[Cdk-commits] [cdk/cdk] 5ad585: First batch of removal of TestClass/-Method use

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  Branch: refs/heads/master
  Home:   https://github.com/cdk/cdk
  Commit: 5ad585becd314ef72ba7c67f8e75109da381e58c
      https://github.com/cdk/cdk/commit/5ad585becd314ef72ba7c67f8e75109da381e58c
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M base/atomtype/src/main/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
    M base/atomtype/src/main/java/org/openscience/cdk/atomtype/mapper/AtomTypeMapper.java
    M base/atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingHandler.java
    M base/atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java
    M base/core/src/main/java/org/openscience/cdk/graph/AllCycles.java
    M base/core/src/main/java/org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
    M base/data/src/main/java/org/openscience/cdk/ConformerContainer.java
    M base/data/src/main/java/org/openscience/cdk/formula/AdductFormula.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/CIPTool.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigand.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/LigancyFourChirality.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/Ligand.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/TerminalLigand.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/VisitedAtoms.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/AtomicNumberRule.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRule.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRule.java
    M descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/MassNumberRule.java
    M storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLReader.java
    M tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java
    M tool/charges/src/main/java/org/openscience/cdk/charges/AtomTypeCharges.java
    M tool/charges/src/main/java/org/openscience/cdk/charges/Electronegativity.java
    M tool/charges/src/main/java/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java
    M tool/charges/src/main/java/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
    M tool/charges/src/main/java/org/openscience/cdk/charges/InductivePartialCharges.java
    M tool/charges/src/main/java/org/openscience/cdk/charges/PiElectronegativity.java
    M tool/charges/src/main/java/org/openscience/cdk/charges/Polarizability.java
    M tool/charges/src/main/java/org/openscience/cdk/charges/StabilizationCharges.java

  Log Message:
  -----------
  First batch of removal of TestClass/-Method use

Change-Id: I6631f26ce3d493e92711fbe67861303c79245843

Signed-off-by: John May <joh...@gm...>


  Commit: ac85c9f773177fd4e51c3174ff0062267c132855
      https://github.com/cdk/cdk/commit/ac85c9f773177fd4e51c3174ff0062267c132855
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M base/core/src/main/java/org/openscience/cdk/CDK.java
    M base/core/src/main/java/org/openscience/cdk/CDKConstants.java
    M base/core/src/main/java/org/openscience/cdk/DynamicFactory.java
    M base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
    M base/core/src/main/java/org/openscience/cdk/config/AtomTypeFactory.java
    M base/core/src/main/java/org/openscience/cdk/config/BODRIsotope.java
    M base/core/src/main/java/org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java
    M base/core/src/main/java/org/openscience/cdk/config/Isotopes.java
    M base/core/src/main/java/org/openscience/cdk/config/NaturalElement.java
    M base/core/src/main/java/org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.java
    M base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeHandler.java
    M base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeReader.java
    M base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java
    M base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java
    M base/core/src/main/java/org/openscience/cdk/exception/CDKException.java
    M base/core/src/main/java/org/openscience/cdk/exception/Intractable.java
    M base/core/src/main/java/org/openscience/cdk/exception/NoSuchAtomException.java
    M base/core/src/main/java/org/openscience/cdk/exception/NoSuchAtomTypeException.java
    M base/core/src/main/java/org/openscience/cdk/graph/AllPairsShortestPaths.java
    M base/core/src/main/java/org/openscience/cdk/graph/BitMatrix.java
    M base/core/src/main/java/org/openscience/cdk/graph/ConnectedComponents.java
    M base/core/src/main/java/org/openscience/cdk/graph/Cycles.java
    M base/core/src/main/java/org/openscience/cdk/graph/EdgeShortCycles.java
    M base/core/src/main/java/org/openscience/cdk/graph/EssentialCycles.java
    M base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java
    M base/core/src/main/java/org/openscience/cdk/graph/GreedyBasis.java
    M base/core/src/main/java/org/openscience/cdk/graph/InitialCycles.java
    M base/core/src/main/java/org/openscience/cdk/graph/JumboPathGraph.java
    M base/core/src/main/java/org/openscience/cdk/graph/MinimumCycleBasis.java
    M base/core/src/main/java/org/openscience/cdk/graph/PathTools.java
    M base/core/src/main/java/org/openscience/cdk/graph/RegularPathGraph.java
    M base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java
    M base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java
    M base/core/src/main/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearch.java
    M base/core/src/main/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearch.java
    M base/core/src/main/java/org/openscience/cdk/ringsearch/RingSearch.java
    M base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java
    M base/core/src/main/java/org/openscience/cdk/tools/LoggingToolFactory.java
    M base/core/src/main/java/org/openscience/cdk/tools/manipulator/BondManipulator.java
    M base/core/src/main/java/org/openscience/cdk/tools/periodictable/PeriodicTable.java

