[med-svn] [ball] branch master updated (17d3449 -> a6a79a1)

Andreas Tille tille at debian.org
Thu Jan 7 10:40:34 UTC 2016


This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository ball.

      from  17d3449   cme fix dpkg-control
       new  e9947a3   Also fetch beta versions
       new  072c9d7   Imported Upstream version 1.4.3~beta1
       new  24e40f4   Merge tag 'upstream/1.4.3_beta1'
       new  a6a79a1   New upstream version, most patches were taken over

The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .gitignore                                         |    3 +
 CMakeLists.txt                                     |  148 +-
 cmake/BALLCompilerSpecific.cmake                   |    4 +
 cmake/BALLComponents.cmake                         |   86 +-
 cmake/BALLConfigBoost.cmake                        |    2 +-
 cmake/BALLConfigNoexcept.cmake                     |   13 +
 cmake/BALLConfigStdStringFeatures.cmake            |   56 +
 cmake/BALLConfiguration.cmake                      |    6 +
 cmake/BALLDoc.cmake                                |   58 +-
 cmake/BALLMacros.cmake                             |   14 +-
 cmake/FindFLEX.cmake                               |    2 +-
 cmake/FindRTfact.cmake                             |   22 +-
 cmake/FindTBB.cmake                                |   19 +-
 cmake/ballaxy/setupBALLAXYDirectories.cmake.in     |    3 +-
 cmake/config.h.in                                  |   36 +-
 data/HTMLBasedInterface/html_de/darstellung.html   |    1 +
 data/HTMLBasedInterface/html_de/index.html         |   14 +-
 .../html_de/lehrer/wiki_tutorial02.html            |   50 +
 .../html_de/lehrer/wiki_tutorial03.html            |   44 +
 .../html_de/lehrer/wiki_tutorial04.html            |   59 +
 .../html_de/lehrer/wiki_tutorial05.html            |   44 +
 .../html_de/lehrer/wiki_tutorial06.html            |   47 +
 .../html_de/lehrer/wiki_tutorial07.html            |   54 +
 .../html_de/lehrer/wiki_tutorial08.html            |   43 +
 .../html_de/lehrer/wiki_tutorial09.html            |   51 +
 .../html_de/lehrer/wiki_tutorial10.html            |   53 +
 .../html_de/lehrer/wiki_tutorial11.html            |   45 +
 data/HTMLBasedInterface/html_de/wiki_tutorial.html |   44 +
 data/HTMLBasedInterface/html_eng/index.html        |    6 +
 .../html_eng/tutorial/tutorial_dialog02.html       |   48 +
 .../html_eng/tutorial/tutorial_dialog03.html       |   47 +
 .../html_eng/tutorial/tutorial_dialog04.html       |   55 +
 .../html_eng/tutorial/tutorial_dialog05.html       |   49 +
 .../html_eng/tutorial/tutorial_dialog06.html       |   44 +
 .../html_eng/tutorial/tutorial_dialog07.html       |   45 +
 .../html_eng/tutorial/tutorial_dialog08.html       |   52 +
 .../html_eng/tutorial/tutorial_dialog09.html       |   46 +
 .../html_eng/tutorial/tutorial_dialog10.html       |   38 +
 .../html_eng/tutorial_dialog.html                  |   53 +
 .../images/ballview_menueleiste.jpg                |  Bin 0 -> 16007 bytes
 .../images/ballview_repraesentation.jpg            |  Bin 0 -> 20933 bytes
 .../images/ballview_uebersicht.jpg                 |  Bin 0 -> 18478 bytes
 .../HTMLBasedInterface/scripts/common_functions.py |   37 +-
 data/HTMLBasedInterface/scripts/connectVIEW.js     |  282 +++
 debian/changelog                                   |    4 +-
 ...X_PENALTY-option-to-bond-order-assignment.patch |   76 -
 ...xed-a-bug-in-the-AssignBondOrderProcessor.patch |   58 -
 ...ilation-of-FTPBondOrderStrategy-Fixes-451.patch |   22 -
 debian/patches/0101-cmake-syntax.patch             |  105 --
 .../0102-fix-boost-compatibility-issue.patch       |   16 -
 ..._OPTIONS-CMake-macro-changed-in-CMake-2.8.patch |   38 -
 debian/patches/HelpSipAmbiguity.patch              |   13 -
 debian/patches/gcc5.diff                           |   58 +-
