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extra.javafiles
META-INF
- MANIFEST.MF
org
- openscience
  - cdk
    - Association.java
    - atomtype
      - MM2AtomTypeMatcher.java
      - MMFF94AtomTypeMatcher.java
    - config
      - data
        electroneg-pauling.txt
        radii-covalent.txt
        radii-vdw.txt
      - ElementPTFactory.java
      - elements
        ElementPTHandler.java
        ElementPTReader.java
      - Elements.java
    - dict
      - data
        cdk.xml
        chemical.xml
        descriptor-algorithms.owl
        emboss.xml
        reaction-processes.owl
    - EnzymeResidueLocator.java
    - exception
      - IncorrectUseOfCDKCoreClassError.java
    - fingerprint
      - data
        maccs.txt
    - geometry
      - alignment
        KabschAlignment.java
      - AtomTools.java
      - IRDFWeightFunction.java
      - Projector.java
      - RDFCalculator.java
      - surface
        NeighborList.java
        NumericalSurface.java
        Tessellate.java
        Triangle.java
    - graph
      - AtomContainerAtomPermutor.java
      - AtomContainerBondPermutor.java
      - AtomContainerPermutor.java
      - invariant
        EquivalentClassPartitioner.java
        exception
        BadMatrixFormatException.java
        IndexOutOfBoundsException.java
        MatrixNotInvertibleException.java
        GIMatrix.java
        HuLuIndexTool.java
      - matrix
        TopologicalMatrix.java
    - index
      - CASNumber.java
    - io
      - CrystClustReader.java
      - CrystClustWriter.java
      - GamessReader.java
      - inchi
        INChIContentProcessorTool.java
        INChIHandler.java
      - INChIPlainTextReader.java
      - INChIReader.java
      - iterator
        IteratingMDLConformerReader.java
      - random
        IRandomAccessChemObjectReader.java
        RandomAccessReader.java
        RandomAccessSDFReader.java
      - ShelXWriter.java
      - VASPReader.java
      - ZMatrixReader.java
    - iupac
      - parser
        AttachedGroup.java
        MoleculeBuilder.java
        NomParser.java
        NomParserConstants.java
        NomParserTokenManager.java
        ParseException.java
        SimpleCharStream.java
        Token.java
        TokenMgrError.java
    - layout
      - templates
        adamantane.cml
        cubane.cml
        diamantane.cml
        templates.list
    - modeling
      - forcefield
        ForceFieldTools.java
    - PeriodicTableElement.java
    - PhysicalConstants.java
    - protein
      - ProteinPocketFinder.java
    - ringsearch
      - FiguerasSSSRFinder.java
    - structgen
      - RandomGenerator.java
    - templates
      - MoleculeFactory.java
      - saturatedhydrocarbons
        IsoAlkanes.java
    - tools
      - AtomTypeTools.java
      - BremserOneSphereHOSECodePredictor.java
      - CDKUtilities.java
      - DataFeaturesTool.java
      - DeAromatizationTool.java
      - features
        MoleculeFeaturesTool.java
      - FixedSizeStack.java
      - GenerateFragments.java
      - GridGenerator.java
      - HOSECodeAnalyser.java
      - PeriodicTable.java
      - SwissArmyKnife.java
    - validate
      - AbstractValidator.java
      - BasicValidator.java
      - CDKValidator.java
      - DictionaryValidator.java
      - Geometry3DValidator.java
      - IValidator.java
      - ValidationReport.java
      - ValidationTest.java
      - ValidatorEngine.java
    - Vibration.java