomNumberMap.put(new Integer(oAtom.getSerial()), oAtom) != null) { + if (atomNumberMap.put(Integer.valueOf(oAtom.getSerial()), oAtom) != null) { logger.warn("Duplicate serial ID found for atom: ", oAtom); } logger.debug("Added HETATM: ", oAtom); @@ -339,7 +338,7 @@ private IChemFile readChemFile(IChemFile oFile) { logger.info("Bonds could not be created when PDB file was read."); logger.debug(exception); } - oSet.addMolecule(molecularStructure); // PaDEL + oSet.addAtomContainer(molecularStructure); // PaDEL } else if ("END ".equalsIgnoreCase(cCol)) { atomNumberMap.clear(); if (isProteinStructure) { @@ -356,7 +355,7 @@ private IChemFile readChemFile(IChemFile oFile) { logger.debug(exception); } } - oSet.addMolecule(oBP); + oSet.addAtomContainer(oBP); } @@ -371,7 +370,7 @@ private IChemFile readChemFile(IChemFile oFile) { logger.info("Bonds could not be created when PDB file was read."); logger.debug(exception); } - oSet.addMolecule(molecularStructure); // PaDEL + oSet.addAtomContainer(molecularStructure); // PaDEL } else if (cCol.equals("MODEL ")) { // OK, start a new model and save the current one first *if* it contains atoms if (isProteinStructure) { @@ -383,7 +382,7 @@ private IChemFile readChemFile(IChemFile oFile) { // setup a new one oBP = new PDBPolymer(); oModel = oFile.getBuilder().newInstance(IChemModel.class); - oSet = oFile.getBuilder().newInstance(IMoleculeSet.class); + oSet = oFile.getBuilder().newInstance(IAtomContainerSet.class); } } else { if (molecularStructure.getAtomCount() > 0) { @@ -392,9 +391,9 @@ private IChemFile readChemFile(IChemFile oFile) { oModel.setMoleculeSet(oSet); oSeq.addChemModel(oModel); // setup a new one - molecularStructure = oFile.getBuilder().newInstance(IMolecule.class); + molecularStructure = oFile.getBuilder().newInstance(IAtomContainer.class); oModel = oFile.getBuilder().newInstance(IChemModel.class); - oSet = oFile.getBuilder().newInstance(IMoleculeSet.class); + oSet = oFile.getBuilder().newInstance(IAtomContainerSet.class); } } } else if ("REMARK".equalsIgnoreCase(cCol)) { @@ -537,9 +536,9 @@ else if ("HELIX ".equalsIgnoreCase(cCol)) { } private void addBond(PDBPolymer obp, int bondAtomNo, int bondedAtomNo) { - IAtom firstAtom = (PDBAtom)atomNumberMap.get(new Integer(bondAtomNo)); - IAtom secondAtom = (PDBAtom)atomNumberMap.get(new Integer(bondedAtomNo)); - if (firstAtom == null) { + IAtom firstAtom = (PDBAtom)atomNumberMap.get(Integer.valueOf(bondAtomNo)); + IAtom secondAtom = (PDBAtom)atomNumberMap.get(Integer.valueOf(bondedAtomNo)); + if (firstAtom == null) { logger.error("Could not find bond start atom in map with serial id: ", bondAtomNo); } if (secondAtom == null) { @@ -592,7 +591,7 @@ private boolean createBondsWithRebondTool(IBioPolymer pol){ } // PaDEL - private boolean createBondsWithRebondTool(IMolecule mol){ + private boolean createBondsWithRebondTool(IAtomContainer mol){ RebondTool tool = new RebondTool(2.0, 0.5, 0.5); try { // configure atoms @@ -714,18 +713,15 @@ private PDBAtom readAtom(String cLine, int lineLength) { return oAtom; } - @TestMethod("testClose") public void close() throws IOException { _oInput.close(); } private void initIOSettings() { - useRebondTool = new BooleanIOSetting("UseRebondTool", IOSetting.LOW, - "Should the PDBReader deduce bonding patterns?", - "false"); - readConnect = new BooleanIOSetting("ReadConnectSection", IOSetting.LOW, - "Should the CONECT be read?", - "true"); + useRebondTool = new BooleanIOSetting("UseRebondTool", IOSetting.Importance.LOW, + "Should the PDBReader deduce bonding patterns?", "false"); + readConnect = new BooleanIOSetting("ReadConnectSection", IOSetting.Importance.LOW, + "Should the CONECT be read?", "true"); } public void customizeJob() { diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELPetitjeanShapeIndexDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELPetitjeanShapeIndexDescriptor.java index bfe765c..bdfe0d9 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELPetitjeanShapeIndexDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELPetitjeanShapeIndexDescriptor.java @@ -19,12 +19,11 @@ */ package libpadeldescriptor; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.geometry.GeometryTools; import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -73,14 +72,12 @@ * @cdk.dictref qsar-descriptors:petitjeanShapeIndex * @cdk.keyword Petit-Jean, shape