 debian/patches/link_against_x11.patch              |    6 +-
 debian/patches/more-gcc5_issues.patch              |   72 -
 debian/patches/nopsboxit.patch                     |    6 +-
 debian/patches/series                              |    8 -
 debian/watch                                       |    4 +-
 include/BALL/DATATYPE/GRAPH/graphAlgorithms.h      |    4 +-
 include/BALL/DATATYPE/string.h                     |  546 +++++-
 include/BALL/DATATYPE/string.iC                    | 1022 ++++++++++-
 include/BALL/DOCKING/COMMON/poseClustering.h       |  151 +-
 include/BALL/FORMAT/HMOFile.h                      |  212 +++
 include/BALL/FORMAT/NMRStarFile.h                  |    4 +-
 include/BALL/FORMAT/SCWRLRotamerFile.h             |   22 +-
 include/BALL/FORMAT/commandlineParser.h            |   28 +-
 include/BALL/FORMAT/lineBasedFile.h                |    3 -
 include/BALL/FORMAT/molFileFactory.h               |   15 +-
 include/BALL/FORMAT/paramFile.h                    |    4 +-
 include/BALL/MATHS/analyticalGeometry.h            |    3 +-
 include/BALL/QSAR/QSARData.h                       |   20 -
 include/BALL/QSAR/classificationValidation.h       |   20 -
 include/BALL/QSAR/kernelModel.h                    |   20 -
 include/BALL/QSAR/latentVariableModel.h            |   20 -
 include/BALL/QSAR/ldaModel.h                       |   20 -
 include/BALL/QSAR/libsvmModel.h                    |   20 -
 include/BALL/QSAR/linearModel.h                    |   20 -
 include/BALL/QSAR/logitModel.h                     |   20 -
 include/BALL/QSAR/mlrModel.h                       |   22 +-
 include/BALL/QSAR/modelFactory.h                   |   22 -
 include/BALL/QSAR/nBModel.h                        |   20 -
 include/BALL/QSAR/nonlinearModel.h                 |   20 -
 include/BALL/QSAR/oplsModel.h                      |   22 +-
 include/BALL/QSAR/pcrModel.h                       |   20 -
 include/BALL/QSAR/plsModel.h                       |   22 +-
 include/BALL/QSAR/registry.h                       |   20 -
 include/BALL/QSAR/regressionModel.h                |   20 -
 include/BALL/QSAR/regressionValidation.h           |   20 -
 include/BALL/QSAR/rrModel.h                        |   22 +-
 include/BALL/QSAR/snBModel.h                       |   20 -
 include/BALL/QSAR/statistics.h                     |   20 -
 include/BALL/QSAR/svmModel.h                       |   20 -
 include/BALL/QSAR/svrModel.h                       |   22 +-
 include/BALL/QSAR/validation.h                     |   20 -
 include/BALL/SCORING/COMMON/diffGridBasedScoring.h |   18 -
 include/BALL/SCORING/COMMON/diffScoringFunction.h  |   18 -
 include/BALL/SCORING/COMMON/gridBasedScoring.h     |   18 -
 include/BALL/SCORING/COMMON/scoreGridSet.h         |   18 -
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 include/BALL/SCORING/COMMON/scoringOptimizer.h     |   18 -
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 include/BALL/SCORING/COMPONENTS/advElectrostatic.h |   18 -
 .../BALL/SCORING/COMPONENTS/aromaticRingStacking.h |   18 -
 include/BALL/SCORING/COMPONENTS/burialDepth.h      |   18 -
 include/BALL/SCORING/COMPONENTS/buriedPolar.h      |   18 -
 include/BALL/SCORING/COMPONENTS/electrostatic.h    |   18 -
 .../SCORING/COMPONENTS/fragmentationalSolvation.h  |   18 -
 include/BALL/SCORING/COMPONENTS/fresnoTypes.h      |   18 -
 include/BALL/SCORING/COMPONENTS/hydrogenBond.h     |   18 -
 include/BALL/SCORING/COMPONENTS/lipophilic.h       |   18 -
 include/BALL/SCORING/COMPONENTS/polarity.h         |   18 -
 .../BALL/SCORING/COMPONENTS/rotationalEntropy.h    |   18 -
 include/BALL/SCORING/COMPONENTS/solvation.h        |   18 -
 include/BALL/SCORING/COMPONENTS/vanDerWaals.h      |   18 -
 include/BALL/SCORING/FUNCTIONS/MMScoring.h         |   18 -