  Log Message:
  -----------
  Second batch of removal of TestClass/-Method use

Change-Id: If9fadf93d75ad0a23d5a20b1714589edd5da5b83

Signed-off-by: John May <joh...@gm...>


  Commit: 415f7cece12488265aaf48f6848f8dd5eb750731
      https://github.com/cdk/cdk/commit/415f7cece12488265aaf48f6848f8dd5eb750731
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java
    M base/core/src/main/java/org/openscience/cdk/graph/SpanningTree.java
    M base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java
    M base/core/src/main/java/org/openscience/cdk/graph/VertexShortCycles.java
    M base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java
    M base/core/src/main/java/org/openscience/cdk/tools/SystemOutLoggingTool.java
    M base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java
    M base/data/src/main/java/org/openscience/cdk/formula/MolecularFormulaSet.java
    M base/dict/src/main/java/org/openscience/cdk/dict/Dictionary.java
    M base/dict/src/main/java/org/openscience/cdk/dict/DictionaryDatabase.java
    M base/dict/src/main/java/org/openscience/cdk/dict/Entry.java
    M base/dict/src/main/java/org/openscience/cdk/dict/EntryReact.java
    M base/dict/src/main/java/org/openscience/cdk/dict/OWLFile.java
    M base/dict/src/main/java/org/openscience/cdk/dict/OWLReact.java
    M descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AminoAcidCountDescriptor.java
    M descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java
    M legacy/src/main/java/org/openscience/cdk/tools/IonizationPotentialTool.java
    M misc/log4j/src/main/java/org/openscience/cdk/tools/LoggingTool.java
    M storage/libiocml/src/main/java/org/openscience/cdk/io/CMLWriter.java
    M storage/libiocml/src/main/java/org/openscience/cdk/io/RssWriter.java
    M storage/pdbcml/src/main/java/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java
    M tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
    M tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java

  Log Message:
  -----------
  Third batch of removal of TestClass/-Method use

Change-Id: Ie265e181192d88ef6643e00c261dded26b33f551

Signed-off-by: John May <joh...@gm...>


  Commit: 1f3633cc497773be81ce9bbae7d165a97f7c6315
      https://github.com/cdk/cdk/commit/1f3633cc497773be81ce9bbae7d165a97f7c6315
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java
    M base/standard/src/main/java/org/openscience/cdk/geometry/BondTools.java
    M base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
    M base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerBondPermutor.java
    M base/standard/src/main/java/org/openscience/cdk/ringsearch/AllRingsFinder.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AminoAcidManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerComparator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
    M base/valencycheck/src/main/java/org/openscience/cdk/tools/AtomTypeAwareSaturationChecker.java
    M base/valencycheck/src/main/java/org/openscience/cdk/tools/CDKHydrogenAdder.java
    M base/valencycheck/src/main/java/org/openscience/cdk/tools/CDKValencyChecker.java
    M base/valencycheck/src/main/java/org/openscience/cdk/tools/SaturationChecker.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomContainerDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomTypeDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/BondDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/ChemObjectDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/ElectronContainerDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/ElementDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/IsotopeDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/LonePairDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/SingleElectronDiff.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/AbstractDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/AbstractDifferenceList.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/AtomTypeHybridizationDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/BondOrderDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/BooleanArrayDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/BooleanDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/ChemObjectDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/DoubleDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/IntegerDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/Point2dDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/Point3dDifference.java
    M misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/StringDifference.java

