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[Cdk-commits] SF.net SVN: cdk: [7620] trunk/cdk-taverna
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From: <tho...@us...> - 2007-01-04 10:17:03
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Revision: 7620
http://svn.sourceforge.net/cdk/?rev=7620&view=rev
Author: thomaskuhn
Date: 2007-01-04 02:16:56 -0800 (Thu, 04 Jan 2007)
Log Message:
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Initial Import of the new maven based cdk-taverna project. This is still under construction so not all old features are currently working!
Added Paths:
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trunk/cdk-taverna/.classpath
trunk/cdk-taverna/.project
trunk/cdk-taverna/ChangeLog
trunk/cdk-taverna/Data/Test_Errors/AtomHybridizationProblem.txt_1166617111900_18151.cml
trunk/cdk-taverna/LICENSE
trunk/cdk-taverna/README
trunk/cdk-taverna/pom.xml
trunk/cdk-taverna/src/
trunk/cdk-taverna/src/main/
trunk/cdk-taverna/src/main/java/
trunk/cdk-taverna/src/main/java/org/
trunk/cdk-taverna/src/main/java/org/openscience/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/CDKTavernaConfig.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/CMLChemFile.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/LocalWorkerCDK.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/aromaticity/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/aromaticity/DetectHueckelAromaticity.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/atomtype/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/atomtype/PerceiveMM2AtomTypes.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/atomtype/PerceiveMMFF94AtomTypes.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/basicutilities/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/basicutilities/CMLChemFileWrapper.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/basicutilities/FileNameGenerator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/basicutilities/StringDoubleConverter.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/bioclipse/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/bioclipse/BioclipseResultViewer.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/charges/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/charges/PartialChargesCalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/filters/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/filters/Has2DCoordinates.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/filters/Has3DCoordinates.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/fingerprint/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/fingerprint/FingerprintCalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/fingerprint/FingerprintCalculatorAPI.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/CDKIOFileWriter.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/CDKIOReader.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/CDKIOReaderIterator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/CDKIOWriter.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/ReadMDLMolFile.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/ReadMDLRXNFile.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/ReadMDLRXNV3000File.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/ReadMDLSDFile.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/ReadSMILESFromFile.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/WriteToMDLMolFile.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/io/writeCMLChemFileToFile.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/isomorphism/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/isomorphism/SubstructureFilter.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/layout/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/layout/StructureDiagramCreator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/modeling/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/modeling/Model3DBuilders.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/modeling/Model3DBuildersWithMM2ForceField.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/modeling/Model3DBuildersWithMMFF94ForceField.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/DescriptorCalculatorLocalWorker.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomCount.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomDegree.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomHybridization.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomHybridizationVSEPR.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomValence.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/BondsToAtom.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/CovalentRadius.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/DistanceToAtom.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/EffectiveAtomPolarizability.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/IPAtomic.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/InductiveAtomicHardness.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/InductiveAtomicSoftness.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/IsProtonInAromaticSystem.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/IsProtonInConjugatedPiSystem.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PartialPiCharge.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PartialSigmaCharge.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PartialTChargeMMFF94.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PartialTChargePEOE.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PeriodicTablePosition.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PiElectronegativity.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/ProtonTotalPartialCharge.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/RDFProton.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/SigmaElectronegativity.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/VdWRadius.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/Weight.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondCount.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialPiCharge.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialSigmaCharge.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialTCharge.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondSigmaElectronegativity.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/ResonancePositiveCharge.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/APol.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCount.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticAtomsCount.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticBondsCount.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BCUTCalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BPol.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CPSACalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CarbonConnectivityOrderOne.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CarbonConnectivityOrderZero.