[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 -
include/BALL/SCORING/COMMON/scoringComponent.h | 18 -
include/BALL/SCORING/COMMON/scoringOptimizer.h | 18 -
include/BALL/SCORING/COMPONENTS/CHPI.h | 18 -
include/BALL/SCORING/COMPONENTS/PB.h | 18 -
include/BALL/SCORING/COMPONENTS/PLP.h | 18 -
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 -
source/APPLICATIONS/QuEasyRun/main.C | 20 -
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 -
source/APPLICATIONS/QuEasyViz/CSVInputDataItem.h | 20 -
source/APPLICATIONS/QuEasyViz/CSVInputDialog.C | 22 +-
source/APPLICATIONS/QuEasyViz/CSVInputDialog.h | 20 -
source/APPLICATIONS/QuEasyViz/SDFInputDataItem.C | 20 -
source/APPLICATIONS/QuEasyViz/SDFInputDataItem.h | 20 -
source/APPLICATIONS/QuEasyViz/SDFInputDialog.C | 20 -
source/APPLICATIONS/QuEasyViz/SDFInputDialog.h | 20 -
source/APPLICATIONS/QuEasyViz/bayesPlotter.C | 22 +-
source/APPLICATIONS/QuEasyViz/bayesPlotter.h | 20 -
source/APPLICATIONS/QuEasyViz/coefficientPlotter.C | 20 -
source/APPLICATIONS/QuEasyViz/coefficientPlotter.h | 20 -
source/APPLICATIONS/QuEasyViz/componentPlotter.C | 23 +-
source/APPLICATIONS/QuEasyViz/componentPlotter.h | 20 -
source/APPLICATIONS/QuEasyViz/connectionManager.C | 22 +-
source/APPLICATIONS/QuEasyViz/connectionManager.h | 20 -
source/APPLICATIONS/QuEasyViz/dataItem.C | 22 +-
source/APPLICATIONS/QuEasyViz/dataItem.h | 20 -
source/APPLICATIONS/QuEasyViz/dataItemScene.C | 22 +-
source/APPLICATIONS/QuEasyViz/dataItemScene.h | 20 -
source/APPLICATIONS/QuEasyViz/dataItemView.C | 20 -
source/APPLICATIONS/QuEasyViz/dataItemView.h | 20 -
source/APPLICATIONS/QuEasyViz/dottedEdge.C | 22 +-
source/APPLICATIONS/QuEasyViz/dottedEdge.h | 20 -
source/APPLICATIONS/QuEasyViz/edge.C | 20 -
source/APPLICATIONS/QuEasyViz/edge.h | 19 -
source/APPLICATIONS/QuEasyViz/exception.C | 20 -
source/APPLICATIONS/QuEasyViz/exception.h | 20 -
source/APPLICATIONS/QuEasyViz/featurePlotter.C | 20 -
source/APPLICATIONS/QuEasyViz/featurePlotter.h | 20 -
.../QuEasyViz/featureSelectionDialog.C | 22 +-
.../QuEasyViz/featureSelectionDialog.h | 20 -
.../APPLICATIONS/QuEasyViz/featureSelectionItem.C | 22 +-
.../APPLICATIONS/QuEasyViz/featureSelectionItem.h | 20 -
source/APPLICATIONS/QuEasyViz/fileBrowser.C | 20 -
source/APPLICATIONS/QuEasyViz/fileBrowser.h | 20 -
source/APPLICATIONS/QuEasyViz/inputDataDialog.C | 20 -
source/APPLICATIONS/QuEasyViz/inputDataDialog.h | 20 -
source/APPLICATIONS/QuEasyViz/inputDataItem.C | 20 -
source/APPLICATIONS/QuEasyViz/inputDataItem.h | 20 -
source/APPLICATIONS/QuEasyViz/inputDataItemIO.C | 30 +-
source/APPLICATIONS/QuEasyViz/inputDataItemIO.h | 19 -
source/APPLICATIONS/QuEasyViz/inputDialog.C | 20 -
source/APPLICATIONS/QuEasyViz/inputDialog.h | 20 -
source/APPLICATIONS/QuEasyViz/inputPartitionItem.C | 19 -
source/APPLICATIONS/QuEasyViz/inputPartitionItem.h | 19 -
source/APPLICATIONS/QuEasyViz/inputPlotter.C | 20 -
source/APPLICATIONS/QuEasyViz/inputPlotter.h | 20 -
source/APPLICATIONS/QuEasyViz/main.C | 19 -
source/APPLICATIONS/QuEasyViz/mainWindow.C | 24 +-
source/APPLICATIONS/QuEasyViz/mainWindow.h | 19 -
.../QuEasyViz/modelConfigurationDialog.C | 21 -
.../QuEasyViz/modelConfigurationDialog.h | 19 -
.../QuEasyViz/modelConfigurationDialogPages.C | 20 -
.../QuEasyViz/modelConfigurationDialogPages.h | 20 -
