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[Cdk-commits] SF.net SVN: cdk: [9983] branches/miguelrojasch/reaction
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From: <eg...@us...> - 2008-01-31 15:37:55
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Revision: 9983
http://cdk.svn.sourceforge.net/cdk/?rev=9983&view=rev
Author: egonw
Date: 2008-01-31 07:37:44 -0800 (Thu, 31 Jan 2008)
Log Message:
-----------
Synched with trunk; merged 9958:9982
Modified Paths:
--------------
branches/miguelrojasch/reaction/.classpath
branches/miguelrojasch/reaction/.externalToolBuilders/EclipsePreBuild.launch
branches/miguelrojasch/reaction/build.xml
branches/miguelrojasch/reaction/javadoc.xml
branches/miguelrojasch/reaction/pmd-migrating.xml
branches/miguelrojasch/reaction/pmd-unused.xml
branches/miguelrojasch/reaction/pmd.xml
branches/miguelrojasch/reaction/src/META-INF/structgen.cdkdepends
branches/miguelrojasch/reaction/src/META-INF/test-extra.cdkdepends
branches/miguelrojasch/reaction/src/META-INF/test-qsarmolecular.cdkdepends
branches/miguelrojasch/reaction/src/META-INF/test-structgen.cdkdepends
branches/miguelrojasch/reaction/src/META-INF/test-valencycheck.cdkdepends
branches/miguelrojasch/reaction/src/org/openscience/cdk/DefaultChemObjectBuilder.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/interfaces/IChemObjectBuilder.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/io/ShelXWriter.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/atomtype/CDKAtomTypeMatcherTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/fingerprint/ExtendedFingerprinterTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/io/MDLReaderTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/io/ShelXWriterTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MdataTests.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MexperimentalTests.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MextraTests.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MioTests.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MstandardTests.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/qsar/descriptors/molecular/AromaticBondsCountDescriptorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/smiles/SmilesGeneratorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/smiles/SmilesParserTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/tools/CDKHydrogenAdderTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/tools/DeAromatizationToolTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/tools/MFAnalyserTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/tools/DeAromatizationTool.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/tools/MFAnalyser.java
branches/miguelrojasch/reaction/tools/nightly.py
Added Paths:
-----------
branches/miguelrojasch/reaction/src/META-INF/formula.cdkdepends
branches/miguelrojasch/reaction/src/META-INF/formula.libdepends
branches/miguelrojasch/reaction/src/META-INF/test-formula.cdkdepends
branches/miguelrojasch/reaction/src/META-INF/test-formula.devellibdepends
branches/miguelrojasch/reaction/src/META-INF/test-formula.libdepends
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/AdductFormula.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IAdductFormula.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IMolecularFormula.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IMolecularFormulaSet.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IsotopePatternGenerator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MassToFormulaTool.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormula.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaChecker.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaManipulator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaRange.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaRangeManipulator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaSet.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaSetManipulator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/ChargeRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/ElementRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/IRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/IsotopePatternRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/MMElementRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/ToleranceRangeRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/FormulaCoverageTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/AdductFormulaTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/IsotopePatternGeneratorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MassToFormulaToolTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaCheckerTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaManipulatorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaRangeManipulatorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaRangeTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaSetManipulatorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaSetTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/ChargeRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/ElementRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/FormulaRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/IsotopePatternRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/MMElementRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/ToleranceRangeRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/modulesuites/MformulaTests.java
Removed Paths:
-------------
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/AdductFormula.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IAdductFormula.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IMolecularFormula.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IMolecularFormulaSet.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IsotopePatternGenerator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MassToFormulaTool.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormula.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaChecker.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaManipulator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaRange.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaRangeManipulator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaSet.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/MolecularFormulaSetManipulator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/ChargeRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/ElementRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/IRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/IsotopePatternRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/MMElementRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/rules/ToleranceRangeRule.