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiChain.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiCluster.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiPath.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiPathCluster.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/EccentricConnectivityIndex.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/GraviationalIndexCalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/HBondAcceptorCount.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/HBondDonorCount.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/IPMolecular.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/KappaShapeIndicesCalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LargestChain.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LargestPiSystem.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LengthOverBreadth.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LongestAliphaticChain.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/MDE.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/MomentOfInertia.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/PetitjeanNumberCalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/PetitjeanShapeIndex.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/RotatableBondsCount.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/RuleOfFiveFilter.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/TPSACalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/TaeAminoAcid.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/VAdjMa.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ValenceCarbonConnectivityOrderOne.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ValenceCarbonConnectivityOrderZero.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WHIMCalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WeightedPath.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WienerNumbers.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/XLogPCalculator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ZagrebIndex.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/reactionevaluator/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/reactionevaluator/ReactionEvaluator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/renderers/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/renderers/CDK2DRenderer.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/smiles/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESGenerator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESParser.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/smiles/SmilesTools.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/structgen/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/structgen/StructureDiagramGenerator.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/tools/
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/tools/CloningCMLChemFile.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/tools/HydrogenTools.java
trunk/cdk-taverna/src/main/resources/
trunk/cdk-taverna/src/main/resources/META-INF/
trunk/cdk-taverna/src/main/resources/META-INF/services/
trunk/cdk-taverna/src/main/resources/META-INF/services/org.embl.ebi.escience.scuflworkers.java.LocalWorker
trunk/cdk-taverna/src/main/resources/localworkers.properties
trunk/cdk-taverna/src/main/resources/taverna.properties
trunk/cdk-taverna/src/test/
trunk/cdk-taverna/src/test/java/
trunk/cdk-taverna/src/test/java/org/
trunk/cdk-taverna/src/test/java/org/openscience/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/CDKTavernaTestCases.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/CDKTavernaTests.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/TavernaTestData.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/aromaticity/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/aromaticity/DetectHueckelAromaticityTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/basicutilities/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/basicutilities/StringDoubleConverterTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/bioclipse/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/bioclipse/BioclipseResultViewerTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/io/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/io/CDKIOFileWriterTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/io/CDKIOReaderTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/io/WriteToMDLMolFileTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/isomorphism/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/isomorphism/SubstructureFilterTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/modeling/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/modeling/Model3DBuildersWithMM2ForceFieldTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/modeling/Model3DBuildersWithMMFF94ForceFieldTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/DescriptorCalculatorLocalWorkerTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomDegreeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomHybridizationTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomHybridizationVSEPRTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/AtomValenceTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/BondsToAtomTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/CovalentRadiusTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/DistanceToAtomTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/EffectiveAtomPolarizabilityTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/IPAtomicTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/InductiveAtomicHardnessTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/InductiveAtomicSoftnessTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/IsProtonInAromaticSystemTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PartialPiChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PartialSigmaChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PartialTChargeMMFF94Test.