  Log Message:
  -----------
  Fourth batch of removal of TestClass/-Method use

Change-Id: I14b814f318daaea5996932999f76bb20630292db

Signed-off-by: John May <joh...@gm...>


  Commit: fb51e91f99976e48b13c905256eaac49b4e84529
      https://github.com/cdk/cdk/commit/fb51e91f99976e48b13c905256eaac49b4e84529
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M misc/extra/src/main/java/org/openscience/cdk/Association.java
    M misc/extra/src/main/java/org/openscience/cdk/config/XMLIsotopeFactory.java
    M misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeHandler.java
    M misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeReader.java
    M misc/extra/src/main/java/org/openscience/cdk/geometry/alignment/KabschAlignment.java
    M misc/extra/src/main/java/org/openscience/cdk/index/CASNumber.java
    M misc/extra/src/main/java/org/openscience/cdk/io/CrystClustReader.java
    M misc/extra/src/main/java/org/openscience/cdk/io/CrystClustWriter.java
    M misc/extra/src/main/java/org/openscience/cdk/io/GamessReader.java
    M misc/extra/src/main/java/org/openscience/cdk/io/INChIPlainTextReader.java
    M misc/extra/src/main/java/org/openscience/cdk/io/INChIReader.java
    M misc/extra/src/main/java/org/openscience/cdk/io/ShelXWriter.java
    M misc/extra/src/main/java/org/openscience/cdk/io/VASPReader.java
    M misc/extra/src/main/java/org/openscience/cdk/io/ZMatrixReader.java
    M misc/extra/src/main/java/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java
    M misc/extra/src/main/java/org/openscience/cdk/reaction/ReactionChain.java
    M misc/extra/src/main/java/org/openscience/cdk/tools/DeAromatizationTool.java
    M storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java
    M storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGenerator.java
    M storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGeneratorFactory.java
    M storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIToStructure.java
    M storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java
    M storage/pdb/src/main/java/org/openscience/cdk/io/PDBWriter.java
    M tool/formula/src/main/java/org/openscience/cdk/formula/IsotopeContainer.java
    M tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePattern.java
    M tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePatternGenerator.java
    M tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePatternManipulator.java
    M tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePatternSimilarity.java
    M tool/formula/src/main/java/org/openscience/cdk/formula/MolecularFormulaChecker.java
    M tool/formula/src/main/java/org/openscience/cdk/formula/MolecularFormulaGenerator.java
    M tool/formula/src/main/java/org/openscience/cdk/formula/MolecularFormulaRange.java
    M tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
    M tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulator.java
    M tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.java
    M tool/fragment/src/main/java/org/openscience/cdk/fragment/ExhaustiveFragmenter.java
    M tool/fragment/src/main/java/org/openscience/cdk/fragment/FragmentUtils.java
    M tool/fragment/src/main/java/org/openscience/cdk/fragment/MurckoFragmenter.java