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/AdductFormulaTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/IsotopePatternGeneratorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MassToFormulaToolTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaCheckerTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaManipulatorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaRangeManipulatorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaRangeTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaSetManipulatorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaSetTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/MolecularFormulaTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/ChargeRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/ElementRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/FormulaRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/IsotopePatternRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/MMElementRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/formula/rules/ToleranceRangeRuleTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/test/tools/IsotopeGeneratorTest.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/tools/IsotopeGenerator.java
branches/miguelrojasch/reaction/src/org/openscience/cdk/tools/MassToFormulaTool.java
Modified: branches/miguelrojasch/reaction/.classpath
===================================================================
--- branches/miguelrojasch/reaction/.classpath 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/.classpath 2008-01-31 15:37:44 UTC (rev 9983)
@@ -1,7 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry excluding="org/openscience/cdk/libio/joelib/Convertor.java|org/openscience/cdk/test/libio/joelib/JOELibIOTest.java" kind="src" path="src"/>
- <classpathentry kind="src" path="perf"/>
<classpathentry kind="lib" path="develjar/ant_doxygen.jar"/>
<classpathentry kind="lib" path="develjar/dbdoclet.jar"/>
<classpathentry kind="lib" path="doc/jar/jabref.jar"/>
Modified: branches/miguelrojasch/reaction/.externalToolBuilders/EclipsePreBuild.launch
===================================================================
--- branches/miguelrojasch/reaction/.externalToolBuilders/EclipsePreBuild.launch 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/.externalToolBuilders/EclipsePreBuild.launch 2008-01-31 15:37:44 UTC (rev 9983)
@@ -1,16 +1,16 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<launchConfiguration type="org.eclipse.ant.AntBuilderLaunchConfigurationType">
+<stringAttribute key="org.eclipse.ant.ui.ATTR_ANT_AUTO_TARGETS" value="preBuild,"/>
+<stringAttribute key="org.eclipse.ui.externaltools.ATTR_RUN_BUILD_KINDS" value="incremental,auto,"/>
<booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
+<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="true"/>
-<booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="false"/>
-<stringAttribute key="org.eclipse.ui.externaltools.ATTR_RUN_BUILD_KINDS" value="incremental,auto,"/>
-<booleanAttribute key="org.eclipse.ant.ui.ATTR_TARGETS_UPDATED" value="true"/>
-<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
-<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>
<booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="false"/>
-<stringAttribute key="org.eclipse.ant.ui.ATTR_ANT_MANUAL_TARGETS" value="preBuild,"/>
-<stringAttribute key="org.eclipse.ant.ui.ATTR_ANT_AUTO_TARGETS" value="preBuild,"/>
<stringAttribute key="org.eclipse.debug.core.ATTR_REFRESH_SCOPE" value="${project}"/>
+<booleanAttribute key="org.eclipse.ant.ui.ATTR_TARGETS_UPDATED" value="true"/>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="false"/>
<stringAttribute key="org.eclipse.ui.externaltools.ATTR_LOCATION" value="${workspace_loc:/cdk/build-eclipse.xml}"/>
+<stringAttribute key="org.eclipse.ant.ui.ATTR_ANT_MANUAL_TARGETS" value="preBuild,"/>
</launchConfiguration>
Modified: branches/miguelrojasch/reaction/build.xml
===================================================================
--- branches/miguelrojasch/reaction/build.xml 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/build.xml 2008-01-31 15:37:44 UTC (rev 9983)
@@ -449,6 +449,7 @@
<antcall target="compile-module"><param name="module" value="control"/></antcall>
<antcall target="compile-module"><param name="module" value="datadebug"/></antcall>
<antcall target="compile-module"><param name="module" value="nonotify"/></antcall>
+ <antcall target="compile-module"><param name="module" value="formula"/></antcall>
<antcall target="compile-module"><param name="module" value="structgen"/></antcall>
<antcall target="compile-module"><param name="module" value="pdb"/></antcall>
<antcall target="compile-module"><param name="module" value="extra"/></antcall>
@@ -474,7 +475,7 @@
<antcall target="compile-module"><param name="module" value="experimental"/></antcall>
<antcall target="compile-module"><param name="module" value="pcore"/></antcall>
<antcall target="compile-module"><param name="module" value="applications"/></antcall>
- <antcall target="compile-module"><param name="module" value="inchi"/></antcall>
+ <antcall target="compile-module"><param name="module" value="inchi"/></antcall>
</target>
<target id="test-dist-all" name="test-dist-all" description="test-dist-all">
@@ -507,6 +508,7 @@
<antcall target="compile-module"><param name="module" value="test-libiomd"/></antcall>
<antcall target="compile-module"><param name="module" value="test-smarts"/></antcall>
<antcall target="compile-module"><param name="module" value="test-pcore"/></antcall>
+ <antcall target="compile-module"><param name="module" value="test-formula"/></antcall>
</target>
<target id="dist-large" name="dist-large" depends="dist-all"
@@ -551,6 +553,7 @@
<includesfile name="${metainf}/inchi.libdepends"/>
<includesfile name="${metainf}/smarts.libdepends"/>
<includesfile name="${metainf}/pcore.libdepends"/>
+ <includesfile name="${metainf}/formula.libdepends"/>
</fileset>
<fileset dir="${dist}/jar">
<include name="cdk-applications.jar"/>
@@ -592,6 +595,7 @@
<include name="cdk-sdg.jar"/>
<include name="cdk-inchi.jar"/>
<include name="cdk-pcore.jar"/>
+ <include name="cdk-formula.jar"/>
</fileset>
</unjar>
@@ -659,6 +663,7 @@
<include name="cdk-sdg.jar"/>
<include name="cdk-inchi.jar"/>
<include name="cdk-pcore.jar"/>
+ <include name="cdk-formula.jar"/>
</fileset>
</unjar>
@@ -714,6 +719,7 @@
<includesfile name="${metainf}/test-weka.libdepends"/>
<includesfile name="${metainf}/test-libiomd.libdepends"/>
<includesfile name="${metainf}/test-pcore.libdepends"/>
+ <includesfile name="${metainf}/test-formula.libdepends"/>
</fileset>