index */ -@TestClass("org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptorTest") public class PaDELPetitjeanShapeIndexDescriptor implements IMolecularDescriptor { private static final String[] names = {"geomRadius", "geomDiameter", "geomShape"}; public PaDELPetitjeanShapeIndexDescriptor() { } - @TestMethod("testGetSpecification") public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#petitjeanShapeIndex", @@ -97,7 +94,6 @@ public DescriptorSpecification getSpecification() { * @throws org.openscience.cdk.exception.CDKException * Description of the Exception */ - @TestMethod("testSetParameters_arrayObject") public void setParameters(Object[] params) throws CDKException { // no parameters for this descriptor } @@ -107,13 +103,11 @@ public void setParameters(Object[] params) throws CDKException { * * @return The parameters value */ - @TestMethod("testGetParameters") public Object[] getParameters() { // no parameters to return return (null); } - @TestMethod(value="testNamesConsistency") public String[] getDescriptorNames() { return names; } @@ -123,7 +117,6 @@ public String[] getDescriptorNames() { * * @return The parameterNames value */ - @TestMethod("testGetParameterNames") public String[] getParameterNames() { // no param names to return return (null); @@ -136,7 +129,6 @@ public String[] getParameterNames() { * @param name Description of the Parameter * @return The parameterType value */ - @TestMethod("testGetParameterType_String") public Object getParameterType(String name) { return (null); } @@ -148,7 +140,6 @@ public Object getParameterType(String name) { * @return A DoubleArrayResult value representing the Petitjean shape indices */ - @TestMethod("testCalculate_IAtomContainer") public DescriptorValue calculate(IAtomContainer container) { DoubleArrayResult retval = new DoubleArrayResult(); @@ -208,10 +199,16 @@ public DescriptorValue calculate(IAtomContainer container) { * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ - @TestMethod("testGetDescriptorResultType") public IDescriptorResult getDescriptorResultType() { return new DoubleArrayResultType(names.length); } + + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELRotatableBondsCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELRotatableBondsCountDescriptor.java index 0db58dc..a5655f0 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELRotatableBondsCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELRotatableBondsCountDescriptor.java @@ -25,8 +25,6 @@ package libpadeldescriptor; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.exception.NoSuchAtomException; import org.openscience.cdk.graph.SpanningTree; @@ -34,6 +32,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IRingSet; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -60,7 +59,6 @@ * @cdk.keyword bond count, rotatable * @cdk.keyword descriptor */ -@TestClass("org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptorTest") public class PaDELRotatableBondsCountDescriptor implements IMolecularDescriptor { private static final String[] names = { "nRotB", "RotBFrac", "nRotBt", "RotBtFrac"}; @@ -77,7 +75,6 @@ public PaDELRotatableBondsCountDescriptor() { } * *@return The specification value */ - @TestMethod("testGetSpecification") public DescriptorSpecification getSpecification() { return new DescriptorSpecification( @@ -87,6 +84,13 @@ public DescriptorSpecification getSpecification() "The Chemistry Development Kit"); } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public String[] getParameterNames() { return null; //To change body of implemented methods use File | Settings | File Templates. @@ -107,7 +111,6 @@ public Object[] getParameters() { return null; //To change body of implemented methods use File | Settings | File Templates. } - @TestMethod(value="testNamesConsistency") /** * Gets the names of descriptors * @@ -125,7 +128,6 @@ public String[] getDescriptorNames() { *@param ac AtomContainer *@return number of rotatable bonds */ - @TestMethod("testCalculate_IAtomContainer") public DescriptorValue calculate(IAtomContainer ac) { int nRotB = 0; @@ -216,7 +218,6 @@ private int getConnectedHCount(IAtomContainer atomContainer, IAtom atom) * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ - @TestMethod("testGetDescriptorResultType") public IDescriptorResult getDescriptorResultType() { return new DoubleArrayResultType(names.length); diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELStandardize.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELStandardize.java index 2fb106d..1bf1005 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELStandardize.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELStandardize.java @@ -7,15 +7,16 @@ import java.util.List; import java.util.logging.Level; import java.util.logging.Logger; +import org.openscience.cdk.AtomContainer; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.DefaultChemObjectBuilder; -import org.openscience.cdk.Molecule; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.exception.InvalidSmilesException; import org.openscience.cdk.graph.ConnectivityChecker; import org.openscience.cdk.interfaces.IAtomType.Hybridization; import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.smiles.SmiFlavor; import org.openscience.cdk.smiles.SmilesGenerator; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.AtomTypeTools; @@ -158,7 +159,7 @@ public IAtomContainer Standardize(IAtomContainer molecule) throws Exception // Tidy up molecule // Assign some properties like ISINRING, ISNOTINRING, ISALIPHATIC to atoms - new AtomTypeTools().assignAtomTypePropertiesToAtom((IMolecule)molecule, false); + new AtomTypeTools().assignAtomTypePropertiesToAtom((IAtomContainer)molecule, false); // Add hydrogens adder.addImplicitHydrogens(molecule); @@ -174,17 +175,17 @@ private IAtomContainer RemoveSalt(IAtomContainer molecule) // Get biggest connected molecule. if (!ConnectivityChecker.isConnected(molecule)) { - IMoleculeSet molSet = ConnectivityChecker.partitionIntoMolecules(molecule); - IMolecule biggest = molSet.getMolecule(0); - for (int i = 1; i < molSet.getMoleculeCount(); i++) + IAtomContainerSet molSet = ConnectivityChecker.partitionIntoMolecules(molecule); + IAtomContainer biggest = molSet.getAtomContainer(0); + for (int i = 1; i < molSet.getAtomContainerCount(); i++) { - if (molSet.getMolecule(i).getBondCount() > biggest.getBondCount()) + if (molSet.getAtomContainer(i).getBondCount() > biggest.getBondCount()) { - biggest = molSet.getMolecule(i); + biggest = molSet.getAtomContainer(i); } } - molecule = (Molecule) biggest; + molecule = (AtomContainer) biggest; } return molecule; } @@ -257,13 +258,15 @@ private void PerceiveAtomTypes(IAtomContainer molecule) throws CDKException private IAtomContainer Dearomatize(IAtomContainer molecule) throws InvalidSmilesException, CDKException { - // Get molecule name. - StringBuffer molName = new StringBuffer(); - molName.setLength(0); - if (molecule.getProperty("cdk:Title")!=null) - { - molName.append(molecule.getProperty("cdk:Title")); - } +// Get molecule name. +StringBuffer molName = new StringBuffer(); // No need to set length to 0 +Object title = molecule.getProperty("cdk:Title"); + +if (title != null) { + molName.append(String.valueOf(title)); // Ensure non-string values are handled +} else { + System.out.println("Title property is null or not found."); +} if (!retain3D_) { @@ -278,7 +281,7 @@ private IAtomContainer Dearomatize(IAtomContainer molecule) throws InvalidSmiles if (!retain3D_) { - molecule = new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles(new SmilesGenerator(true).createSMILES(molecule)); + molecule = new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles(new SmilesGenerator(SmiFlavor.Canonical | SmiFlavor.Stereo).createSMILES(molecule)); molecule.setProperty("cdk:Title", molName.toString()); } @@ -295,7 +298,7 @@ private IAtomContainer StandardizeTautomers(IAtomContainer molecule) throws CDKE molName.setLength(0); if (molecule.getProperty("cdk:Title")!=null) { - molName.append(molecule.getProperty("cdk:Title")); + molName.append((CharSequence) molecule.getProperty("cdk:Title")); } // Add hydrogens. Necessary for InChITautomerGenerator. @@ -373,7 +376,7 @@ else if (smrkMan.applyTransformation(molecule, reaction)) lastPosTransform = curPos; if (!retain3D_) { - molecule = new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles(new SmilesGenerator(true).createSMILES(molecule)); + molecule = new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles(new SmilesGenerator(SmiFlavor.Default).createSMILES(molecule)); molecule.setProperty("cdk:Title", molName.toString()); } } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWHIMDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWHIMDescriptor.java