  Log Message:
  -----------
  Fifth batch of removal of TestClass/-Method use

Change-Id: Id4e8ecf935cc519f529766dc1b3efe1b16b0078d

Signed-off-by: John May <joh...@gm...>


  Commit: 1951f68de16afbb9df56ddf86e4a7a1009a0ae0b
      https://github.com/cdk/cdk/commit/1951f68de16afbb9df56ddf86e4a7a1009a0ae0b
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M storage/ioformats/src/main/java/org/openscience/cdk/io/FormatFactory.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ABINITFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ADFFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Aces2Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/AlchemyFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/BGFFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/BSFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CACheFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CDKOWLFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CDKSourceCodeFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CIFFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CMLFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CMLRSSFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CRK2DFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CRK3DFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CTXFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CacaoCartesianFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CacaoInternalFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Chem3D_Cartesian_1Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Chem3D_Cartesian_2Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ChemDrawFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ChemtoolFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CrystClustFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/DMol3Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/DOCK5Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/DaltonFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/FingerprintFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GROMOS96Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GamessFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian03Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian90Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian92Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian94Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian95Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian98Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GaussianInputFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GhemicalMMFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GhemicalSPMFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/HINFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/INChIFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/INChIPlainTextFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/JMEFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/JaguarFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLRXNFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLRXNV3000Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLV2000Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLV3000Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MMODFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC2002Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC2007Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC2009Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC2012Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC7Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC7InputFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC93Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC97Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MPQCFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MacroModelFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MoSSOutputFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Mol2Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/NWChemFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PCModelFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PDBFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PDBMLFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PMPFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/POVRayFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PQSChemFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemASNFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemSubstancesASNFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/QChemFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/RGroupQueryFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/RawCopyFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SDFFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SMARTSFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SMILESFIXFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SMILESFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SVGFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ShelXFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SpartanFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SybylDescriptorFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/TinkerMM2Format.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/TinkerXYZFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/TurboMoleFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/UniChemXYZFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/VASPFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ViewmolFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/XEDFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/XYZFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/YasaraFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ZMatrixFormat.java
    M storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ZindoFormat.java

  Log Message:
  -----------
  Sixth batch of removal of TestClass/-Method use

Change-Id: I8a89eaa2059dab5b7bf67042dcb5811b810961ad

Signed-off-by: John May <joh...@gm...>


  Commit: 9424578dab5c8e4f0718533a968b7758018e59af
      https://github.com/cdk/cdk/commit/9424578dab5c8e4f0718533a968b7758018e59af
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M base/silent/src/main/java/org/openscience/cdk/silent/AdductFormula.java
    M base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormula.java
    M base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormulaSet.java
    M storage/smiles/src/main/java/org/openscience/cdk/fingerprint/LingoFingerprinter.java
    M storage/smiles/src/main/java/org/openscience/cdk/io/MoSSOutputReader.java
    M storage/smiles/src/main/java/org/openscience/cdk/io/SMILESReader.java
    M storage/smiles/src/main/java/org/openscience/cdk/io/SMILESWriter.java
    M storage/smiles/src/main/java/org/openscience/cdk/io/iterator/IteratingSMILESReader.java
    M storage/smiles/src/main/java/org/openscience/cdk/normalize/Normalizer.java
    M storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java
    M storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java
    M storage/smiles/src/main/java/org/openscience/cdk/smiles/DeduceBondSystemTool.java
    M storage/smiles/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java
    M storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
    M storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java

  Log Message:
  -----------
  Seventh batch of removal of TestClass/-Method use

Change-Id: I775a4001013bf778d1ed7b2a80ea826eff4b5351

Signed-off-by: John May <joh...@gm...>


  Commit: 00bd54cddae68fb87269b6d1aa3decdeba1d8cb1
      https://github.com/cdk/cdk/commit/00bd54cddae68fb87269b6d1aa3decdeba1d8cb1
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/CircularFingerprinter.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/EStateFingerprinter.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/KlekotaRothFingerprinter.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/MACCSFingerprinter.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/RandomNumber.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathWalker.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SimpleAtomCanonicalizer.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SimpleAtomComparator.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/StandardSubstructureSets.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/similarity/DistanceMoment.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/similarity/LingoSimilarity.java
    M descriptor/fingerprint/src/main/java/org/openscience/cdk/similarity/Tanimoto.java
    M tool/group/src/main/java/org/openscience/cdk/group/AbstractDiscretePartitionRefiner.java
    M tool/group/src/main/java/org/openscience/cdk/group/AtomDiscretePartitionRefiner.java
    M tool/group/src/main/java/org/openscience/cdk/group/BondDiscretePartitionRefiner.java
    M tool/group/src/main/java/org/openscience/cdk/group/BondEquitablePartitionRefiner.java
    M tool/group/src/main/java/org/openscience/cdk/group/Partition.java
    M tool/group/src/main/java/org/openscience/cdk/group/Permutation.java
    M tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java