<fileset dir="${dist}/jar">
<include name="cdk-test-core.jar"/>
@@ -742,6 +748,7 @@
<include name="cdk-test-weka.jar"/>
<include name="cdk-test-libiomd.jar"/>
<include name="cdk-test-pcore.jar"/>
+ <include name="cdk-test-formula.jar"/>
</fileset>
</unjar>
@@ -985,6 +992,7 @@
<antcall target="test-module"><param name="module" value="inchi"/></antcall>
<antcall target="test-module"><param name="module" value="structgen"/></antcall>
<antcall target="test-module"><param name="module" value="libiomd"/></antcall>
+ <antcall target="test-module"><param name="module" value="formula"/></antcall>
</target>
<target id="limitations" name="limitations" depends="noJunit, dist-all"
Modified: branches/miguelrojasch/reaction/javadoc.xml
===================================================================
--- branches/miguelrojasch/reaction/javadoc.xml 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/javadoc.xml 2008-01-31 15:37:44 UTC (rev 9983)
@@ -123,6 +123,7 @@
<antcall target="doccheck-module"><param name="module" value="io"/></antcall>
<antcall target="doccheck-module"><param name="module" value="inchi"/></antcall>
<antcall target="doccheck-module"><param name="module" value="extra"/></antcall>
+ <antcall target="doccheck-module"><param name="module" value="formula"/></antcall>
<antcall target="doccheck-module"><param name="module" value="render"/></antcall>
<antcall target="doccheck-module"><param name="module" value="reaction"/></antcall>
<antcall target="doccheck-module"><param name="module" value="libio-cml"/></antcall>
Modified: branches/miguelrojasch/reaction/pmd-migrating.xml
===================================================================
--- branches/miguelrojasch/reaction/pmd-migrating.xml 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/pmd-migrating.xml 2008-01-31 15:37:44 UTC (rev 9983)
@@ -37,6 +37,7 @@
<antcall target="test-module"><param name="module" value="atomtype"/></antcall>
<antcall target="test-module"><param name="module" value="io"/></antcall>
<antcall target="test-module"><param name="module" value="extra"/></antcall>
+ <antcall target="test-module"><param name="module" value="formula"/></antcall>
<antcall target="test-module"><param name="module" value="render"/></antcall>
<antcall target="test-module"><param name="module" value="reaction"/></antcall>
<antcall target="test-module"><param name="module" value="libio-cml"/></antcall>
Modified: branches/miguelrojasch/reaction/pmd-unused.xml
===================================================================
--- branches/miguelrojasch/reaction/pmd-unused.xml 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/pmd-unused.xml 2008-01-31 15:37:44 UTC (rev 9983)
@@ -37,6 +37,7 @@
<antcall target="test-module"><param name="module" value="atomtype"/></antcall>
<antcall target="test-module"><param name="module" value="io"/></antcall>
<antcall target="test-module"><param name="module" value="extra"/></antcall>
+ <antcall target="test-module"><param name="module" value="formula"/></antcall>
<antcall target="test-module"><param name="module" value="render"/></antcall>
<antcall target="test-module"><param name="module" value="reaction"/></antcall>
<antcall target="test-module"><param name="module" value="libio-cml"/></antcall>
Modified: branches/miguelrojasch/reaction/pmd.xml
===================================================================
--- branches/miguelrojasch/reaction/pmd.xml 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/pmd.xml 2008-01-31 15:37:44 UTC (rev 9983)
@@ -37,6 +37,7 @@
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="atomtype"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="io"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="extra"/></antcall>
+ <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="formula"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="render"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="reaction"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="libio-cml"/></antcall>
Copied: branches/miguelrojasch/reaction/src/META-INF/formula.cdkdepends (from rev 9982, trunk/cdk/src/META-INF/formula.cdkdepends)
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/formula.cdkdepends (rev 0)
+++ branches/miguelrojasch/reaction/src/META-INF/formula.cdkdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -0,0 +1,4 @@
+cdk-core.jar
+cdk-extra.jar
+cdk-interfaces.jar
+cdk-standard.jar
\ No newline at end of file
Copied: branches/miguelrojasch/reaction/src/META-INF/formula.libdepends (from rev 9982, trunk/cdk/src/META-INF/formula.libdepends)
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/formula.libdepends (rev 0)
+++ branches/miguelrojasch/reaction/src/META-INF/formula.libdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -0,0 +1,2 @@
+vecmath1.2-1.14.jar
+
Modified: branches/miguelrojasch/reaction/src/META-INF/structgen.cdkdepends
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/structgen.cdkdepends 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/META-INF/structgen.cdkdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -2,3 +2,4 @@
cdk-core.jar
cdk-standard.jar
cdk-nonotify.jar
+cdk-formula.jar
Modified: branches/miguelrojasch/reaction/src/META-INF/test-extra.cdkdepends
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/test-extra.cdkdepends 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/META-INF/test-extra.cdkdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -21,3 +21,4 @@
cdk-smiles.jar
cdk-charges.jar
cdk-test.jar
+cdk-formula.jar
Copied: branches/miguelrojasch/reaction/src/META-INF/test-formula.cdkdepends (from rev 9982, trunk/cdk/src/META-INF/test-formula.cdkdepends)
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/test-formula.cdkdepends (rev 0)
+++ branches/miguelrojasch/reaction/src/META-INF/test-formula.cdkdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -0,0 +1,11 @@
+cdk-interfaces.jar
+cdk-data.jar
+cdk-nonotify.jar
+cdk-core.jar
+cdk-standard.jar
+cdk-test.jar
+cdk-formula.jar
+cdk-extra.jar
+cdk-smiles.jar
+cdk-valencycheck.jar
+cdk-atomtype.jar
Copied: branches/miguelrojasch/reaction/src/META-INF/test-formula.devellibdepends (from rev 9982, trunk/cdk/src/META-INF/test-formula.devellibdepends)
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/test-formula.devellibdepends (rev 0)
+++ branches/miguelrojasch/reaction/src/META-INF/test-formula.devellibdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -0,0 +1,2 @@
+junit-4.3.1.jar
+
Copied: branches/miguelrojasch/reaction/src/META-INF/test-formula.libdepends (from rev 9982, trunk/cdk/src/META-INF/test-formula.libdepends)
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/test-formula.libdepends (rev 0)