 include/BALL/SCORING/FUNCTIONS/PBScoring.h         |   18 -
 include/BALL/SCORING/FUNCTIONS/PLPScoring.h        |   18 -
 include/BALL/SCORING/FUNCTIONS/gridedMM.h          |   18 -
 include/BALL/SCORING/FUNCTIONS/gridedPLP.h         |   18 -
 include/BALL/SCORING/FUNCTIONS/rescoring.h         |   18 -
 include/BALL/SCORING/FUNCTIONS/rescoring1D.h       |   18 -
 include/BALL/SCORING/FUNCTIONS/rescoring3D.h       |   18 -
 include/BALL/SCORING/FUNCTIONS/rescoring4D.h       |   18 -
 include/BALL/STRUCTURE/RMSDMinimizer.h             |    5 -
 include/BALL/STRUCTURE/binaryFingerprintMethods.h  |   14 +-
 include/BALL/STRUCTURE/residueChecker.h            |    2 +-
 include/BALL/SYSTEM/MPISupport.h                   |    8 +-
 include/BALL/SYSTEM/fileSystem.h                   |    5 +
 include/BALL/VIEW/DIALOGS/materialSettings.h       |    1 -
 include/BALL/VIEW/KERNEL/message.h                 |    7 +-
 include/BALL/VIEW/KERNEL/stage.h                   |   20 +-
 include/BALL/VIEW/KERNEL/stringStub.h              |    1 -
 .../BALL/VIEW/RENDERING/RENDERERS/XML3DRenderer.h  |   16 +-
 include/BALL/VIEW/RENDERING/RENDERERS/glRenderer.h |    7 +
 include/BALL/VIEW/RENDERING/RENDERERS/renderer.h   |   43 +-
 .../BALL/VIEW/RENDERING/RENDERERS/rtfactRenderer.h |  174 +-
 include/BALL/VIEW/WIDGETS/geometricControl.h       |    2 +-
 include/BALL/VIEW/WIDGETS/molecularStructure.h     |    4 +
 include/BALL/VIEW/WIDGETS/scene.h                  |   78 +-
 source/APPLICATIONS/BALLVIEW/aboutDialog.ui        |    6 +-
 source/APPLICATIONS/BALLVIEW/demoTutorialDialog.C  |    2 +-
 source/APPLICATIONS/QuEasyRun/CMakeLists.txt       |    4 +-
 source/APPLICATIONS/QuEasyRun/featureSelector.C    |   20 -
 source/APPLICATIONS/QuEasyRun/inputPartitioner.C   |   20 -
 source/APPLICATIONS/QuEasyRun/inputReader.C        |   20 -
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 source/APPLICATIONS/QuEasyRun/modelCreator.C       |   20 -
 source/APPLICATIONS/QuEasyRun/predictor.C          |   20 -
 source/APPLICATIONS/QuEasyRun/validator.C          |   20 -
 source/APPLICATIONS/QuEasyViz/CMakeLists.txt       |    5 +
 source/APPLICATIONS/QuEasyViz/CSVInputDataItem.C   |   20 -
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 source/APPLICATIONS/QuEasyViz/connectionManager.C  |   22 +-
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 source/APPLICATIONS/QuEasyViz/dataItem.C           |   22 +-
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 source/APPLICATIONS/QuEasyViz/fileBrowser.C        |   20 -
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 source/APPLICATIONS/QuEasyViz/inputDataItem.C      |   20 -
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 source/APPLICATIONS/QuEasyViz/inputDataItemIO.C    |   30 +-
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 source/APPLICATIONS/TOOLS/AddMissingAtoms.C        |  100 +
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 source/APPLICATIONS/TOOLS/BondOrderAssigner.C      |   67 +-
 source/APPLICATIONS/TOOLS/CMakeLists.txt           |    6 +-
 .../TOOLS/CalculateBindingFreeEnergy.C             |  126 ++
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 .../TOOLS/CalculateSolvationFreeEnergy.C           |  109 ++
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 source/APPLICATIONS/TOOLS/CrystalGenerator.C       |   39 +-
 source/APPLICATIONS/TOOLS/DBExporter.C             |    4 +-
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 source/APPLICATIONS/TOOLS/DockPoseClustering.C     |  180 +-
 .../TOOLS/ExtractClustersFromWardTree.C            |  170 ++
 source/APPLICATIONS/TOOLS/ExtractProteinChains.C   |  122 ++
 source/APPLICATIONS/TOOLS/ExtractProteinSequence.C |   75 +
 .../TOOLS/FingerprintSimilarityClustering.C        |  487 +++--