  Log Message:
  -----------
  Eight batch of removal of TestClass/-Method use

Change-Id: Idc38c12924feba45ed7c10d65f9c3db7aaa92cf6

Signed-off-by: John May <joh...@gm...>


  Commit: ffa58589a454ec50ed00403ea1f284c23d695b3f
      https://github.com/cdk/cdk/commit/ffa58589a454ec50ed00403ea1f284c23d695b3f
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M storage/io/src/main/java/org/openscience/cdk/io/CDKSourceCodeWriter.java
    M storage/io/src/main/java/org/openscience/cdk/io/CIFReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/CMLReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/CTXReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/Gaussian03Reader.java
    M storage/io/src/main/java/org/openscience/cdk/io/Gaussian98Reader.java
    M storage/io/src/main/java/org/openscience/cdk/io/GhemicalMMReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/HINReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/HINWriter.java
    M storage/io/src/main/java/org/openscience/cdk/io/IChemObjectIO.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLRXNReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLRXNV2000Reader.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLRXNV3000Reader.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLRXNWriter.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
    M storage/io/src/main/java/org/openscience/cdk/io/MDLValence.java
    M storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java
    M storage/io/src/main/java/org/openscience/cdk/io/Mol2Writer.java
    M storage/io/src/main/java/org/openscience/cdk/io/Mopac7Reader.java
    M storage/io/src/main/java/org/openscience/cdk/io/PCCompoundASNReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/PCCompoundXMLReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/PCSubstanceXMLReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/PMPReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/RGroupQueryReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/RGroupQueryWriter.java
    M storage/io/src/main/java/org/openscience/cdk/io/SDFWriter.java
    M storage/io/src/main/java/org/openscience/cdk/io/ShelXReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/XYZReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/XYZWriter.java
    M storage/io/src/main/java/org/openscience/cdk/io/cml/CMLModuleStack.java
    M storage/io/src/main/java/org/openscience/cdk/io/cml/CMLStack.java
    M storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingPCCompoundASNReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingPCCompoundXMLReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/iterator/event/EventCMLReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/program/GaussianInputWriter.java
    M storage/io/src/main/java/org/openscience/cdk/io/program/Mopac7Writer.java
    M storage/io/src/main/java/org/openscience/cdk/io/random/RandomAccessReader.java
    M storage/io/src/main/java/org/openscience/cdk/io/random/RandomAccessSDFReader.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/AbstractHashGenerator.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/AllEquivalentCyclicSet.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/AtomSuppression.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomEncoder.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomHashGenerator.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/BasicMoleculeHashGenerator.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/ConjugatedAtomEncoder.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/HashGeneratorMaker.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSet.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSetUnion.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/PerturbedAtomHashGenerator.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/SeedGenerator.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/Suppressed.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/SuppressedAtomHashGenerator.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/Xorshift.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/BasicPermutationParity.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/CombinedPermutationParity.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBond2DParity.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBond3DParity.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBondElementEncoderFactory.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricCumulativeDoubleBondFactory.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactory.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricParity.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricTetrahedralEncoderFactory.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometryEncoder.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/MultiStereoEncoder.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral2DParity.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral3DParity.java
    M tool/hash/src/main/java/org/openscience/cdk/hash/stereo/TetrahedralElementEncoderFactory.java