+++ branches/miguelrojasch/reaction/src/META-INF/test-formula.libdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -0,0 +1,5 @@
+Jama-1.0.1.jar
+jgrapht-0.6.0.jar
+log4j.jar
+vecmath1.2-1.14.jar
+xom-1.1.jar
Modified: branches/miguelrojasch/reaction/src/META-INF/test-qsarmolecular.cdkdepends
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/test-qsarmolecular.cdkdepends 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/META-INF/test-qsarmolecular.cdkdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -17,3 +17,4 @@
cdk-test.jar
cdk-test-qsar.jar
cdk-test-qsarbond.jar
+cdk-formula.jar
Modified: branches/miguelrojasch/reaction/src/META-INF/test-structgen.cdkdepends
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/test-structgen.cdkdepends 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/META-INF/test-structgen.cdkdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -9,3 +9,4 @@
cdk-smiles.jar
cdk-extra.jar
cdk-test.jar
+cdk-formula.jar
Modified: branches/miguelrojasch/reaction/src/META-INF/test-valencycheck.cdkdepends
===================================================================
--- branches/miguelrojasch/reaction/src/META-INF/test-valencycheck.cdkdepends 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/META-INF/test-valencycheck.cdkdepends 2008-01-31 15:37:44 UTC (rev 9983)
@@ -9,3 +9,4 @@
cdk-valencycheck.jar
cdk-smiles.jar
cdk-test.jar
+cdk-formula.jar
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/DefaultChemObjectBuilder.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/DefaultChemObjectBuilder.java 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/DefaultChemObjectBuilder.java 2008-01-31 15:37:44 UTC (rev 9983)
@@ -60,7 +60,6 @@
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.interfaces.ISingleElectron;
import org.openscience.cdk.interfaces.IStrand;
-import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.protein.data.PDBAtom;
import org.openscience.cdk.protein.data.PDBMonomer;
import org.openscience.cdk.protein.data.PDBPolymer;
@@ -143,11 +142,11 @@
return new Bond(atom1, atom2);
}
- public IBond newBond(IAtom atom1, IAtom atom2, Order order) {
+ public IBond newBond(IAtom atom1, IAtom atom2, IBond.Order order) {
return new Bond(atom1, atom2, order);
}
- public IBond newBond(IAtom atom1, IAtom atom2, Order order, int stereo) {
+ public IBond newBond(IAtom atom1, IAtom atom2, IBond.Order order, int stereo) {
return new Bond(atom1, atom2, order, stereo);
}
@@ -232,7 +231,7 @@
public IMolecule newMolecule(IAtomContainer container) {
return new Molecule(container);
}
-
+
public IMonomer newMonomer () {
return new Monomer();
}
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java 2008-01-31 15:37:44 UTC (rev 9983)
@@ -522,7 +522,7 @@
return null;
} else if (atom.getHybridization() != CDKConstants.UNSET &&
(atom.getFormalCharge() == CDKConstants.UNSET ||
- atom.getFormalCharge() == 0)) {
+ atom.getFormalCharge() != 0)) {
if (atom.getHybridization() == Hybridization.SP2 &&
atom.getFormalCharge() == +1) {
IAtomType type = getAtomType("S.plus");
Modified: branches/miguelrojasch/reaction/src/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java 2008-01-31 15:37:44 UTC (rev 9983)
@@ -43,8 +43,8 @@
* @cdk.created 2006-01-13
* @cdk.keyword fingerprint
* @cdk.keyword similarity
- * @cdk.module standard
- * @cdk.svnrev $Revision: 9162 $
+ * @cdk.module extra
+ * @cdk.svnrev $Revision: 9162 $
*
* @see org.openscience.cdk.fingerprint.Fingerprinter
*/
Copied: branches/miguelrojasch/reaction/src/org/openscience/cdk/formula (from rev 9982, trunk/cdk/src/org/openscience/cdk/formula)
Deleted: branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/AdductFormula.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/formula/AdductFormula.java 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/AdductFormula.java 2008-01-31 15:37:44 UTC (rev 9983)
@@ -1,351 +0,0 @@
-/* $RCSfile$
- * $Author: egonw $
- * $Date: 2007-09-03 12:53:05 +0200 (Mon, 03 Sep 2007) $
- * $Revision: 8848 $
- *
- * Copyright (C) 2007 Miguel Rojasch <mig...@us...>
- *
- * Contact: cdk...@li...
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-package org.openscience.cdk.formula;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
-import org.openscience.cdk.interfaces.IIsotope;
-import org.openscience.cdk.formula.IMolecularFormula;
-
-/**
- * Class defining an adduct object in a MolecularFormula. It maintains
- * a list of list IMolecularFormula.<p>
- *
- * Examples:
- * <ul>
- * <li><code>[C2H4O2+Na]+</code></li>
- * </ul>
- *
- * @cdk.module formula
- * @author miguelrojasch
- * @cdk.created 2007-11-20
- * @cdk.keyword molecular formula
- */
-@TestClass("org.openscience.cdk.test.formula.AdductFormulaTest")
-public class AdductFormula implements Iterable<IMolecularFormula>, IAdductFormula, Cloneable{
-
- /**
- * Determines if a de-serialized object is compatible with this class.
- *
- * This value must only be changed if and only if the new version
- * of this class is imcompatible with the old version. See Sun docs
- * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
- * /serialization/spec/version.doc.html>details</a>.
- */
- private static final long serialVersionUID = -811384981700039389L;
-
- /** Internal List of IMolecularFormula. */
- private List<IMolecularFormula> components;
-
- /**
- * Constructs an empty AdductFormula.
- *
- * @see #AdductFormula(IMolecularFormula)
- */
- public AdductFormula() {
- components = new ArrayList<IMolecularFormula>();
- }
-
- /**
- * Constructs an AdductFormula with a copy AdductFormula of another
- * AdductFormula (A shallow copy, i.e., with the same objects as in
- * the original AdductFormula).
- *
- * @param formula An MolecularFormula to copy from
- * @see #AdductFormula()
- */
- public AdductFormula(IMolecularFormula formula) {
- components = new ArrayList<IMolecularFormula>();
- components.add(0, formula);
- }
-
- /**
- * Adds an molecularFormula to this chemObject.
- *
- * @param formula The molecularFormula to be added to this chemObject
- */
- @TestMethod("testAddMolecularFormula_IMolecularFormula")
- public void addMolecularFormula(IMolecularFormula formula) {
- components.add(formula);
- }
- /**
- * Adds all molecularFormulas in the AdductFormula to this chemObject.
- *
- * @param formulaSet The MolecularFormulaSet
- */
- @TestMethod("testAdd_IMolecularFormulaSet")
- public void add(IMolecularFormulaSet formulaSet) {
-
- for (IMolecularFormula mf : formulaSet.molecularFormulas()){
- addMolecularFormula(mf);
- }
- /*
- * notifyChanged() is called by addAtomContainer()
- */
- }
-
- /**
- * True, if the AdductFormula contains the given IIsotope object and not
- * the instance. The method looks for other isotopes which has the same
- * symbol, natural abundance and exact mass.