index 349c902..4310c4d 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWHIMDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWHIMDescriptor.java @@ -32,6 +32,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -77,6 +78,13 @@ public PaDELWHIMDescriptor() } } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWeightDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWeightDescriptor.java index a1c85c8..91918a2 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWeightDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWeightDescriptor.java @@ -26,12 +26,12 @@ package libpadeldescriptor; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.config.Isotopes; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IIsotope; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -74,7 +74,6 @@ * @cdk.set qsar-descriptors * @cdk.dictref qsar-descriptors:weight */ -@TestClass("org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptorTest") public class PaDELWeightDescriptor implements IMolecularDescriptor { private String elementName = "*"; @@ -98,7 +97,6 @@ public PaDELWeightDescriptor() { } * * @return An object containing the descriptor specification */ - @TestMethod("testGetSpecification") public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#weight", @@ -115,7 +113,6 @@ public DescriptorSpecification getSpecification() { *is not of type String *@see #getParameters */ - @TestMethod("testSetParameters_arrayObject") public void setParameters(Object[] params) throws CDKException { if (params.length > 1) { throw new CDKException("weight only expects one parameter"); @@ -134,7 +131,6 @@ public void setParameters(Object[] params) throws CDKException { * @return The parameters value * @see #setParameters */ - @TestMethod("testGetParameters") public Object[] getParameters() { // return the parameters as used for the descriptor calculation Object[] params = new Object[1]; @@ -142,7 +138,6 @@ public Object[] getParameters() { return params; } - @TestMethod(value="testNamesConsistency") public String[] getDescriptorNames() { String name = "w"; if (elementName.equals("*")) @@ -167,7 +162,6 @@ private DescriptorValue getDummyDescriptorValue(Exception e) { * is specified as the element symbol make sure that the AtomContainer has hydrogens. *@return The total weight of atoms of the specified element type */ - @TestMethod("testCalculate_IAtomContainer") public DescriptorValue calculate(IAtomContainer container) { double weight = 0; if (elementName.equals("*")) { @@ -175,7 +169,7 @@ public DescriptorValue calculate(IAtomContainer container) { int maxAtoms = 0; for (int i = 0; i < container.getAtomCount(); i++) { //logger.debug("WEIGHT: "+container.getAtomAt(i).getSymbol() +" " +IsotopeFactory.getInstance().getMajorIsotope( container.getAtomAt(i).getSymbol() ).getExactMass()); - weight += IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass(); + weight += Isotopes.getInstance().getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass(); Integer hcount = container.getAtom(i).getImplicitHydrogenCount(); if (hcount == CDKConstants.UNSET) hcount = 0; weight += (hcount * 1.00782504); @@ -196,10 +190,10 @@ public DescriptorValue calculate(IAtomContainer container) { } else if (elementName.equals("H")) { try { - IIsotope h=IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope("H"); + IIsotope h=Isotopes.getInstance().getMajorIsotope("H"); for (int i = 0; i < container.getAtomCount(); i++) { if (container.getAtom(i).getSymbol().equals(elementName)) { - weight += IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass(); + weight += Isotopes.getInstance().getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass(); } else { weight += (container.getAtom(i).getImplicitHydrogenCount() * h.getExactMass()); @@ -213,7 +207,7 @@ else if (elementName.equals("H")) { try { for (int i = 0; i < container.getAtomCount(); i++) { if (container.getAtom(i).getSymbol().equals(elementName)) { - weight += IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass(); + weight += Isotopes.getInstance().getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass(); } } } catch (Exception e) { @@ -237,7 +231,6 @@ else if (elementName.equals("H")) { * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ - @TestMethod("testGetDescriptorResultType") public IDescriptorResult getDescriptorResultType() { if (elementName.equals("*")) return new DoubleArrayResultType(2); else return new DoubleResult(0.0); @@ -249,7 +242,6 @@ public IDescriptorResult getDescriptorResultType() { * *@return The parameterNames value */ - @TestMethod("testGetParameterNames") public String[] getParameterNames() { String[] params = new String[1]; params[0] = "elementSymbol"; @@ -263,9 +255,16 @@ public String[] getParameterNames() { *@param name Description of the Parameter *@return An Object whose class is that of the parameter requested */ - @TestMethod("testGetParameterType_String") public Object getParameterType(String name) { return ""; } + + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWeightedPathDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWeightedPathDescriptor.java index ba42496..b9a4f18 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWeightedPathDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PaDELWeightedPathDescriptor.java @@ -19,12 +19,11 @@ */ package libpadeldescriptor; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -83,7 +82,6 @@ * @cdk.set qsar-descriptors * @cdk.dictref qsar-descriptors:weightedPath */ -@TestClass("org.openscience.cdk.qsar.descriptors.molecular.WeightedPathDescriptorTest") public class PaDELWeightedPathDescriptor implements IMolecularDescriptor { private static final String[] names = { @@ -93,7 +91,6 @@ public class PaDELWeightedPathDescriptor implements IMolecularDescriptor { public PaDELWeightedPathDescriptor() { } - @TestMethod("testGetSpecification") public DescriptorSpecification getSpecification() { return new DescriptorSpecification( "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#weightedPath", @@ -110,7 +107,6 @@ public DescriptorSpecification getSpecification() { * @throws org.openscience.cdk.exception.CDKException * Description of the Exception */ - @TestMethod("testSetParameters_arrayObject") public void setParameters(Object[] params) throws CDKException { // no parameters for this descriptor } @@ -120,13 +116,11 @@ public void setParameters(Object[] params) throws CDKException { * * @return The parameters value */ - @TestMethod("testGetParameters") public Object[] getParameters() { // no parameters to return return (null); } - @TestMethod(value="testNamesConsistency") public String[] getDescriptorNames() { return names; } @@ -136,7 +130,6 @@ public String[] getDescriptorNames() { * * @return The parameterNames value */ - @TestMethod("testGetParameterNames") public String[] getParameterNames() { // no param names to return return (null); @@ -149,7 +142,6 @@ public String[] getParameterNames() { * @param name Description of the Parameter * @return The parameterType value */ - @TestMethod("testGetParameterType_String") public Object getParameterType(String name) { return (null); } @@ -161,7 +153,6 @@ public Object getParameterType(String name) { * @return A DoubleArrayResult value representing the weighted path values */ - @TestMethod("testCalculate_IAtomContainer") public DescriptorValue calculate(IAtomContainer container) { IAtomContainer local = AtomContainerManipulator.removeHydrogens(container); int natom = local.getAtomCount(); @@ -262,7 +253,6 @@ public DescriptorValue calculate(IAtomContainer container) { * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating * the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object */ - @TestMethod("testGetDescriptorResultType") public IDescriptorResult getDescriptorResultType() { return new DoubleArrayResultType(5); } @@ -283,6 +273,13 @@ private double[] getPathWeights(List pathList, IAtomContainer atomContainer) { return pathWts; } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/PathCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/PathCountDescriptor.java index 62d9a4b..01b1857 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/PathCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/PathCountDescriptor.java @@ -34,6 +34,7 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IBond.Order; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -72,6 +73,13 @@ public PathCountDescriptor() names[index++] = "R_TpiPCTPC"; } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/RDFDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/RDFDescriptor.java index c22a499..3cb04c5 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/RDFDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/RDFDescriptor.java @@ -30,6 +30,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -70,6 +71,13 @@ public RDFDescriptor() } } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/RingCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/RingCountDescriptor.java index 0d5b07a..c4dff94 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/RingCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/RingCountDescriptor.java @@ -31,6 +31,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IRingSet; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -145,6 +146,13 @@ public RingCountDescriptor() { } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/ShortestPaths.java b/libPaDEL-Descriptor/src/libpadeldescriptor/ShortestPaths.java index 8fbc019..72998cc 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/ShortestPaths.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/ShortestPaths.java @@ -27,7 +27,6 @@ import org.openscience.cdk.interfaces.IAtomContainer; import java.util.Arrays; -import org.openscience.cdk.annotations.TestMethod; /** * Find and reconstruct the shortest paths from a given start atom to any other @@ -105,7 +104,6 @@ public final class ShortestPaths { * computed * {@code AllPairsShortestPaths} */ - @TestMethod("testConstructor_Container_Empty,testConstructor_Container_Null,testConstructor_Container_MissingAtom") public ShortestPaths(IAtomContainer container, IAtom start) { this(GraphUtil.toAdjList(container), container, container .getAtomNumber(start)); @@ -302,10 +300,7 @@ private void compute(final int[][] adjacent, final int[] ordering) { * @see #atomsTo(int) * @see #atomsTo(org.openscience.cdk.interfaces.IAtom) */ - @TestMethod("testPathTo_Int_Simple,testPathTo_Int_Benzene,testPathTo_Int_Norbornane," + - "testPathTo_Int_Spiroundecane,testPathTo_Int_Pentadecaspiro," + - "testPathTo_Int_OutOfBoundsIndex,testPathTo_Int_NegativeIndex," + - "testPathTo_Int_Disconnected") + public int[] pathTo(int end) { if (end < 0 || end >= routeTo.length) @@ -344,10 +339,7 @@ public int[] pathTo(int end) { * @see #atomsTo(int) * @see #pathTo(int) */ - @TestMethod("testPathTo_Atom_Simple,testPathTo_Atom_Benzene,testPathTo_Atom_Norbornane," + - "testPathTo_Atom_Spiroundecane,testPathTo_Atom_Pentadecaspiro," + - "testPathTo_Atom_MissingAtom,testPathTo_Atom_Null," + - "testPathTo_Atom_Disconnected") + public int[] pathTo(IAtom end) { return pathTo(container.getAtomNumber(end)); } @@ -362,7 +354,6 @@ public int[] pathTo(IAtom end) { * @return whether the path to the end only passed through vertices * preceding the start */ - @TestMethod("testIsPrecedingPathTo_OutOfBounds,testIsPrecedingPathTo") public boolean isPrecedingPathTo(int end) { return (end >= 0 || end < routeTo.length) && precedes[end]; } @@ -397,9 +388,7 @@ public boolean isPrecedingPathTo(int end) { * @param end the end vertex * @return all shortest paths from the start to the end vertex */ - @TestMethod("testPathsTo_Int_Simple,testPathsTo_Int_Benzene,testPathsTo_Int_Spiroundecane," + - "testPathsTo_Int_Norbornane,testPathsTo_Int_OutOfBoundsIndex," + - "testPathsTo_Int_NegativeIndex,testPathsTo_Int_Disconnected") + public int[][] pathsTo(int end) { if (end < 0 || end >= routeTo.length) @@ -441,10 +430,7 @@ public int[][] pathsTo(int end) { * @param end the end atom * @return all shortest paths from the start to the end vertex */ - @TestMethod("testPathsTo_Atom_Simple,testPathsTo_Atom_Benzene,testPathsTo_Atom_Spiroundecane," + - "testPathsTo_Atom_Norbornane,testPathsTo_Atom_Pentadecaspiro," + - "testPathsTo_Atom_MissingAtom,testPathsTo_Atom_Null," + - "testPathsTo_Atom_Disconnected") + public int[][] pathsTo(IAtom end) { return pathsTo(container.getAtomNumber(end)); } @@ -478,8 +464,7 @@ public int[][] pathsTo(IAtom end) { * @see #pathTo(int) * @see #pathTo(org.openscience.cdk.interfaces.IAtom) */ - @TestMethod("testAtomsTo_Int_Simple,testAtomsTo_Int_Benzene,testAtomsTo_Int_Disconnected," + - "testAtomsTo_Int_OutOfBoundsIndex,testAtomsTo_Int_NegativeIndex") + public IAtom[] atomsTo(int end) { int[] path = pathTo(end); @@ -524,8 +509,7 @@ public IAtom[] atomsTo(int end) { * @see #pathTo(int) * @see #pathTo(org.openscience.cdk.interfaces.IAtom) */ - @TestMethod("testAtomsTo_Atom_Simple,testAtomsTo_Atom_Benzene,testAtomsTo_Atom_Disconnected," + - "testAtomsTo_Atom_MissingAtom,testAtomsTo_Atom_Null") + public IAtom[] atomsTo(IAtom end) { return atomsTo(container.getAtomNumber(end)); } @@ -549,10 +533,7 @@ public IAtom[] atomsTo(IAtom end) { * returned * @return the number of paths to the end vertex */ - @TestMethod("testNPathsTo_Int_Simple,testNPathsTo_Int_Benzene,testNPathsTo_Int_Norbornane," + - "testNPathsTo_Int_Spiroundecane,testNPathsTo_Int_Pentadecaspiro," + - "testNPathsTo_Int_Disconnected," + - "testNPathsTo_Int_OutOfBoundIndex,testNPathsTo_Int_NegativeIndex") + public int nPathsTo(int end) { return (end < 0 || end >= nPathsTo.length) ? 