  Log Message:
  -----------
  Nineth batch of removal of TestClass/-Method use

Change-Id: I243499103e48362ecc19f24f9618328ae36e4423

Signed-off-by: John May <joh...@gm...>


  Commit: 15f009893cd5766b5eedcee7ed561b433d448bbe
      https://github.com/cdk/cdk/commit/15f009893cd5766b5eedcee7ed561b433d448bbe
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java
    M base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java
    M base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java
    M base/standard/src/main/java/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java
    M base/standard/src/main/java/org/openscience/cdk/dict/DictRef.java
    M base/standard/src/main/java/org/openscience/cdk/exception/InvalidSmilesException.java
    M base/standard/src/main/java/org/openscience/cdk/exception/UnsupportedChemObjectException.java
    M base/standard/src/main/java/org/openscience/cdk/fingerprint/BitSetFingerprint.java
    M base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java
    M base/standard/src/main/java/org/openscience/cdk/fingerprint/FingerprinterTool.java
    M base/standard/src/main/java/org/openscience/cdk/fingerprint/GraphOnlyFingerprinter.java
    M base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java
    M base/standard/src/main/java/org/openscience/cdk/fingerprint/IntArrayCountFingerprint.java
    M base/standard/src/main/java/org/openscience/cdk/geometry/CrystalGeometryTools.java
    M base/standard/src/main/java/org/openscience/cdk/geometry/volume/VABCVolume.java
    M base/standard/src/main/java/org/openscience/cdk/graph/ConnectivityChecker.java
    M base/standard/src/main/java/org/openscience/cdk/graph/EdmondsMaximumMatching.java
    M base/standard/src/main/java/org/openscience/cdk/graph/Matching.java
    M base/standard/src/main/java/org/openscience/cdk/graph/Permutor.java
    M base/standard/src/main/java/org/openscience/cdk/graph/invariant/CanonicalLabeler.java
    M base/standard/src/main/java/org/openscience/cdk/graph/invariant/MorganNumbersTools.java
    M base/standard/src/main/java/org/openscience/cdk/graph/matrix/ConnectionMatrix.java
    M base/standard/src/main/java/org/openscience/cdk/graph/rebond/Bspt.java
    M base/standard/src/main/java/org/openscience/cdk/graph/rebond/Point.java
    M base/standard/src/main/java/org/openscience/cdk/graph/rebond/RebondTool.java
    M base/standard/src/main/java/org/openscience/cdk/group/DisjointSetForest.java
    M base/standard/src/main/java/org/openscience/cdk/isomorphism/IsomorphismTester.java
    M base/standard/src/main/java/org/openscience/cdk/math/FortranFormat.java
    M base/standard/src/main/java/org/openscience/cdk/math/MathTools.java
    M base/standard/src/main/java/org/openscience/cdk/math/Primes.java
    M base/standard/src/main/java/org/openscience/cdk/math/RandomNumbersTool.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/DescriptorSpecification.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/DescriptorValue.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/BooleanResult.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/BooleanResultType.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/DoubleArrayResult.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/DoubleArrayResultType.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/DoubleResult.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/DoubleResultType.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/IntegerArrayResult.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/IntegerArrayResultType.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/IntegerResult.java
    M base/standard/src/main/java/org/openscience/cdk/qsar/result/IntegerResultType.java
    M base/standard/src/main/java/org/openscience/cdk/ringsearch/RingPartitioner.java
    M base/standard/src/main/java/org/openscience/cdk/smiles/InvPair.java
    M base/standard/src/main/java/org/openscience/cdk/stereo/CyclicCarbohydrateRecognition.java
    M base/standard/src/main/java/org/openscience/cdk/stereo/FischerRecognition.java
    M base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java
    M base/standard/src/main/java/org/openscience/cdk/stereo/StereoTool.java
    M base/standard/src/main/java/org/openscience/cdk/tools/ElementComparator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/FormatStringBuffer.java
    M base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/IDCreator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerSetManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomTypeManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ChemFileManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ChemModelManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ChemSequenceManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/MoleculeSetManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionSchemeManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionSetManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingSetManipulator.java
    M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingSizeComparator.java
    M base/standard/src/main/java/org/openscience/cdk/validate/ProblemMarker.java
    M descriptor/signature/src/main/java/org/openscience/cdk/fingerprint/SignatureFingerprinter.java
    M descriptor/signature/src/main/java/org/openscience/cdk/signature/AtomSignature.java
    M descriptor/signature/src/main/java/org/openscience/cdk/signature/MoleculeFromSignatureBuilder.java
    M descriptor/signature/src/main/java/org/openscience/cdk/signature/MoleculeSignature.java
    M descriptor/signature/src/main/java/org/openscience/cdk/signature/Orbit.java
    M descriptor/signature/src/main/java/org/openscience/cdk/signature/SignatureQuotientGraph.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtomInvariants.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java
    M tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
    M tool/smsd/src/main/java/org/openscience/cdk/normalize/SMSDNormalizer.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/Isomorphism.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultBondMatcher.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultMCSPlusAtomMatcher.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultRGraphAtomMatcher.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultVFAtomMatcher.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultVFBondMatcher.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/McGregor.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/McGregorChecks.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/McgregorHelper.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/QueryProcessor.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/TargetProcessor.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/BKKCKCF.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/ExactMapping.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/GenerateCompatibilityGraph.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlus.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlusHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCS.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRGraph.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMap.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRNode.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKSubGraphHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/single/SingleMapping.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/single/SingleMappingHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibMCSHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibSubStructureHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibTurboHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/builder/EdgeBuilder.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/builder/NodeBuilder.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/builder/VFQueryBuilder.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IEdge.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IMapper.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/INode.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IQuery.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IQueryCompiler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IState.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/map/Match.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/map/VFMCSMapper.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/map/VFMapper.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/map/VFState.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/query/QueryCompiler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/filters/PostFilter.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/global/TimeOut.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/helper/BinaryTree.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/helper/BondEnergy.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/helper/FinalMappings.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/helper/LabelContainer.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/interfaces/AbstractMCS.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/interfaces/AbstractMCSAlgorithm.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/interfaces/AbstractSubGraph.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/interfaces/Algorithm.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/interfaces/IFinalMapping.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/interfaces/IMCSBase.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/tools/BondEnergies.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulator.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/tools/MolHandler.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/tools/MoleculeSanityCheck.java
    M tool/smsd/src/main/java/org/openscience/cdk/smsd/tools/TimeManager.java