- *
- * @param isotope The IIsotope this AdductFormula is searched for
- * @return True, if the AdductFormula contains the given isotope object
- */
- @TestMethod("testContains_IIsotope")
- public boolean contains(IIsotope isotope) {
- for(Iterator<IIsotope> it = isotopes(); it.hasNext(); ) {
- IIsotope thisIsotope = it.next();
- if(isTheSame(thisIsotope, isotope)){
- return true;
- }
- }
- return false;
- }
-
- /**
- * Returns the partial charge of this Adduct. If the charge
- * has not been set the return value is Double.NaN.
- *
- * @return the charge of this Adduct
- *
- * @see #setCharge
- */
- @TestMethod("testGetCharge")
- public Double getCharge() {
- Double charge = 0.0;
- Iterator<IMolecularFormula> componentIterator = components.iterator();
- while (componentIterator.hasNext()) {
- charge += componentIterator.next().getCharge();
- }
- return charge;
- }
-
- /**
- * Checks a set of Nodes for the occurrence of the isotope in the
- * adduct formula from a particular isotope. It returns 0 if the does not exist.
- *
- * @param isotope The IIsotope to look for
- * @return The occurrence of this isotope in this adduct
- * @see #getIsotopeCount()
- */
- @TestMethod("testGetIsotopeCount_IIsotope")
- public int getIsotopeCount(IIsotope isotope) {
- int count = 0;
- Iterator<IMolecularFormula> componentIterator = components.iterator();
- while (componentIterator.hasNext()) {
- count += componentIterator.next().getIsotopeCount(isotope);
- }
- return count;
- }
-
- /**
- * Checks a set of Nodes for the number of different isotopes in the
- * adduct formula.
- *
- * @return The the number of different isotopes in this adduct formula
- * @see #getIsotopeCount(IIsotope)
- */
- @TestMethod("testGetIsotopeCount")
- public int getIsotopeCount() {
- return isotopesList().size();
- }
-
-
- /**
- * Returns an Iterator for looping over all isotopes in this adduct formula.
- *
- * @return An Iterator with the isotopes in this adduct formula
- */
- @TestMethod("testIsotopes")
- public Iterator<IIsotope> isotopes() {
- return isotopesList().iterator();
- }
-
- /**
- * Returns a List for looping over all isotopes in this adduct formula.
- *
- * @return A List with the isotopes in this adduct formula
- */
- private List<IIsotope> isotopesList() {
- List<IIsotope> isotopes = new ArrayList<IIsotope>();
- Iterator<IMolecularFormula> componentIterator = components.iterator();
- while (componentIterator.hasNext()) {
- Iterator<IIsotope> compIsotopes = componentIterator.next().isotopes();
- while (compIsotopes.hasNext()) {
- IIsotope isotope = compIsotopes.next();
- if (!isotopes.contains(isotope)) {
- isotopes.add(isotope);
- }
- }
- }
- return isotopes;
- }
-
- /**
- * No use this method. The charge is defined in each
- * IMolecularFormula.
- *
- * @param charge The partial charge
- * @deprecated
- *
- * @see #getCharge
- */
- @TestMethod("testSetCharge")
- public void setCharge(Double charge) {
- throw new java.lang.IllegalAccessError();
- }
-
- /**
- * Returns an Iterable for looping over all IMolecularFormula
- * in this adduct formula.
- *
- * @return An Iterable with the IMolecularFormula in this adduct formula
- */
- @TestMethod("testMolecularFormulas")
- public Iterable<IMolecularFormula> molecularFormulas() {
- return components;
- }
-
- /**
- * Returns an Iterator for looping over all IMolecularFormula
- * in this adduct formula.
- *
- * @return An Iterator with the IMolecularFormula in this adduct formula
- */
- @TestMethod("testIterator")
- public Iterator<IMolecularFormula> iterator() {
- return components.iterator();
- }
-
- /**
- * Returns the number of MolecularFormulas in this AdductFormula.
- *
- * @return The number of MolecularFormulas in this AdductFormula
- */
- @TestMethod("testSize")
- public int size() {
- return components.size();
- }
-
- /**
- * True, if the AdductFormula contains the given IMolecularFormula object.
- *
- * @param formula The IMolecularFormula this AdductFormula is searched for
- * @return True, if the AdductFormula contains the given IMolecularFormula object
- */
- @TestMethod("testContains_IMolecularFormula")
- public boolean contains(IMolecularFormula formula) {
- return components.contains(formula);
- }
-
- /**
- *
- * Returns the MolecularFormula at position <code>number</code> in the
- * chemObject.
- *
- * @param number The position of the IMolecularFormula to be returned.
- * @return The IMolecularFormula at position <code>number</code> .
- */
- @TestMethod("testGetMolecularFormulas_int")
- public IMolecularFormula getMolecularFormula(int position) {
- return components.get(position);
- }
-
- /**
- * Removes all IMolecularFormula from this chemObject.
- */
- @TestMethod("testRemoveAllMolecularFormulas")
- public void removeAllMolecularFormulas() {
- components.clear();
- }
-
- /**
- * Removes an IMolecularFormula from this chemObject.
- *
- * @param formula The IMolecularFormula to be removed from this chemObject
- */
- @TestMethod("testRemoveMolecularFormula_IMolecularFormula")
- public void removeMolecularFormula(IMolecularFormula formula) {
- components.remove(formula);
- }
-
- /**
- * Removes an MolecularFormula from this chemObject.