0 : nPathsTo[end]; } @@ -578,10 +559,6 @@ public int nPathsTo(int end) { * returned * @return the number of paths to the end vertex */ - @TestMethod("testNPathsTo_Atom_Simple,testNPathsTo_Atom_Benzene,testNPathsTo_Atom_Norbornane," + - "testNPathsTo_Atom_Spiroundecane,testNPathsTo_Atom_Pentadecaspiro," + - "testNPathsTo_Atom_Disconnected," + - "testNPathsTo_Atom_MissingAtom,testNPathsTo_Atom_Null") public int nPathsTo(IAtom end) { return nPathsTo(container.getAtomNumber(end)); } @@ -622,10 +599,6 @@ public int nPathsTo(IAtom end) { * @return distance to this vertex * @see #distanceTo(org.openscience.cdk.interfaces.IAtom) */ - @TestMethod("testDistanceTo_Int_Simple,testDistanceTo_Int_OutOfBoundIndex," + - "testDistanceTo_Int_NegativeIndex,testDistanceTo_Int_Disconnected," + - "testDistanceTo_Int_Benzene,testDistanceTo_Int_Spiroundecane," + - "testDistanceTo_Int_Pentadecaspiro") public int distanceTo(int end) { return (end < 0 || end >= nPathsTo.length) ? Integer.MAX_VALUE : distTo[end]; @@ -668,9 +641,6 @@ public int distanceTo(int end) { * @return distance to the given atom * @see #distanceTo(int) */ - @TestMethod("testDistanceTo_Atom_Simple,testDistanceTo_Atom_MissingAtom,testDistanceTo_Atom_Null," + - "testDistanceTo_Atom_Disconnected,testDistanceTo_Atom_Benzene," + - "testDistanceTo_Atom_Spiroundecane,testDistanceTo_Atom_Pentadecaspiro") public int distanceTo(IAtom end) { return distanceTo(container.getAtomNumber(end)); } diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/SubstructureFingerprintCount.java b/libPaDEL-Descriptor/src/libpadeldescriptor/SubstructureFingerprintCount.java index b92fdf6..1550662 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/SubstructureFingerprintCount.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/SubstructureFingerprintCount.java @@ -29,6 +29,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.fingerprint.StandardSubstructureSets; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -74,6 +75,13 @@ public DescriptorSpecification getSpecification() { "PaDEL"); } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public String[] getParameterNames() { return null; //To change body of implemented methods use File | Settings | File Templates. @@ -136,7 +144,7 @@ public DescriptorValue calculate(IAtomContainer container) { try { DoubleArrayResult retval = new DoubleArrayResult(); - SMARTSQueryTool sqt = new SMARTSQueryTool("C"); + SMARTSQueryTool sqt = new SMARTSQueryTool("C", builder); for (int i = 0; i < smarts.length; i++) { String pattern = smarts[i]; diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalChargeDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalChargeDescriptor.java index 3b0905c..538edc5 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalChargeDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalChargeDescriptor.java @@ -30,6 +30,7 @@ import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.graph.matrix.AdjacencyMatrix; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -81,6 +82,13 @@ public TopologicalChargeDescriptor() { } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalDescriptor.java index b288ec8..c87d947 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalDescriptor.java @@ -30,6 +30,7 @@ import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.graph.matrix.AdjacencyMatrix; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -68,6 +69,13 @@ public TopologicalDescriptor() { } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalDistanceMatrixDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalDistanceMatrixDescriptor.java index f872a42..49ea662 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalDistanceMatrixDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/TopologicalDistanceMatrixDescriptor.java @@ -32,6 +32,7 @@ import org.openscience.cdk.graph.matrix.TopologicalMatrix; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -69,6 +70,13 @@ public TopologicalDistanceMatrixDescriptor() } } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/WalkCountDescriptor.java b/libPaDEL-Descriptor/src/libpadeldescriptor/WalkCountDescriptor.java index a2f86b6..d51a057 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/WalkCountDescriptor.