source/APPLICATIONS/QuEasyViz/modelItem.C | 22 +-
source/APPLICATIONS/QuEasyViz/modelItem.h | 19 -
.../APPLICATIONS/QuEasyViz/modelPropertiesDialog.C | 21 -
.../APPLICATIONS/QuEasyViz/modelPropertiesDialog.h | 20 -
source/APPLICATIONS/QuEasyViz/partitioningItem.C | 20 -
source/APPLICATIONS/QuEasyViz/partitioningItem.h | 20 -
source/APPLICATIONS/QuEasyViz/pipeline.C | 19 -
source/APPLICATIONS/QuEasyViz/pipeline.h | 20 -
source/APPLICATIONS/QuEasyViz/plotter.C | 21 -
source/APPLICATIONS/QuEasyViz/plotter.h | 20 -
source/APPLICATIONS/QuEasyViz/predictionItem.C | 21 -
source/APPLICATIONS/QuEasyViz/predictionItem.h | 20 -
source/APPLICATIONS/QuEasyViz/predictionPlotter.C | 22 +-
source/APPLICATIONS/QuEasyViz/predictionPlotter.h | 20 -
.../QuEasyViz/predictionResultDialog.C | 22 -
.../QuEasyViz/predictionResultDialog.h | 20 -
source/APPLICATIONS/QuEasyViz/validationDialog.C | 22 +-
source/APPLICATIONS/QuEasyViz/validationDialog.h | 21 -
source/APPLICATIONS/QuEasyViz/validationItem.C | 22 -
source/APPLICATIONS/QuEasyViz/validationItem.h | 20 -
.../QuEasyViz/validationResultDialog.C | 25 -
.../QuEasyViz/validationResultDialog.h | 20 -
source/APPLICATIONS/TOOLS/AddMissingAtoms.C | 100 +
source/APPLICATIONS/TOOLS/BindingDBCleaner.C | 23 +-
source/APPLICATIONS/TOOLS/BondOrderAssigner.C | 67 +-
source/APPLICATIONS/TOOLS/CMakeLists.txt | 6 +-
.../TOOLS/CalculateBindingFreeEnergy.C | 126 ++
source/APPLICATIONS/TOOLS/CalculateEnergy.C | 279 +++
.../TOOLS/CalculateSolvationFreeEnergy.C | 109 ++
source/APPLICATIONS/TOOLS/Converter.C | 108 +-
source/APPLICATIONS/TOOLS/CrystalGenerator.C | 39 +-
source/APPLICATIONS/TOOLS/DBExporter.C | 4 +-
source/APPLICATIONS/TOOLS/DBImporter.C | 4 +-
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 +-
source/APPLICATIONS/TOOLS/GalaxyConfigGenerator.C | 56 +-
source/APPLICATIONS/TOOLS/LigandFileSplitter.C | 517 +++---
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 +
.../TOOLS/TrajectoryFile2PDBSplitter.C | 49 +-
source/APPLICATIONS/TOOLS/VendorFinder.C | 4 +-
source/APPLICATIONS/TOOLS/sources.cmake | 14 +-
source/APPLICATIONS/TOOLS/stringStub.C | 9 -
source/APPLICATIONS/TOOLS/tool_conf.xml.section | 131 ++
source/APPLICATIONS/UTILITIES/pdb2dcd.C | 33 +-
source/DATATYPE/string.C | 25 +-
source/DOCKING/COMMON/poseClustering.C | 686 +++++--
source/DOCKING/COMMON/staticLigandFragment.C | 18 -
source/DOCKING/COMMON/structurePreparer.C | 18 -
source/DOCKING/GENETICDOCK/rotateBond.C | 24 +-
source/DOCKING/IMGDOCK/IMGDock.C | 18 -
source/DOCKING/geometricFit.C | 16 +-
source/EXAMPLES/PDBChecker.C | 1 +
.../{PRESENTABALL => BALLAXY}/CMakeLists.txt | 23 +-
.../EXTENSIONS/BALLAXY/include/BALLaxyInterface.h | 87 +
.../BALLAXY/include/BALLaxyInterfacePreferences.h | 57 +
.../include/BALLaxyPlugin.h} | 16 +-
.../EXTENSIONS/BALLAXY/source/BALLaxyInterface.C | 417 +++++
.../BALLAXY/source/BALLaxyInterfacePreferences.C | 51 +
.../BALLAXY/source/BALLaxyInterfacePreferences.ui | 220 +++
source/EXTENSIONS/BALLAXY/source/BALLaxyPlugin.C | 69 +
.../{PRESENTABALL => BALLAXY}/source/logo.png | Bin
source/EXTENSIONS/BALLAXY/source/logo.qrc | 5 +
source/EXTENSIONS/BALLPluginComponents.cmake | 2 -
source/EXTENSIONS/CMakeLists.txt | 5 +
source/EXTENSIONS/PRESENTABALL/CMakeLists.txt | 10 +-