- *
- * @param pos The position of the MolecularFormula to be removed from this chemObject
- */
- @TestMethod("testRemoveMolecularFormula_int")
- public void removeMolecularFormula(int position) {
- components.remove(position);
- }
- /**
- * Clones this AdductFormula object and its content.
- *
- * @return The cloned object
- */
- @TestMethod("testClone")
- public Object clone() throws CloneNotSupportedException {
-
-// /* it is not a super class of chemObject */
-// AdductFormula clone = (AdductFormula) super.clone();
-// // start from scratch
-// clone.removeAllMolecularFormulas();
-// // clone all molecularFormulas
-// Iterator<IMolecularFormula> iterForm = this.molecularFormulas();
-// while(iterForm.hasNext()){
-// clone.addMolecularFormula((IMolecularFormula) iterForm.next().clone());
-// }
-
- AdductFormula clone = new AdductFormula();
- for(IMolecularFormula form: this.molecularFormulas()){
- clone.addMolecularFormula((IMolecularFormula) form.clone());
- }
- return clone;
- }
-
- /**
- * Compare to IIsotope. The method doesn't compare instance but if they
- * have the same symbol, natural abundance and exact mass.
- *
- * @param isotopeOne The first Isotope to compare
- * @param isotopeTwo The second Isotope to compare
- * @return True, if both isotope are the same
- */
- private boolean isTheSame(IIsotope isotopeOne, IIsotope isotopeTwo) {
-
- if(isotopeOne.getSymbol() != isotopeTwo.getSymbol() )
- return false;
- if(isotopeOne.getNaturalAbundance() != isotopeTwo.getNaturalAbundance() )
- return false;
- if(isotopeOne.getExactMass() != isotopeTwo.getExactMass() )
- return false;
-
- return true;
- }
-}
Copied: branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/AdductFormula.java (from rev 9982, trunk/cdk/src/org/openscience/cdk/formula/AdductFormula.java)
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/AdductFormula.java (rev 0)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/AdductFormula.java 2008-01-31 15:37:44 UTC (rev 9983)
@@ -0,0 +1,351 @@
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2007-09-03 12:53:05 +0200 (Mon, 03 Sep 2007) $
+ * $Revision: 8848 $
+ *
+ * Copyright (C) 2007 Miguel Rojasch <mig...@us...>
+ *
+ * Contact: cdk...@li...
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.formula;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
+import org.openscience.cdk.interfaces.IIsotope;
+import org.openscience.cdk.formula.IMolecularFormula;
+
+/**
+ * Class defining an adduct object in a MolecularFormula. It maintains
+ * a list of list IMolecularFormula.<p>
+ *
+ * Examples:
+ * <ul>
+ * <li><code>[C2H4O2+Na]+</code></li>
+ * </ul>
+ *
+ * @cdk.module formula
+ * @author miguelrojasch
+ * @cdk.created 2007-11-20
+ * @cdk.keyword molecular formula
+ */
+@TestClass("org.openscience.cdk.test.formula.AdductFormulaTest")
+public class AdductFormula implements Iterable<IMolecularFormula>, IAdductFormula, Cloneable{
+
+ /**
+ * Determines if a de-serialized object is compatible with this class.
+ *
+ * This value must only be changed if and only if the new version
+ * of this class is imcompatible with the old version. See Sun docs
+ * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
+ * /serialization/spec/version.doc.html>details</a>.
+ */
+ private static final long serialVersionUID = -811384981700039389L;
+
+ /** Internal List of IMolecularFormula. */
+ private List<IMolecularFormula> components;
+
+ /**
+ * Constructs an empty AdductFormula.
+ *
+ * @see #AdductFormula(IMolecularFormula)
+ */
+ public AdductFormula() {
+ components = new ArrayList<IMolecularFormula>();
+ }
+
+ /**
+ * Constructs an AdductFormula with a copy AdductFormula of another
+ * AdductFormula (A shallow copy, i.e., with the same objects as in
+ * the original AdductFormula).
+ *
+ * @param formula An MolecularFormula to copy from
+ * @see #AdductFormula()
+ */
+ public AdductFormula(IMolecularFormula formula) {
+ components = new ArrayList<IMolecularFormula>();
+ components.add(0, formula);
+ }
+
+ /**
+ * Adds an molecularFormula to this chemObject.
+ *
+ * @param formula The molecularFormula to be added to this chemObject
+ */
+ @TestMethod("testAddMolecularFormula_IMolecularFormula")
+ public void addMolecularFormula(IMolecularFormula formula) {
+ components.add(formula);
+ }
+ /**
+ * Adds all molecularFormulas in the AdductFormula to this chemObject.
+ *
+ * @param formulaSet The MolecularFormulaSet
+ */
+ @TestMethod("testAdd_IMolecularFormulaSet")
+ public void add(IMolecularFormulaSet formulaSet) {
+
+ for (IMolecularFormula mf : formulaSet.molecularFormulas()){
+ addMolecularFormula(mf);
+ }
+ /*
+ * notifyChanged() is called by addAtomContainer()
+ */
+ }
+
+ /**
+ * True, if the AdductFormula contains the given IIsotope object and not
+ * the instance. The method looks for other isotopes which has the same
+ * symbol, natural abundance and exact mass.
+ *
+ * @param isotope The IIsotope this AdductFormula is searched for
+ * @return True, if the AdductFormula contains the given isotope object
+ */
+ @TestMethod("testContains_IIsotope")
+ public boolean contains(IIsotope isotope) {
+ for(Iterator<IIsotope> it = isotopes(); it.hasNext(); ) {
+ IIsotope thisIsotope = it.next();
+ if(isTheSame(thisIsotope, isotope)){
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns the partial charge of this Adduct. If the charge
+ * has not been set the return value is Double.NaN.