 .../TOOLS/FingerprintSimilaritySearch.C            |    7 +-
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 source/APPLICATIONS/TOOLS/MolecularFileConverter.C |   18 +-
 source/APPLICATIONS/TOOLS/PDBRMSDCalculator.C      |  308 ++++
 source/APPLICATIONS/TOOLS/PeptideBuilder.C         |   24 +-
 source/APPLICATIONS/TOOLS/PoseIndices2PDB.C        |  149 ++
 source/APPLICATIONS/TOOLS/ProteinProtonator.C      |  122 +-
 source/APPLICATIONS/TOOLS/RMSDCalculator.C         |   12 +-
 source/APPLICATIONS/TOOLS/RemoveWater.C            |   75 +
 source/APPLICATIONS/TOOLS/ResidueChecker.C         |  199 ++
 source/APPLICATIONS/TOOLS/SideChainGridBuilder.C   |    8 +-
 .../APPLICATIONS/TOOLS/Split2ConnectedComponents.C |   94 +-
 .../TOOLS/Trajectory2RigidTransformation.C         |   91 +
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 source/APPLICATIONS/TOOLS/VendorFinder.C           |    4 +-
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 source/DATATYPE/string.C                           |   25 +-
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 source/QSAR/snBModel.C                             |   20 -
 source/QSAR/statistics.C                           |   20 -
 source/QSAR/svmModel.C                             |   20 -
 source/QSAR/svrModel.C                             |   22 +-
 source/QSAR/validation.C                           |   20 -
 source/SCORING/COMMON/diffGridBasedScoring.C       |   18 -
 source/SCORING/COMMON/diffScoringFunction.C        |   18 -
 source/SCORING/COMMON/gridBasedScoring.C           |   18 -
 source/SCORING/COMMON/scoreGridSet.C               |   18 -
 source/SCORING/COMMON/scoringComponent.C           |   18 -
 source/SCORING/COMMON/scoringOptimizer.C           |   18 -
 source/SCORING/COMPONENTS/CHPI.C                   |   20 -
 source/SCORING/COMPONENTS/PB.C                     |   17 -
 source/SCORING/COMPONENTS/PLP.C                    |   18 -
 source/SCORING/COMPONENTS/advElectrostatic.C       |   18 -
 source/SCORING/COMPONENTS/aromaticRingStacking.C   |   18 -
 source/SCORING/COMPONENTS/burialDepth.C            |   18 -
 source/SCORING/COMPONENTS/buriedPolar.C            |   19 -
 source/SCORING/COMPONENTS/electrostatic.C          |   18 -
 .../SCORING/COMPONENTS/fragmentationalSolvation.C  |   18 -
 source/SCORING/COMPONENTS/fresnoTypes.C            |   18 -
 source/SCORING/COMPONENTS/hydrogenBond.C           |   19 -
 source/SCORING/COMPONENTS/lipophilic.C             |   18 -
 source/SCORING/COMPONENTS/polarity.C               |   18 -
 source/SCORING/COMPONENTS/rotationalEntropy.C      |   18 -
 source/SCORING/COMPONENTS/solvation.C              |   18 -
 source/SCORING/COMPONENTS/vanDerWaals.C            |   18 -
 source/SCORING/FUNCTIONS/MMScoring.C               |   18 -
 source/SCORING/FUNCTIONS/PBScoring.C               |   20 +-
 source/SCORING/FUNCTIONS/PLPScoring.C              |   18 -
 source/SCORING/FUNCTIONS/gridedMM.C                |   17 -
 source/SCORING/FUNCTIONS/gridedPLP.C               |   18 -
 source/SCORING/FUNCTIONS/rescoring.C               |   18 -
 source/SCORING/FUNCTIONS/rescoring1D.C             |   18 -
 source/SCORING/FUNCTIONS/rescoring3D.C             |   18 -
 source/SCORING/FUNCTIONS/rescoring4D.C             |   19 -
 source/STRUCTURE/assignBondOrderProcessor.C        |   11 +
 source/STRUCTURE/binaryFingerprintMethods.C        |  308 +---
 source/STRUCTURE/logP.C                            |    2 +
 source/STRUCTURE/numericalSAS.C                    |    5 +-
 source/STRUCTURE/residueChecker.C                  |    8 +-
 source/STRUCTURE/smartsParserLexer.l               |    2 +
 source/STRUCTURE/smilesParserLexer.l               |    2 +
 source/SYSTEM/MPISupport.C                         |   14 +-
 source/SYSTEM/fileSystem.C                         |   13 +