  Log Message:
  -----------
  Tenth batch of removal of TestClass/-Method use

Change-Id: I7309ad45514b94812fae210322e0b6d0473bee41

Signed-off-by: John May <joh...@gm...>


  Commit: 1c0410bfffe8f33cb7eaa17d5530544996941cce
      https://github.com/cdk/cdk/commit/1c0410bfffe8f33cb7eaa17d5530544996941cce
  Author: Egon Willighagen <eg...@us...>
  Date:   2015-01-16 (Fri, 16 Jan 2015)

  Changed paths:
    M descriptor/qsar/src/main/java/org/openscience/cdk/qsar/DescriptorException.java
    M descriptor/qsar/src/main/java/org/openscience/cdk/tools/AtomicProperties.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomDegreeDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomValenceDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/BondsToAtomDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/DistanceToAtomDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PeriodicTablePositionDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonAffinityHOSEDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptor.java
    M descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/VdWRadiusDescriptor.java
    M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/AtomicNumberDifferenceDescriptor.java
    M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java
    M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptor.java
    M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java
    M descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/graph/matrix/TopologicalMatrix.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/DescriptorEngine.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/APolDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AtomCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorCharge.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMass.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizability.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BPolDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BondCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/CarbonTypesDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/EccentricConnectivityIndexDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FMFDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FractionalPSADescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FragmentComplexityDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/GravitationalIndexDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondDonorCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/KappaShapeIndicesDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/KierHallSmartsDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LongestAliphaticChainDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MannholdLogPDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanNumberDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanShapeIndexDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/SmallRingDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/VABCDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WeightDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WeightedPathDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WienerNumbersDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java
    M descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ZagrebIndexDescriptor.java
    M display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java
    M display/render/src/main/java/org/openscience/cdk/renderer/color/CDK2DAtomColors.java
    M display/render/src/main/java/org/openscience/cdk/renderer/color/CDKAtomColors.java
    M display/render/src/main/java/org/openscience/cdk/renderer/color/CPKAtomColors.java
    M display/render/src/main/java/org/openscience/cdk/renderer/color/PartialAtomicChargeColors.java
    M display/render/src/main/java/org/openscience/cdk/renderer/color/RasmolColors.java
    M display/render/src/main/java/org/openscience/cdk/renderer/elements/TextElement.java
    M display/render/src/main/java/org/openscience/cdk/renderer/generators/parameter/AbstractGeneratorParameter.java
    M display/renderawt/src/main/java/org/openscience/cdk/render...
 
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