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/WalkCountDescriptor.java @@ -30,6 +30,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.matrix.AdjacencyMatrix; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -67,6 +68,13 @@ public WalkCountDescriptor() names[index++] = "TSRW"; } + private IChemObjectBuilder builder; + + @Override + public void initialise(IChemObjectBuilder builder) { + this.builder = builder; + } + @Override public DescriptorSpecification getSpecification() { return new DescriptorSpecification( diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/libPaDELDescriptorMaster.java b/libPaDEL-Descriptor/src/libpadeldescriptor/libPaDELDescriptorMaster.java index 8288472..d0ca72a 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/libPaDELDescriptorMaster.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/libPaDELDescriptorMaster.java @@ -305,10 +305,11 @@ private boolean PaDELReaderHasNext() } else { - if (molStructure.getProperty("cdk:Title")!=null && - !((String)molStructure.getProperty("cdk:Title")).trim().isEmpty()) - { - name.append(molStructure.getProperty("cdk:Title")); + if (molStructure.getProperty("cdk:Title") != null) { + String title = String.valueOf(molStructure.getProperty("cdk:Title")); + if (!title.trim().isEmpty()) { + name.append(title); // Now there is no ambiguity + } } else { diff --git a/libPaDEL-Descriptor/src/libpadeldescriptor/libPaDELDescriptorWorker.java b/libPaDEL-Descriptor/src/libpadeldescriptor/libPaDELDescriptorWorker.java index bc85bdd..70e8437 100644 --- a/libPaDEL-Descriptor/src/libpadeldescriptor/libPaDELDescriptorWorker.java +++ b/libPaDEL-Descriptor/src/libpadeldescriptor/libPaDELDescriptorWorker.java @@ -9,8 +9,10 @@ import java.util.logging.Level; import java.util.logging.Logger; import libpadeljobs.Worker; + +import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.modeling.builder3d.ModelBuilder3D; import org.openscience.cdk.modeling.builder3d.TemplateHandler3D; @@ -110,8 +112,9 @@ public void DoJob() { // Calculate 3D coordinates. TemplateHandler3D template = TemplateHandler3D.getInstance(); - ModelBuilder3D mb3d = ModelBuilder3D.getInstance(template,job.getForcefield()); - molecule = (IAtomContainer) mb3d.generate3DCoordinates((IMolecule) molecule, true); + IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance(); + ModelBuilder3D mb3d = ModelBuilder3D.getInstance(template, job.getForcefield(), builder); + molecule = (IAtomContainer) mb3d.generate3DCoordinates((IAtomContainer) molecule, true); } catch (Exception ex) { @@ -126,7 +129,7 @@ public void DoJob() { try { - cdk_descriptor.setMolecule((IAtomContainer)molecule.clone()); + cdk_descriptor.setAtomContainer((IAtomContainer)molecule.clone()); cdk_descriptor.run(); } catch (Exception ex) @@ -140,7 +143,7 @@ public void DoJob() { try { - cdk_fingerprint.setMolecule((IAtomContainer)molecule.clone()); + cdk_fingerprint.setAtomContainer((IAtomContainer)molecule.clone()); cdk_fingerprint.run(); } catch (Exception ex) @@ -154,7 +157,7 @@ public void DoJob() { try { - cdk_fingerprint_count.setMolecule((IAtomContainer)molecule.clone()); + cdk_fingerprint_count.setAtomContainer((IAtomContainer)molecule.clone()); cdk_fingerprint_count.run(); } catch (Exception ex) @@ -172,7 +175,7 @@ public void DoJob() { try { - cdk_descriptor.setMolecule((IAtomContainer)molecule.clone()); + cdk_descriptor.setAtomContainer((IAtomContainer)molecule.clone()); cdk_descriptor.start(); } catch (Exception ex) @@ -185,7 +188,7 @@ public void DoJob() { try { - cdk_fingerprint.setMolecule((IAtomContainer)molecule.clone()); + cdk_fingerprint.setAtomContainer((IAtomContainer)molecule.clone()); cdk_fingerprint.start(); } catch (Exception ex) @@ -198,7 +201,7 @@ public void DoJob() { try { - cdk_fingerprint_count.setMolecule((IAtomContainer)molecule.clone()); + cdk_fingerprint_count.setAtomContainer((IAtomContainer)molecule.clone()); cdk_fingerprint_count.start(); } catch (Exception ex)