# # ChangeLog for src/Graph # # Generated by Trac 1.4.4 # Jan 4, 2025, 12:43:48 PM Tue, 03 Apr 2012 08:00:19 GMT Frederik Heber [108968] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) FIX: Rewrite of BondGraph's CreateAdjacency() and ... Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [8e1f901] * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) molecule uses AtomIdSet now, rename getAtoms -> getAtomIds(). - ... Wed, 22 Feb 2012 11:29:04 GMT Frederik Heber [826e8c] * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (modified) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) Introduced new LinkedCell into BondGraph. - new convenience ... Wed, 22 Feb 2012 11:28:28 GMT Frederik Heber [44f53e] * src/Analysis/analysis_correlation.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/WorldTime.cpp (modified) Made various verbosities a lot less annoying. - LinkedCell_Model ... Fri, 17 Feb 2012 15:24:20 GMT Frederik Heber [52ed5b] * src/Atom/atom_bondedparticle.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) Ids handed out by molecule now start with 1. - this required some ... Wed, 04 Jan 2012 14:28:40 GMT Frederik Heber [0aa122] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/AtomStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) Updated all source files's copyright note to current year 2012. Mon, 02 Jan 2012 13:34:28 GMT Frederik Heber [6bd7e0] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/linkedcell.hpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.hpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/CandidateForTesselation.hpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/ellipsoid.hpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/tesselationhelpers.hpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/triangleintersectionlist.hpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.hpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) * src/molecule.hpp (modified) Renamed old LinkedCell class to LinkedCell_deprecated. - this is ... Wed, 28 Dec 2011 15:30:06 GMT Frederik Heber [6f0841] * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomSet.hpp (moved) * src/Atom/AtomicInfo.cpp (moved) * src/Atom/AtomicInfo.hpp (moved) * src/Atom/Makefile.am (added) * src/Atom/TesselPoint.cpp (moved) * src/Atom/TesselPoint.hpp (moved) * src/Atom/atom.cpp (moved) * src/Atom/atom.hpp (moved) * src/Atom/atom_atominfo.cpp (moved) * src/Atom/atom_atominfo.hpp (moved) * src/Atom/atom_bondedparticle.cpp (moved) * src/Atom/atom_bondedparticle.hpp (moved) * src/Atom/atom_bondedparticleinfo.cpp (moved) * src/Atom/atom_bondedparticleinfo.hpp (moved) * src/Atom/atom_graphnode.cpp (moved) * src/Atom/atom_graphnode.hpp (moved) * src/Atom/atom_graphnodeinfo.cpp (moved) * src/Atom/atom_graphnodeinfo.hpp (moved) * src/Atom/atom_observable.cpp (moved) * src/Atom/atom_observable.hpp (moved) * src/Atom/atom_particleinfo.cpp (moved) * src/Atom/atom_particleinfo.hpp (moved) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/LinkedCell/PointCloudAdaptor.hpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/Makefile.am (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Thermostat.hpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Shifted all modules related to atoms into own subfolder src/Atom/ - ... Wed, 28 Dec 2011 15:30:06 GMT Frederik Heber [53c7fc] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/LinkedCell/IPointCloud.hpp (moved) * src/LinkedCell/PointCloudAdaptor.hpp (moved) * src/LinkedCell/linkedcell.cpp (moved) * src/LinkedCell/linkedcell.hpp (moved) * src/Makefile.am (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.hpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) Moved linkedcell.[ch]pp and related files to folder src/LinkedCell. ... Wed, 28 Dec 2011 15:25:49 GMT Frederik Heber [59fff1] * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Tesselation/BoundaryMaps.hpp (modified) * src/Tesselation/boundary.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) Replaced the molecule::const_iterator by a true const version of the ... Wed, 28 Dec 2011 15:24:58 GMT Frederik Heber [d103d3] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/TesselPoint.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_observable.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) Added additional check in CodeCheck's project disclaimer for current ... Wed, 28 Dec 2011 15:24:24 GMT Frederik Heber [68c923] * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (modified) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Box.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/IPointCloud.hpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) Lots of small compiler warning fixes. Issues: - non-virtual ... Wed, 28 Dec 2011 15:24:23 GMT Frederik Heber [de29ad6] * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) Some optimization to speed up Subgraph dissections. - Replaced ... Fri, 04 Nov 2011 15:20:22 GMT Frederik Heber [42c9e2] * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.hpp (modified) FIX: getKeys() and getValues() are now simply internal functions of ... Thu, 03 Nov 2011 19:44:01 GMT Frederik Heber [47d041] * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Element/periodentafel.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Views/StreamStringView.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) HUGE: Removed all calls to Log(), eLog(), replaced by LOG() and ... Wed, 26 Oct 2011 15:02:53 GMT Frederik Heber [07a47e] * configure.ac (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.def (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/BondsPerShortestPath.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/HydrogenSaturation_enum.hpp (added) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/PowerSetGenerator.