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PartialTChargePEOETest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PeriodicTablePositionTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PiContactDetectionTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/PiElectronegativityTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/ProtonTotalPartialChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/RDFProtonTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/SigmaElectronegativityTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/VdWRadiusTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/atomic/WeightTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialPiChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialSigmaChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondPartialTChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/BondSigmaElectronegativityTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/bond/ResonancePositiveChargeTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/APolTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AminoAcidCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticAtomsCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/AromaticBondsCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BCUTCalculatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/BPolTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CPSACalculatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CarbonConnectivityOrderOneTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/CarbonConnectivityOrderZeroTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiChainTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiClusterTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiPathClusterTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ChiPathTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/EccentricConnectivityIndexTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/GraviationalIndexCalculatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/HBondAcceptorCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/HBondDonorCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/IPMolecularTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/KappaShapeIndicesCalculatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LargestChainTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LargestPiSystemTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LengthOverBreadthTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/LongestAliphaticChainTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/MDETest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/MomentOfInertiaTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/PetitjeanNumberCalculatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/PetitjeanShapeIndexTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/RotatableBondsCountTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/RuleOfFiveTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/TPSACalculatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/TaeAminoAcidTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/VAdjMaTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ValenceCarbonConnectivityOrderOneTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ValenceCarbonConnectivityOrderZeroTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WHIMCalculatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WeightedPathTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/WienerNumbersTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/XLogPCalculatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/qsar/descriptors/molecular/ZagrebIndexTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/reactionevaluator/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/reactionevaluator/ReactionEvaluatorTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/smiles/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/smiles/SmilesToolsTest.java
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/tools/
trunk/cdk-taverna/src/test/java/org/openscience/cdk/applications/taverna/tools/CloningCMLChemFileTest.java
Added: trunk/cdk-taverna/.classpath
===================================================================
--- trunk/cdk-taverna/.classpath (rev 0)
+++ trunk/cdk-taverna/.classpath 2007-01-04 10:16:56 UTC (rev 7620)
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="src/main/java"/>
+ <classpathentry kind="src" path="src/test/java"/>
+ <classpathentry excluding="**" kind="src" output="src/main/resources" path="src/main/resources"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Added: trunk/cdk-taverna/.project
===================================================================
--- trunk/cdk-taverna/.project (rev 0)
+++ trunk/cdk-taverna/.project 2007-01-04 10:16:56 UTC (rev 7620)
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>cdk-taverna</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.maven.ide.eclipse.maven2Builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.maven.ide.eclipse.maven2Nature</nature>
+ </natures>
+</projectDescription>
Added: trunk/cdk-taverna/ChangeLog
===================================================================
--- trunk/cdk-taverna/ChangeLog (rev 0)
+++ trunk/cdk-taverna/ChangeLog 2007-01-04 10:16:56 UTC (rev 7620)
@@ -0,0 +1,76 @@
+Statistics:
+---------------------------------
+ 2 Renderer
+78 LocalWorker processors
+19 APIConsumer processors
+
+74 Unit-Test
+0 Errors
+6 Fail (Main reason are the missing 3D coordinates of the test data set)
+
+20070103
+---------------------------------
+* Major Change of the build system to Maven
+* So some old feature are currently missing or commented out
+
+20060704
+---------------------------------
+* Integrate the current cdk.jar
+* Update to the taverna version 1.4
+* Added all new QSAR descriptors, integrate the QSAR bond package
+* Integrate a linear regression model -> uses a connection to 'R' via the JRI
+
+20060418
+---------------------------------
+* Added all available Atomic QSAR - Descriptors of the cdk
+* Added all available Molecular QSAR - Descriptors of the cdk
+* Changes the package structure to get it consitent
+
+20060326
+---------------------------------
+* Changes the QSAR Descriptors to local worker
+* Added Junit tests for the apiconsumer and local worker
+* Added a Detect Hueckel Aromaticity local worker
+* Added a FileWriter local worker which output a cml file
+* Added a smiles generator
+* Added a CloneCMLChemfile local worker
+
+20051229
+---------------------------------
+* Pass around CMLChemFile instead of a CML string
+* Removed old workflow examples
+
+20051018
+---------------------------------
+* Added a build.xml to be able to create a distributable jar
+* Renamed APIConsumer XML and include it in the jar so that
+ Taverna picks it up automatically
+
+20051017
+---------------------------------
+* Added a number of QSAR descriptors as separate processors
+* Added two filters: has3DCoordinates and has2DCoordinates
+* Relicensed rest of the code to LGPL
+
+20051016
+---------------------------------
+* Relicensed most of the code to LGPL as requested
+* Added a processors: RuleOfFiveFilter, FingerPrinter,
+ PerceiveMMFF94AtomTypes
+
+20051008
+---------------------------------
+* added a LocalWorker for perceiving MM2 atom types
+
+20050930
+---------------------------------
+* added new processors:
+ - reading of SMILES files
+ - building of 3D models using MM2 and MMFF94 force fields
+ - adding explicit hydrogens
+* added two new example workflows, including one that uses
+ WWMM web services
+
+20050927
+---------------------------------
+* refactored to pass CML strings between processors
Added: trunk/cdk-taverna/Data/Test_Errors/AtomHybridizationProblem.txt_1166617111900_18151.cml
===================================================================
--- trunk/cdk-taverna/Data/Test_Errors/AtomHybridizationProblem.txt_1166617111900_18151.cml (rev 0)
