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[Cdk-commits] SF.net SVN: cdk:[12456] cdk/trunk
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From: <eg...@us...> - 2008-09-24 10:18:33
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Revision: 12456
http://cdk.svn.sourceforge.net/cdk/?rev=12456&view=rev
Author: egonw
Date: 2008-09-24 10:18:00 +0000 (Wed, 24 Sep 2008)
Log Message:
-----------
Merged with branch cdk-1.2.x
Modified Paths:
--------------
cdk/trunk/.classpath
cdk/trunk/META-INF/MANIFEST.MF
cdk/trunk/build.properties
cdk/trunk/build.xml
cdk/trunk/src/META-INF/test-libiocml.cdkdepends
cdk/trunk/src/main/org/openscience/cdk/Association.java
cdk/trunk/src/main/org/openscience/cdk/CDKConstants.java
cdk/trunk/src/main/org/openscience/cdk/FragmentAtom.java
cdk/trunk/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
cdk/trunk/src/main/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
cdk/trunk/src/main/org/openscience/cdk/atomtype/mapper/AtomTypeMapper.java
cdk/trunk/src/main/org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java
cdk/trunk/src/main/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingHandler.java
cdk/trunk/src/main/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java
cdk/trunk/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl
cdk/trunk/src/main/org/openscience/cdk/fingerprint/Fingerprinter.java
cdk/trunk/src/main/org/openscience/cdk/fingerprint/GraphOnlyFingerprinter.java
cdk/trunk/src/main/org/openscience/cdk/geometry/alignment/KabschAlignment.java
cdk/trunk/src/main/org/openscience/cdk/graph/PathTools.java
cdk/trunk/src/main/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java
cdk/trunk/src/main/org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
cdk/trunk/src/main/org/openscience/cdk/inchi/InChIGenerator.java
cdk/trunk/src/main/org/openscience/cdk/index/CASNumber.java
cdk/trunk/src/main/org/openscience/cdk/interfaces/IAtomType.java
cdk/trunk/src/main/org/openscience/cdk/interfaces/IChemObjectBuilder.java
cdk/trunk/src/main/org/openscience/cdk/interfaces/IElement.java
cdk/trunk/src/main/org/openscience/cdk/io/CMLWriter.java
cdk/trunk/src/main/org/openscience/cdk/io/ReaderFactory.java
cdk/trunk/src/main/org/openscience/cdk/io/SMILESReader.java
cdk/trunk/src/main/org/openscience/cdk/io/cml/CMLCoreModule.java
cdk/trunk/src/main/org/openscience/cdk/io/cml/PDBConvention.java
cdk/trunk/src/main/org/openscience/cdk/io/iterator/IteratingSMILESReader.java
cdk/trunk/src/main/org/openscience/cdk/libio/cml/Convertor.java
cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java
cdk/trunk/src/main/org/openscience/cdk/similarity/Tanimoto.java
cdk/trunk/src/main/org/openscience/cdk/smiles/DeduceBondSystemTool.java
cdk/trunk/src/main/org/openscience/cdk/smiles/SmilesGenerator.java
cdk/trunk/src/main/org/openscience/cdk/smiles/SmilesParser.java
cdk/trunk/src/main/org/openscience/cdk/tools/CDKHydrogenAdder.java
cdk/trunk/src/main/org/openscience/cdk/tools/CDKValencyChecker.java
cdk/trunk/src/main/org/openscience/cdk/tools/HOSECodeGenerator.java
cdk/trunk/src/main/org/openscience/cdk/tools/Normalizer.java
cdk/trunk/src/main/org/openscience/cdk/tools/PeriodicTable.java
cdk/trunk/src/main/org/openscience/cdk/tools/SaturationChecker.java
cdk/trunk/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java
cdk/trunk/src/main/org/openscience/cdk/tools/diff/AtomDiff.java
cdk/trunk/src/main/org/openscience/cdk/tools/diff/ElementDiff.java
cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/BondManipulator.java
cdk/trunk/src/test/org/openscience/cdk/AssociationTest.java
cdk/trunk/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
cdk/trunk/src/test/org/openscience/cdk/charges/AtomTypeChargesTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/AtomtypeCoverageTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/CoverageAnnotationTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/ExtraCoverageTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/InchiCoverageTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/QsarproteinCoverageTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/ReactionCoverageTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/SmilesCoverageTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/ValencycheckCoverageTest.java
cdk/trunk/src/test/org/openscience/cdk/fingerprint/FingerprinterTest.java
cdk/trunk/src/test/org/openscience/cdk/fingerprint/MACCSFingerprinterTest.java
cdk/trunk/src/test/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java
cdk/trunk/src/test/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java
cdk/trunk/src/test/org/openscience/cdk/graph/matrix/AdjacencyMatrixTest.java
cdk/trunk/src/test/org/openscience/cdk/inchi/InChIGeneratorTest.java
cdk/trunk/src/test/org/openscience/cdk/index/CASNumberTest.java
cdk/trunk/src/test/org/openscience/cdk/io/cml/CML23FragmentsTest.java
cdk/trunk/src/test/org/openscience/cdk/io/cml/CML2Test.java
cdk/trunk/src/test/org/openscience/cdk/io/cml/CML2WriterTest.java
cdk/trunk/src/test/org/openscience/cdk/io/cml/CMLRoundTripTest.java
cdk/trunk/src/test/org/openscience/cdk/io/cml/cml23TestFramework.xml