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/CyclicStructureAnalysis.hpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeLeafClass.hpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/moleculelist.cpp (modified) Replaced enable/disable-hydrogen by internal switch. - changes in ... Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [42127c] * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/MoleculeListClass.hpp (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/World.cpp (modified) * src/config.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) Extracted definition of MoleculeListClass and put into own header module. Tue, 25 Oct 2011 12:08:03 GMT Frederik Heber [d3abb1] * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Makefile.am (modified) * src/MoleculeLeafClass.cpp (added) * src/MoleculeLeafClass.hpp (added) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) Extracted MoleculeLeafClass into own module. - removed some ... Tue, 25 Oct 2011 12:08:02 GMT Frederik Heber [708798] * src/Graph/Makefile.am (modified) FIX: removed -version-info from libMolecuilderGraph. - it's just a ... Tue, 25 Oct 2011 12:08:02 GMT Frederik Heber [ec87e4] * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.hpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (added) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp (added) * src/Graph/unittests/Makefile.am (modified) * src/molecule_fragmentation.cpp (modified) Rewrite of CheckAgainstAdjacencyFile. - we now construct two ... Thu, 20 Oct 2011 13:20:09 GMT Frederik Heber [539f32] * src/Graph/BondGraph.cpp (modified) Enhanced BondGraph::CreateAdjacency() a bit. Thu, 20 Oct 2011 13:20:03 GMT Frederik Heber [9317be] * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) Replaced molecule::atomVector by World::AtomComposite everywhere. Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [829761] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) New function BondGraph::CleanupBondLengthTable(). - allows for ... Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [1ac24b] * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.hpp (modified) Added unit test function SerializationTest to BondGraphUnitTest. Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [f007a1] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) Added serialization capability to class BondGraph. - note that we ... Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber [9b6663] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.hpp (modified) Added operator==() to BondGraph. - also added new unit test ... Mon, 17 Oct 2011 20:17:51 GMT Frederik Heber [a9b86d] * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/EnergyMatrix.cpp (added) * src/Fragmentation/EnergyMatrix.hpp (added) * src/Fragmentation/ForceMatrix.cpp (added) * src/Fragmentation/ForceMatrix.hpp (added) * src/Fragmentation/HessianMatrix.cpp (added) * src/Fragmentation/HessianMatrix.hpp (added) * src/Fragmentation/KeySetsContainer.cpp (added) * src/Fragmentation/KeySetsContainer.hpp (added) * src/Fragmentation/Makefile.am (added) * src/Fragmentation/MatrixContainer.cpp (added) * src/Fragmentation/MatrixContainer.hpp (added) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/defs.hpp (added) * src/Fragmentation/helpers.cpp (added) * src/Fragmentation/helpers.hpp (added) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/parser.cpp (deleted) * src/Fragmentation/parser.hpp (deleted) * src/Graph/BondGraph.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) Split up modules parser.[ch]pp into one module per class. - fixed ... Mon, 17 Oct 2011 16:18:54 GMT Frederik Heber [3bdb6d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/Hbondangle.db (moved) * src/Element/Hbonddistance.db (moved) * src/Element/Makefile.am (added) * src/Element/element.cpp (moved) * src/Element/element.hpp (moved) * src/Element/elements.db (moved) * src/Element/elements_db.cpp (moved) * src/Element/elements_db.hpp (moved) * src/Element/orbitals.db (moved) * src/Element/periodentafel.cpp (moved) * src/Element/periodentafel.hpp (moved) * src/Element/valence.db (moved) * src/Formula.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ElementUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/PeriodentafelUnitTest.cpp (modified) Moved all stuff related to elements into own subfolder and has its ... Fri, 14 Oct 2011 14:08:41 GMT Frederik Heber [629e43] * src/Graph/unittests/BondGraphUnitTest.cpp (moved) * src/Graph/unittests/BondGraphUnitTest.hpp (moved) * src/Graph/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Moved unitests on BondGraph into subfolder src/Graph/unittests. - ... Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber [bc28b0] * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/analyzer.cpp (moved) * src/Fragmentation/datacreator.cpp (moved) * src/Fragmentation/datacreator.hpp (moved) * src/Fragmentation/joiner.cpp (moved) * src/Fragmentation/parser.cpp (moved) * src/Fragmentation/parser.hpp (moved) * src/Graph/BondGraph.cpp (modified) * src/Makefile.am (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) Moved modules associated with fragmentation into source subfolder ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [5e2f80] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) BondedParticle no more hands out non-const ListOfBonds. - the few ... Thu, 06 Oct 2011 16:06:10 GMT Frederik Heber [db7e6d] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) BondedParticle:: register and unregister are private. - adding and ... Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber [455573] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Large Commit: SUBDIRS in src/Makefile.am replaced by include. - ... Fri, 08 Apr 2011 15:48:50 GMT Frederik Heber [bf4b9f] * LinearAlgebra/.gitignore (added) * LinearAlgebra/AUTHORS (added) * LinearAlgebra/COPYING (added) * LinearAlgebra/ChangeLog (added) * LinearAlgebra/INSTALL (added) * LinearAlgebra/LinearAlgebra-debug.pc.in (added) * LinearAlgebra/LinearAlgebra.pc.in (moved) * LinearAlgebra/Makefile.am (added) * LinearAlgebra/NEWS (added) * LinearAlgebra/README (added) * LinearAlgebra/bootstrap (added) * LinearAlgebra/build-aux/README (added) * LinearAlgebra/configure.ac (added) * LinearAlgebra/doc/Doxyfile (added) * LinearAlgebra/doc/Makefile.am (added) * LinearAlgebra/libLinearAlgebra_config.h.in (added) * LinearAlgebra/m4 (added) * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/defs.hpp (moved) * LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.hpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * LinearAlgebra/src/unittests/Makefile.am (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.hpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (added) * LinearAlgebra/src/unittests/UnitTestMain.cpp (added) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * LinearAlgebra/tests/CodeChecks/Makefile.am (added) * LinearAlgebra/tests/CodeChecks/atlocal.in (added) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (added) * LinearAlgebra/tests/CodeChecks/testsuite.at (added) * Makefile.am (modified) * bootstrap (modified) * build-aux/README (added) * config/depcomp (deleted) * config/install-sh (deleted) * config/ltmain.sh (deleted) * config/missing (deleted) * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra from folder src/ into distinct sub-package. - ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [255829] * configure.ac (modified) * src/BoundaryPolygonSet.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/OutputTemperature.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Formula.hpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Helpers/Makefile.am (deleted) * src/Helpers/defs.hpp (modified) * src/Helpers/helpers.cpp (deleted) * src/Helpers/helpers.hpp (modified) * src/Makefile.am (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) Removed Helpers.hpp, deleted Helpers.cpp and libMoleCuilderHelpers.la ... Fri, 11 Mar 2011 12:38:30 GMT Frederik Heber [13a953] * src/Graph/CheckAgainstAdjacencyFile.cpp (added) * src/Graph/CheckAgainstAdjacencyFile.hpp (added) * src/Graph/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Moved molecule::CheckAdjacencyAgainstFile() into functor in Graph/. ... Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber [2d4334] * src/Graph/BuildInducedSubgraph.cpp (added) * src/Graph/BuildInducedSubgraph.hpp (added) * src/Graph/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Moved BuildInducedSubgraph from molecule into functor in Graph/. - ... Wed, 02 Mar 2011 21:53:09 GMT Frederik Heber [efe516] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) Removed bond::nr. - has only been used by BreadthFirstSearchAdd. - ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [49c059] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (added) * src/Graph/DepthFirstSearchAnalysis.hpp (added) * src/Graph/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * tests/Fragmentations/defs.in (modified) * tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Molecules/MoleculeById/post/id4_missing.xyz (moved) * tests/regression/Selection/Molecules/MoleculeById/post/water_id4.xyz (moved) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-molecules-by-name.at (modified) Moved DepthFirstSearchAnalysis into functor in Graph/. Smaller ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [e73ad9a] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Graph/CyclicStructureAnalysis.cpp (added) * src/Graph/CyclicStructureAnalysis.hpp (added) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Moved CyclicStructureAnalysis from molecule_graph.cpp into own ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [09ac12] * src/Graph/ConnectedSubgraph.cpp (added) * src/Graph/ConnectedSubgraph.hpp (added) * src/Graph/Makefile.am (modified) Added new class ConnectedSubgraph. - inherits list. - will ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [111387] * src/Graph/BreadthFirstSearchAdd.hpp (modified) FIX: BreadthFirstSearchAdd header only includes GraphEdge, not bond ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [129204] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Bond/GraphEdge.cpp (added) * src/Bond/GraphEdge.hpp (added) * src/Bond/bond.cpp (moved) * src/Bond/bond.hpp (moved) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/Makefile.am (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/graph.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Moved bond.* to Bond/, new class GraphEdge which contains graph parts ... Wed, 02 Mar 2011 21:53:07 GMT Frederik Heber [766ba5] * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/bond.cpp (modified) * src/bond.hpp (modified) bond::GetColor() is now static function bond::getColorName(). Wed, 02 Mar 2011 21:53:07 GMT Frederik Heber [53d6b2] * configure.ac (modified) * src/Graph/BreadthFirstSearchAdd.cpp (added) * src/Graph/BreadthFirstSearchAdd.hpp (added) * src/Graph/Makefile.am (added) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Moved unused function BreadthFirstSearchAdd and subfunctions into ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [632508] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Graph/BondGraph.cpp (moved) * src/Graph/BondGraph.hpp (moved) * src/Makefile.am (modified) * src/World.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) Moved files bondgraph.?pp -> Graph/BondGraph.?pp.