+++ trunk/cdk-taverna/Data/Test_Errors/AtomHybridizationProblem.txt_1166617111900_18151.cml 2007-01-04 10:16:56 UTC (rev 7620)
@@ -0,0 +1,247 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="C" formalCharge="0" hydrogenCount="3"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="3"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="S"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="O" formalCharge="-1" hydrogenCount="1"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a3" elementType="C" formalCharge="0" hydrogenCount="3"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="S"/>
+ <bond id="b2" atomRefs2="a3 a2" order="S"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="O" formalCharge="0" hydrogenCount="0"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="3"/>
+ <atom id="a3" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a4" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a5" elementType="C" formalCharge="0" hydrogenCount="3"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="S"/>
+ <bond id="b2" atomRefs2="a3 a1" order="S"/>
+ <bond id="b3" atomRefs2="a4 a3" order="S"/>
+ <bond id="b4" atomRefs2="a5 a4" order="S"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="C" formalCharge="0" hydrogenCount="0"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a3" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="D"/>
+ <bond id="b2" atomRefs2="a3 a1" order="D"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="O" formalCharge="-1" hydrogenCount="1"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a3" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a4" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a5" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a6" elementType="C" formalCharge="0" hydrogenCount="0"/>
+ <atom id="a7" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a8" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a9" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a10" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a11" elementType="C" formalCharge="0" hydrogenCount="0"/>
+ <atom id="a12" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a13" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="S"/>
+ <bond id="b2" atomRefs2="a3 a2" order="S"/>
+ <bond id="b3" atomRefs2="a4 a3" order="D"/>
+ <bond id="b4" atomRefs2="a5 a4" order="S"/>
+ <bond id="b5" atomRefs2="a6 a5" order="S"/>
+ <bond id="b6" atomRefs2="a7 a6" order="A"/>
+ <bond id="b7" atomRefs2="a8 a7" order="A"/>
+ <bond id="b8" atomRefs2="a9 a8" order="A"/>
+ <bond id="b9" atomRefs2="a10 a9" order="A"/>
+ <bond id="b10" atomRefs2="a11 a10" order="A"/>
+ <bond id="b11" atomRefs2="a11 a6" order="A"/>
+ <bond id="b12" atomRefs2="a12 a11" order="S"/>
+ <bond id="b13" atomRefs2="a13 a12" order="D"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="O" formalCharge="0" hydrogenCount="0"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a3" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a4" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a5" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a6" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a7" elementType="N" formalCharge="0" hydrogenCount="2"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="S"/>
+ <bond id="b2" atomRefs2="a3 a2" order="S"/>
+ <bond id="b3" atomRefs2="a4 a3" order="D"/>
+ <bond id="b4" atomRefs2="a5 a1" order="S"/>
+ <bond id="b5" atomRefs2="a6 a5" order="S"/>
+ <bond id="b6" atomRefs2="a7 a6" order="S"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="C" formalCharge="0" hydrogenCount="3"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a3" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a4" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a5" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a6" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a7" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a8" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a9" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a10" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a11" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a12" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a13" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a14" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a15" elementType="C" formalCharge="0" hydrogenCount="3"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="S"/>
+ <bond id="b2" atomRefs2="a3 a2" order="S"/>
+ <bond id="b3" atomRefs2="a4 a3" order="S"/>
+ <bond id="b4" atomRefs2="a5 a4" order="S"/>
+ <bond id="b5" atomRefs2="a6 a5" order="S"/>
+ <bond id="b6" atomRefs2="a7 a6" order="S"/>
+ <bond id="b7" atomRefs2="a8 a7" order="S"/>
+ <bond id="b8" atomRefs2="a9 a8" order="S"/>
+ <bond id="b9" atomRefs2="a10 a9" order="S"/>
+ <bond id="b10" atomRefs2="a11 a10" order="S"/>
+ <bond id="b11" atomRefs2="a12 a11" order="S"/>
+ <bond id="b12" atomRefs2="a13 a12" order="S"/>
+ <bond id="b13" atomRefs2="a14 a13" order="S"/>
+ <bond id="b14" atomRefs2="a15 a14" order="S"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="O" formalCharge="-1" hydrogenCount="1"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a3" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a4" elementType="C" formalCharge="0" hydrogenCount="1"/>
+ <atom id="a5" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a6" elementType="O" formalCharge="0" hydrogenCount="1"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="S"/>
+ <bond id="b2" atomRefs2="a3 a2" order="S"/>
+ <bond id="b3" atomRefs2="a4 a3" order="D"/>
+ <bond id="b4" atomRefs2="a5 a4" order="S"/>
+ <bond id="b5" atomRefs2="a6 a5" order="S"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<cml dictRef="cdk:document" xmlns="http://www.xml-cml.org/schema">
+ <list dictRef="cdk:sequence">
+ <list dictRef="cdk:model">
+ <list>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a1" elementType="N" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a2" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a3" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a4" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a5" elementType="C" formalCharge="0" hydrogenCount="2"/>
+ <atom id="a6" elementType="N" formalCharge="0" hydrogenCount="2"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a2 a1" order="S"/>
+ <bond id="b2" atomRefs2="a3 a2" order="S"/>
+ <bond id="b3" atomRefs2="a4 a3" order="S"/>
+ <bond id="b4" atomRefs2="a5 a4" order="S"/>
+ <bond id="b5" atomRefs2="a6 a5" order="S"/>
+ </bondArray>
+ </molecule>
+ </list>
+ </list>
+ </list>
+</cml>
Added: trunk/cdk-taverna/LICENSE
===================================================================
--- trunk/cdk-taverna/LICENSE (rev 0)
+++ trunk/cdk-taverna/LICENSE 2007-01-04 10:16:56 UTC (rev 7620)
@@ -0,0 +1,458 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
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+ Everyone is permitted to copy and distribute verbatim copies
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