.../PRESENTABALL/include/HTMLBasedInterface.h | 31 +-
.../PRESENTABALL/include/PresentaBALLPlugin.h | 3 +
.../PRESENTABALL/include/PresentaBALLSettings.h | 55 +
.../PRESENTABALL/source/HTMLBasedInterface.C | 158 +-
.../PRESENTABALL/source/PresentaBALLPlugin.C | 12 +-
.../PRESENTABALL/source/PresentaBALLSettings.C | 58 +
.../PRESENTABALL/source/PresentaBALLSettings.ui | 62 +
source/EXTENSIONS/SPACENAV/CMakeLists.txt | 5 +
.../SPACENAV/source/spaceNavigatorPlugin.C | 3 +-
source/EXTENSIONS/VRPN/CMakeLists.txt | 5 +
source/EXTENSIONS/VRPNHD/CMakeLists.txt | 5 +
source/EXTENSIONS/XML3D/CMakeLists.txt | 9 +-
source/EXTENSIONS/XML3D/Makefile | 20 -
source/FORMAT/CIFParserLexer.l | 2 +
source/FORMAT/HMOFile.C | 448 +++++
source/FORMAT/NMRStarFile.C | 55 +-
source/FORMAT/PDBFileDetails.C | 2 +-
source/FORMAT/SCWRLRotamerFile.C | 20 +-
source/FORMAT/commandlineParser.C | 245 +--
source/FORMAT/dockResultFile.C | 4 +
source/FORMAT/lineBasedFile.C | 9 +-
source/FORMAT/molFileFactory.C | 637 ++++---
source/FORMAT/paramFile.C | 19 +
source/FORMAT/sources.cmake | 2 +-
source/KERNEL/expressionParserLexer.l | 2 +
source/MOLMEC/AMBER/GAFFCESParserLexer.l | 2 +
source/MOLMEC/COMMON/snapShotManager.C | 1 -
source/PLUGIN/pluginManager.C | 9 +-
source/PYTHON/EXTENSIONS/BALL/BALLCore.sip | 6 +-
source/PYTHON/EXTENSIONS/BALL/HMOFile.sip | 62 +
source/PYTHON/EXTENSIONS/BALL/NMRStarFile.sip | 4 +-
source/PYTHON/EXTENSIONS/BALL/RMSDMinimizer.sip | 40 +-
source/PYTHON/EXTENSIONS/BALL/XYZFile.sip | 12 +-
.../EXTENSIONS/BALL/aromaticityProcessor.sip | 54 +
source/PYTHON/EXTENSIONS/BALL/assignTypes.sip | 74 +
source/PYTHON/EXTENSIONS/BALL/exception.sip | 676 +++----
source/PYTHON/EXTENSIONS/BALL/file.sip | 20 +-
source/PYTHON/EXTENSIONS/BALL/fragmentDB.sip | 3 +-
source/PYTHON/EXTENSIONS/BALL/molFileFactory.sip | 5 +
source/PYTHON/EXTENSIONS/BALL/options.sip | 28 +-
source/PYTHON/EXTENSIONS/BALL/string.sip | 13 +-
source/PYTHON/EXTENSIONS/TEST/Makefile.lst | 43 -
source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip | 10 +-
source/PYTHON/EXTENSIONS/VIEW/serverWidget.sip | 22 +-
source/PYTHON/Makefile.win | 30 -
source/QSAR/Model.C | 22 +-
source/QSAR/QSARData.C | 20 -
source/QSAR/allModel.C | 20 -
source/QSAR/bayesModel.C | 20 -
source/QSAR/classificationModel.C | 20 -
source/QSAR/classificationValidation.C | 20 -
source/QSAR/configIO.C | 20 -
source/QSAR/exception.C | 20 -
source/QSAR/featureSelection.C | 20 -
source/QSAR/fitModel.C | 20 -
source/QSAR/gpModel.C | 20 -
source/QSAR/kernel.C | 20 -
source/QSAR/kernelModel.C | 20 -
source/QSAR/knnModel.C | 20 -
source/QSAR/kpcrModel.C | 20 -
source/QSAR/kplsModel.C | 20 -
source/QSAR/latentVariableModel.C | 20 -
source/QSAR/ldaModel.C | 20 -
source/QSAR/libsvmModel.C | 22 +-
source/QSAR/linearModel.C | 20 -
source/QSAR/logitModel.C | 20 -
source/QSAR/mlrModel.C | 22 +-
source/QSAR/modelFactory.C | 20 -
source/QSAR/nBModel.C | 20 -
source/QSAR/nonlinearModel.C | 20 -
source/QSAR/oplsModel.C | 22 +-
source/QSAR/pcrModel.C | 20 -
source/QSAR/plsModel.C | 22 +-
source/QSAR/registry.C | 20 -
source/QSAR/regressionModel.C | 20 -
source/QSAR/regressionValidation.C | 20 -
source/QSAR/rrModel.C | 22 +-
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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