 source/TEST/CMakeLists.txt                         |   14 +-
 source/TEST/FileSystem_test.C                      |    9 +
 source/TEST/HMOFile_test.C                         |  201 ++
 source/TEST/Makefile.lst                           |  291 ---
 source/TEST/NMRStarFile_test.C                     |    2 +-
 source/TEST/PDBFile_test.C                         |    4 +-
 source/TEST/PoseClustering_test.C                  |  487 ++++-
 source/TEST/SCWRLRotamerFile_test.C                |   28 +-
 source/TEST/Socket_test.C                          |    2 +
 source/TEST/cmake/BALLTestExecutables.cmake        |    1 +
 source/TEST/data/HMOFile_test.hmo                  | 1936 ++++++++++++++++++++
 source/TEST/data/HMOFile_test_no_charge.hmo        | 1932 +++++++++++++++++++
 source/TEST/data/PoseClustering_transformFile.dat  |    8 +
 source/TEST/data/PoseClustering_wardtree.dat       |    1 +
 source/TEST/stringStub.C                           |    9 -
 source/VIEW/DIALOGS/coloringSettingsDialog.C       |   17 +-
 source/VIEW/DIALOGS/displayProperties.C            |   13 +-
 source/VIEW/DIALOGS/lightSettings.C                |    5 +-
 source/VIEW/DIALOGS/materialSettings.C             |  132 +-
 source/VIEW/DIALOGS/materialSettings.ui            |   48 -
 source/VIEW/DIALOGS/stageSettings.ui               |    2 +-
 source/VIEW/KERNEL/MODES/editMode.C                |    4 +
 source/VIEW/KERNEL/representationManager.C         |    1 +
 source/VIEW/KERNEL/shortcutRegistry.C              |    2 -
 source/VIEW/KERNEL/sources.cmake                   |    1 -
 source/VIEW/KERNEL/stage.C                         |   10 +-
 source/VIEW/KERNEL/stringStub.C                    |    9 -
 source/VIEW/RENDERING/RENDERERS/XML3DRenderer.C    |   96 +-
 source/VIEW/RENDERING/RENDERERS/glRenderer.C       |   64 +-
 source/VIEW/RENDERING/RENDERERS/rtfactRenderer.C   | 1394 +++++++++++---
 source/VIEW/RENDERING/renderSetup.C                |   17 +-
 source/VIEW/WIDGETS/geometricControl.C             |   98 +-
 source/VIEW/WIDGETS/molecularControl.C             |   23 +-
 source/VIEW/WIDGETS/molecularStructure.C           |    8 +-
 source/VIEW/WIDGETS/scene.C                        |  279 +--
 443 files changed, 16731 insertions(+), 8172 deletions(-)
 create mode 100644 cmake/BALLConfigNoexcept.cmake
 create mode 100644 cmake/BALLConfigStdStringFeatures.cmake
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial02.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial03.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial04.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial05.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial06.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial07.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial08.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial09.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial10.html
 create mode 100644 data/HTMLBasedInterface/html_de/lehrer/wiki_tutorial11.html
 create mode 100644 data/HTMLBasedInterface/html_de/wiki_tutorial.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog02.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog03.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog04.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog05.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog06.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog07.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog08.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog09.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial/tutorial_dialog10.html
 create mode 100644 data/HTMLBasedInterface/html_eng/tutorial_dialog.html
 create mode 100644 data/HTMLBasedInterface/images/ballview_menueleiste.jpg