+ *
+ * @return the charge of this Adduct
+ *
+ * @see #setCharge
+ */
+ @TestMethod("testGetCharge")
+ public Double getCharge() {
+ Double charge = 0.0;
+ Iterator<IMolecularFormula> componentIterator = components.iterator();
+ while (componentIterator.hasNext()) {
+ charge += componentIterator.next().getCharge();
+ }
+ return charge;
+ }
+
+ /**
+ * Checks a set of Nodes for the occurrence of the isotope in the
+ * adduct formula from a particular isotope. It returns 0 if the does not exist.
+ *
+ * @param isotope The IIsotope to look for
+ * @return The occurrence of this isotope in this adduct
+ * @see #getIsotopeCount()
+ */
+ @TestMethod("testGetIsotopeCount_IIsotope")
+ public int getIsotopeCount(IIsotope isotope) {
+ int count = 0;
+ Iterator<IMolecularFormula> componentIterator = components.iterator();
+ while (componentIterator.hasNext()) {
+ count += componentIterator.next().getIsotopeCount(isotope);
+ }
+ return count;
+ }
+
+ /**
+ * Checks a set of Nodes for the number of different isotopes in the
+ * adduct formula.
+ *
+ * @return The the number of different isotopes in this adduct formula
+ * @see #getIsotopeCount(IIsotope)
+ */
+ @TestMethod("testGetIsotopeCount")
+ public int getIsotopeCount() {
+ return isotopesList().size();
+ }
+
+
+ /**
+ * Returns an Iterator for looping over all isotopes in this adduct formula.
+ *
+ * @return An Iterator with the isotopes in this adduct formula
+ */
+ @TestMethod("testIsotopes")
+ public Iterator<IIsotope> isotopes() {
+ return isotopesList().iterator();
+ }
+
+ /**
+ * Returns a List for looping over all isotopes in this adduct formula.
+ *
+ * @return A List with the isotopes in this adduct formula
+ */
+ private List<IIsotope> isotopesList() {
+ List<IIsotope> isotopes = new ArrayList<IIsotope>();
+ Iterator<IMolecularFormula> componentIterator = components.iterator();
+ while (componentIterator.hasNext()) {
+ Iterator<IIsotope> compIsotopes = componentIterator.next().isotopes();
+ while (compIsotopes.hasNext()) {
+ IIsotope isotope = compIsotopes.next();
+ if (!isotopes.contains(isotope)) {
+ isotopes.add(isotope);
+ }
+ }
+ }
+ return isotopes;
+ }
+
+ /**
+ * No use this method. The charge is defined in each
+ * IMolecularFormula.
+ *
+ * @param charge The partial charge
+ * @deprecated
+ *
+ * @see #getCharge
+ */
+ @TestMethod("testSetCharge")
+ public void setCharge(Double charge) {
+ throw new java.lang.IllegalAccessError();
+ }
+
+ /**
+ * Returns an Iterable for looping over all IMolecularFormula
+ * in this adduct formula.
+ *
+ * @return An Iterable with the IMolecularFormula in this adduct formula
+ */
+ @TestMethod("testMolecularFormulas")
+ public Iterable<IMolecularFormula> molecularFormulas() {
+ return components;
+ }
+
+ /**
+ * Returns an Iterator for looping over all IMolecularFormula
+ * in this adduct formula.
+ *
+ * @return An Iterator with the IMolecularFormula in this adduct formula
+ */
+ @TestMethod("testIterator")
+ public Iterator<IMolecularFormula> iterator() {
+ return components.iterator();
+ }
+
+ /**
+ * Returns the number of MolecularFormulas in this AdductFormula.
+ *
+ * @return The number of MolecularFormulas in this AdductFormula
+ */
+ @TestMethod("testSize")
+ public int size() {
+ return components.size();
+ }
+
+ /**
+ * True, if the AdductFormula contains the given IMolecularFormula object.
+ *
+ * @param formula The IMolecularFormula this AdductFormula is searched for
+ * @return True, if the AdductFormula contains the given IMolecularFormula object
+ */
+ @TestMethod("testContains_IMolecularFormula")
+ public boolean contains(IMolecularFormula formula) {
+ return components.contains(formula);
+ }
+
+ /**
+ *
+ * Returns the MolecularFormula at position <code>number</code> in the
+ * chemObject.
+ *
+ * @param number The position of the IMolecularFormula to be returned.
+ * @return The IMolecularFormula at position <code>number</code> .
+ */
+ @TestMethod("testGetMolecularFormulas_int")
+ public IMolecularFormula getMolecularFormula(int position) {
+ return components.get(position);
+ }
+
+ /**
+ * Removes all IMolecularFormula from this chemObject.
+ */
+ @TestMethod("testRemoveAllMolecularFormulas")
+ public void removeAllMolecularFormulas() {
+ components.clear();
+ }
+
+ /**
+ * Removes an IMolecularFormula from this chemObject.
+ *
+ * @param formula The IMolecularFormula to be removed from this chemObject
+ */
+ @TestMethod("testRemoveMolecularFormula_IMolecularFormula")
+ public void removeMolecularFormula(IMolecularFormula formula) {
+ components.remove(formula);
+ }
+
+ /**
+ * Removes an MolecularFormula from this chemObject.
+ *
+ * @param pos The position of the MolecularFormula to be removed from this chemObject
+ */
+ @TestMethod("testRemoveMolecularFormula_int")
+ public void removeMolecularFormula(int position) {
+ components.remove(position);
+ }
+ /**
+ * Clones this AdductFormula object and its content.