cdk/trunk/src/test/org/openscience/cdk/io/iterator/IteratingSMILESReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MextraTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MlibiocmlTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MreactionTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MsmilesTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MstandardTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MvalencycheckTests.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorChargeTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMassTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizabilityTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/similarity/TanimotoTest.java
cdk/trunk/src/test/org/openscience/cdk/smiles/SmilesGeneratorTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/CDKHydrogenAdderTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/CDKValencyCheckerTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogens.java
cdk/trunk/src/test/org/openscience/cdk/tools/HOSECodeGeneratorTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/NormalizerTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/SaturationCheckerTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java
Added Paths:
-----------
cdk/trunk/jar/jumbo-with-fix-by-jonalv.jar
cdk/trunk/src/test/data/cml/olaCmlAtomType.cml
cdk/trunk/src/test/org/openscience/cdk/io/cml/CDKRoundTripTest.java
cdk/trunk/src/test/org/openscience/cdk/io/cml/CMLRoundTripTool.java
Modified: cdk/trunk/.classpath
===================================================================
--- cdk/trunk/.classpath 2008-09-24 09:46:12 UTC (rev 12455)
+++ cdk/trunk/.classpath 2008-09-24 10:18:00 UTC (rev 12456)
@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
+ <classpathentry exported="true" kind="lib" path="jar/jumbo-with-fix-by-jonalv.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
<classpathentry kind="src" path="src/main"/>
Modified: cdk/trunk/META-INF/MANIFEST.MF
===================================================================
--- cdk/trunk/META-INF/MANIFEST.MF 2008-09-24 09:46:12 UTC (rev 12455)
+++ cdk/trunk/META-INF/MANIFEST.MF 2008-09-24 10:18:00 UTC (rev 12456)
@@ -1,8 +1,8 @@
Manifest-Version: 1.0
Bundle-ManifestVersion: 2
-Bundle-Name: CDK plugin
+Bundle-Name: Chemistry Development Kit (CDK)
Bundle-SymbolicName: org.openscience.cdk;singleton:=true
-Bundle-Version: 1.1.0.A20080903
+Bundle-Version: 1.1.0.A20080911
Bundle-Vendor: The Chemistry Development Kit Project
Bundle-ActivationPolicy: lazy
Export-Package: javax.vecmath,
@@ -121,4 +121,4 @@
develjar/com-sun-tools-doclets-Taglet.jar,
develjar/junit-4.3.1.jar,
jar/xercesImpl.jar,
- jar/jumbo-5.4.2-b2.jar
+ jar/jumbo-with-fix-by-jonalv.jar
Modified: cdk/trunk/build.properties
===================================================================
--- cdk/trunk/build.properties 2008-09-24 09:46:12 UTC (rev 12455)
+++ cdk/trunk/build.properties 2008-09-24 10:18:00 UTC (rev 12456)
@@ -7,4 +7,5 @@
develjar/com-sun-tools-doclets-Taglet.jar,\
develjar/com-sun-javadoc.jar,\
META-INF/MANIFEST.MF,\
+ jar/jumbo-with-fix-by-jonalv.jar
Modified: cdk/trunk/build.xml
===================================================================
--- cdk/trunk/build.xml 2008-09-24 09:46:12 UTC (rev 12455)
+++ cdk/trunk/build.xml 2008-09-24 10:18:00 UTC (rev 12456)
@@ -85,6 +85,38 @@
<echo message=" optimization: ${optimization}" />
</target>
+ <!-- Tasks that will be used to clean up ${basedir} after test runs.
+ We only cleanup files in the top level directory, but keep the
+ cdk.log file, ince it might be important for debugging
+ -->
+
+ <target id="tcSnapshot" name="tcSnapshot">
+ <copy todir="oldfiles" includeEmptyDirs="false">
+ <fileset dir="${basedir}" includes="*" excludes="cdk.log"/>
+ </copy>
+ </target>
+
+ <target id="tcCleanup" name="tcCleanup">
+ <copy todir="newfiles" includeEmptyDirs="false">
+ <fileset dir="${basedir}" includes="*" excludes="cdk.log"/>
+ </copy>
+ <foreach target="tcRemoveNewFiles" param="file.to.delete">
+ <path>
+ <fileset id="result" dir="newfiles">
+ <different targetdir="oldfiles" ignoreFileTimes="true"/>
+ </fileset>
+ </path>
+ </foreach>
+ <delete dir="oldfiles"/>
+ <delete dir="newfiles"/>
+ </target>
+
+ <target name="tcRemoveNewFiles">
+ <basename property="file.basename" file="${file.to.delete}"/>
+ <delete file="${file.basename}"/>
+ </target>
+
+ <!-- See what platform were on -->
<target id="checkPlatforms" name="checkPlatforms">
<condition property="isMacOsX">
<and>
@@ -1030,7 +1062,10 @@
if="junit.present">
<echo message="Testing classes for CDK's ${module} module." />
-
+
+ <!-- take the directory snapshot -->
+ <antcall target="tcSnapshot" />
+
<!-- check for availability for meta info files -->
<available file="${metainf}/test-${module}.cdkdepends" property="module.cdkdepends.present"/>
<available file="${metainf}/test-${module}.libdepends" property="module.libdepends.present"/>
@@ -1065,7 +1100,11 @@
<formatter type="brief" />
</test>
</junit>
- </target>
+
+ <!-- cleanup after ourselves -->
+ <antcall target="tcCleanup" />
+
+ </target>
<target id="test-all" name="test-all" depends="noJunit, dist-all, test-dist-all, jarTestdata"
description="Performs a full JUnit test for the CDK."
Added: cdk/trunk/jar/jumbo-with-fix-by-jonalv.jar
===================================================================
--- cdk/trunk/jar/jumbo-with-fix-by-jonalv.jar (rev 0)
+++ cdk/trunk/jar/jumbo-with-fix-by-jonalv.jar 2008-09-24 10:18:00 UTC (rev 12456)
@@ -0,0 +1,15669 @@
+PK
+ |