 create mode 100644 data/HTMLBasedInterface/images/ballview_repraesentation.jpg
 create mode 100644 data/HTMLBasedInterface/images/ballview_uebersicht.jpg
 create mode 100644 data/HTMLBasedInterface/scripts/connectVIEW.js
 delete mode 100644 debian/patches/0008-Added-MAX_PENALTY-option-to-bond-order-assignment.patch
 delete mode 100644 debian/patches/0009-Fixed-a-bug-in-the-AssignBondOrderProcessor.patch
 delete mode 100644 debian/patches/0010-Fix-compilation-of-FTPBondOrderStrategy-Fixes-451.patch
 delete mode 100644 debian/patches/0101-cmake-syntax.patch
 delete mode 100644 debian/patches/0102-fix-boost-compatibility-issue.patch
 delete mode 100644 debian/patches/0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
 delete mode 100644 debian/patches/HelpSipAmbiguity.patch
 delete mode 100644 debian/patches/more-gcc5_issues.patch
 create mode 100644 include/BALL/FORMAT/HMOFile.h
 delete mode 100644 include/BALL/VIEW/KERNEL/stringStub.h
 create mode 100644 source/APPLICATIONS/TOOLS/AddMissingAtoms.C
 create mode 100644 source/APPLICATIONS/TOOLS/CalculateBindingFreeEnergy.C
 create mode 100644 source/APPLICATIONS/TOOLS/CalculateEnergy.C
 create mode 100644 source/APPLICATIONS/TOOLS/CalculateSolvationFreeEnergy.C
 create mode 100644 source/APPLICATIONS/TOOLS/ExtractClustersFromWardTree.C
 create mode 100644 source/APPLICATIONS/TOOLS/ExtractProteinChains.C
 create mode 100644 source/APPLICATIONS/TOOLS/ExtractProteinSequence.C
 create mode 100644 source/APPLICATIONS/TOOLS/PDBRMSDCalculator.C
 create mode 100644 source/APPLICATIONS/TOOLS/PoseIndices2PDB.C
 create mode 100644 source/APPLICATIONS/TOOLS/RemoveWater.C
 create mode 100644 source/APPLICATIONS/TOOLS/ResidueChecker.C
 create mode 100644 source/APPLICATIONS/TOOLS/Trajectory2RigidTransformation.C
 delete mode 100644 source/APPLICATIONS/TOOLS/stringStub.C
 create mode 100644 source/APPLICATIONS/TOOLS/tool_conf.xml.section
 copy source/EXTENSIONS/{PRESENTABALL => BALLAXY}/CMakeLists.txt (67%)
 create mode 100644 source/EXTENSIONS/BALLAXY/include/BALLaxyInterface.h
 create mode 100644 source/EXTENSIONS/BALLAXY/include/BALLaxyInterfacePreferences.h
 copy source/EXTENSIONS/{PRESENTABALL/include/PresentaBALLPlugin.h => BALLAXY/include/BALLaxyPlugin.h} (75%)
 create mode 100644 source/EXTENSIONS/BALLAXY/source/BALLaxyInterface.C
 create mode 100644 source/EXTENSIONS/BALLAXY/source/BALLaxyInterfacePreferences.C
 create mode 100644 source/EXTENSIONS/BALLAXY/source/BALLaxyInterfacePreferences.ui
 create mode 100644 source/EXTENSIONS/BALLAXY/source/BALLaxyPlugin.C
 copy source/EXTENSIONS/{PRESENTABALL => BALLAXY}/source/logo.png (100%)
 create mode 100644 source/EXTENSIONS/BALLAXY/source/logo.qrc
 create mode 100644 source/EXTENSIONS/PRESENTABALL/include/PresentaBALLSettings.h
 create mode 100644 source/EXTENSIONS/PRESENTABALL/source/PresentaBALLSettings.C
 create mode 100644 source/EXTENSIONS/PRESENTABALL/source/PresentaBALLSettings.ui
 delete mode 100644 source/EXTENSIONS/XML3D/Makefile
 create mode 100644 source/FORMAT/HMOFile.C
 create mode 100644 source/PYTHON/EXTENSIONS/BALL/HMOFile.sip
 create mode 100644 source/PYTHON/EXTENSIONS/BALL/aromaticityProcessor.sip
 create mode 100644 source/PYTHON/EXTENSIONS/BALL/assignTypes.sip
 delete mode 100644 source/PYTHON/EXTENSIONS/TEST/Makefile.lst
 delete mode 100755 source/PYTHON/Makefile.win
 create mode 100644 source/TEST/HMOFile_test.C
 delete mode 100644 source/TEST/Makefile.lst
 create mode 100644 source/TEST/data/HMOFile_test.hmo
 create mode 100644 source/TEST/data/HMOFile_test_no_charge.hmo
 create mode 100644 source/TEST/data/PoseClustering_transformFile.dat
 create mode 100644 source/TEST/data/PoseClustering_wardtree.dat
 delete mode 100644 source/TEST/stringStub.C
 delete mode 100644 source/VIEW/KERNEL/stringStub.C

-- 
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