+ *
+ * @return The cloned object
+ */
+ @TestMethod("testClone")
+ public Object clone() throws CloneNotSupportedException {
+
+// /* it is not a super class of chemObject */
+// AdductFormula clone = (AdductFormula) super.clone();
+// // start from scratch
+// clone.removeAllMolecularFormulas();
+// // clone all molecularFormulas
+// Iterator<IMolecularFormula> iterForm = this.molecularFormulas();
+// while(iterForm.hasNext()){
+// clone.addMolecularFormula((IMolecularFormula) iterForm.next().clone());
+// }
+
+ AdductFormula clone = new AdductFormula();
+ for(IMolecularFormula form: this.molecularFormulas()){
+ clone.addMolecularFormula((IMolecularFormula) form.clone());
+ }
+ return clone;
+ }
+
+ /**
+ * Compare to IIsotope. The method doesn't compare instance but if they
+ * have the same symbol, natural abundance and exact mass.
+ *
+ * @param isotopeOne The first Isotope to compare
+ * @param isotopeTwo The second Isotope to compare
+ * @return True, if both isotope are the same
+ */
+ private boolean isTheSame(IIsotope isotopeOne, IIsotope isotopeTwo) {
+
+ if(isotopeOne.getSymbol() != isotopeTwo.getSymbol() )
+ return false;
+ if(isotopeOne.getNaturalAbundance() != isotopeTwo.getNaturalAbundance() )
+ return false;
+ if(isotopeOne.getExactMass() != isotopeTwo.getExactMass() )
+ return false;
+
+ return true;
+ }
+}
Deleted: branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IAdductFormula.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/formula/IAdductFormula.java 2008-01-31 10:07:16 UTC (rev 9982)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IAdductFormula.java 2008-01-31 15:37:44 UTC (rev 9983)
@@ -1,105 +0,0 @@
-/* $RCSfile$
- * $Author: egonw $
- * $Date: 2007-09-03 12:53:05 +0200 (Mon, 03 Sep 2007) $
- * $Revision: 8848 $
- *
- * Copyright (C) 2007 Miguel Rojasch <mig...@us...>
- *
- * Contact: cdk...@li...
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-package org.openscience.cdk.formula;
-
-import java.util.Iterator;
-
-import org.openscience.cdk.interfaces.IIsotope;
-
-/**
- * Class defining an adduct object in a MolecularFormula. It maintains
- * a list of list IMolecularFormula.<p>
- *
- * Examples:
- * <ul>
- * <li><code>[C2H4O2+Na]+</code></li>
- * </ul>
- *
- * @cdk.module formula
- * @author miguelrojasch
- * @cdk.created 2007-11-20
- * @cdk.keyword molecular formula
- */
-public interface IAdductFormula extends IMolecularFormulaSet{
-
- /**
- * Checks a set of Nodes for the occurrence of the isotope in the
- * adduct formula from a particular isotope. It returns 0 if the does not exist.
- *
- * @param isotope The IIsotope to look for
- * @return The occurrence of this isotope in this adduct
- * @see #getIsotopeCount()
- */
- public int getIsotopeCount(IIsotope isotope);
-
- /**
- * Checks a set of Nodes for the number of different isotopes in the
- * adduct formula.
- *
- * @return The the number of different isotopes in this adduct formula
- * @see #getIsotopeCount(IIsotope)
- */
- public int getIsotopeCount();
-
- /**
- * Returns an Iterator for looping over all isotopes in this adduct formula.
- *
- * @return An Iterator with the isotopes in this adduct formula
- */
- public Iterator<IIsotope> isotopes();
-
- /**
- * Returns the partial charge of this Adduct. If the charge
- * has not been set the return value is Double.NaN.
- *
- * @return the charge of this Adduct
- *
- * @see #setCharge
- */
- public Double getCharge();
-
- /**
- * True, if the AdductFormula contains the given IIsotope object.
- *
- * @param isotope The IIsotope this AdductFormula is searched for
- * @return True, if the AdductFormula contains the given isotope object
- */
- public boolean contains(IIsotope isotope);
-
- /**
- * Sets the partial charge of this adduct formula.
- *
- * @param charge The partial charge
- *
- * @see #getCharge
- */
- public void setCharge(Double charge) ;
-
- /**
- * Clones this IAdductFormula object and its content.
- *
- * @return The cloned object
- */
- public Object clone() throws CloneNotSupportedException ;
-}
Copied: branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IAdductFormula.java (from rev 9982, trunk/cdk/src/org/openscience/cdk/formula/IAdductFormula.java)
===================================================================
--- branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IAdductFormula.java (rev 0)
+++ branches/miguelrojasch/reaction/src/org/openscience/cdk/formula/IAdductFormula.java 2008-01-31 15:37:44 UTC (rev 9983)
@@ -0,0 +1,105 @@
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2007-09-03 12:53:05 +0200 (Mon, 03 Sep 2007) $
+ * $Revision: 8848 $
+ *
+ * Copyright (C) 2007 Miguel Rojasch <mig...@us...>
+ *
+ * Contact: cdk...@li...
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.formula;
+
+import java.util.Iterator;
+
+import org.openscience.cdk.interfaces.IIsotope;
+
+/**
+ * Class defining an adduct object in a MolecularFormula. It maintains
+ * a list of list IMolecularFormula.<p>
+ *
+ * Examples:
+ * <ul>
+ * <li><code>[C2H4O2+Na]+</code></li>
+ * </ul>
+ *
+ * @cdk.module formula
+ * @author miguelrojasch
+ * @cdk.created 2007-11-20
+ * @cdk.keyword molecular formula
+ */
+public interface IAdductFormula extends IMolecularFormulaSet{
+
+ /**
+ * Checks a set of Nodes for the occurrence of the isotope in the
+ * adduct formula from a particular isotope. It returns 0 if the does not exist.
+ *
+ * @param isotope The IIsotope to look for
+ * @return The occurrence of this isotope in this adduct
+ * @see #getIsotopeCount()
+ */
+ public int getIsotopeCount(IIsotope isotope);
+
+ /**
+ * Checks a set of Nodes for the number of different isotopes in the
+ * adduct formula.
+...
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