[med-svn] [ball] 03/04: Merge tag 'upstream/1.4.3_beta1'
Andreas Tille
tille at debian.org
Thu Jan 7 10:40:35 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ball.
commit 24e40f4d9b634df8562d051d64f12f7ff3088095
Merge: e9947a3 072c9d7
Author: Andreas Tille <tille at debian.org>
Date: Thu Jan 7 10:30:46 2016 +0100
Merge tag 'upstream/1.4.3_beta1'
Upstream version 1.4.3~beta1
.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 +-
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data/HTMLBasedInterface/html_de/wiki_tutorial.html | 44 +
data/HTMLBasedInterface/html_eng/index.html | 6 +
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.../images/ballview_uebersicht.jpg | Bin 0 -> 18478 bytes
.../HTMLBasedInterface/scripts/common_functions.py | 37 +-
data/HTMLBasedInterface/scripts/connectVIEW.js | 282 +++
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 +-
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include/BALL/QSAR/linearModel.h | 20 -
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include/BALL/QSAR/mlrModel.h | 22 +-
include/BALL/QSAR/modelFactory.h | 22 -
include/BALL/QSAR/nBModel.h | 20 -
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include/BALL/QSAR/oplsModel.h | 22 +-
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include/BALL/SCORING/COMPONENTS/burialDepth.h | 18 -
include/BALL/SCORING/COMPONENTS/buriedPolar.h | 18 -
include/BALL/SCORING/COMPONENTS/electrostatic.h | 18 -
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include/BALL/SCORING/COMPONENTS/fresnoTypes.h | 18 -
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include/BALL/SCORING/COMPONENTS/lipophilic.h | 18 -
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include/BALL/SCORING/COMPONENTS/solvation.h | 18 -
include/BALL/SCORING/COMPONENTS/vanDerWaals.h | 18 -
include/BALL/SCORING/FUNCTIONS/MMScoring.h | 18 -
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include/BALL/STRUCTURE/binaryFingerprintMethods.h | 14 +-
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include/BALL/SYSTEM/MPISupport.h | 8 +-
include/BALL/SYSTEM/fileSystem.h | 5 +
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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 +-
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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 +
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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 +
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.../BALLAXY/source/BALLaxyInterfacePreferences.C | 51 +
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source/EXTENSIONS/BALLAXY/source/BALLaxyPlugin.C | 69 +
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source/EXTENSIONS/SPACENAV/CMakeLists.txt | 5 +
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source/FORMAT/HMOFile.C | 448 +++++
source/FORMAT/NMRStarFile.C | 55 +-
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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 +-
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source/PYTHON/EXTENSIONS/BALL/HMOFile.sip | 62 +
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source/QSAR/nonlinearModel.C | 20 -
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source/TEST/Makefile.lst | 291 ---
source/TEST/NMRStarFile_test.C | 2 +-
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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 +--
429 files changed, 16720 insertions(+), 7697 deletions(-)
--
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