#
# ChangeLog for src/Atom/atom_bondedparticle.hpp
#
# Generated by Trac 1.4.4
# Jan 9, 2025, 9:57:23 AM

Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber <heber@…> [c6719d]
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)

	FIX: atom_bondedparticle signatures changed to more const versions.
 ...


Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber <heber@…> [f01769]
	* src/Actions/AtomAction/ChangeElementAction.cpp (modified)
	* src/Actions/FillAction/FillRegularGridAction.cpp (modified)
	* src/Actions/FillAction/FillSurfaceAction.cpp (modified)
	* src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/RemoveAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified)
	* src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.cpp (modified)
	* src/Actions/WorldAction/RepeatBoxAction.def (modified)
	* src/Analysis/analysis_bonds.cpp (modified)
	* src/Analysis/analysis_correlation.cpp (modified)
	* src/Atom/AtomSet.hpp (modified)
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/AtomIdSet.cpp (modified)
	* src/AtomIdSet.hpp (modified)
	* src/Bond/BondInfo.cpp (modified)
	* src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified)
	* src/Filling/unittests/ClusterUnitTest.cpp (modified)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/Graph.cpp (modified)
	* src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified)
	* src/Graph/AdjacencyList.cpp (modified)
	* src/Graph/BuildInducedSubgraph.cpp (modified)
	* src/Graph/BuildInducedSubgraph.hpp (modified)
	* src/Parameters/Specifics/Value_molecule.cpp (modified)
	* src/Parameters/StreamOperators.hpp (modified)
	* src/Parameters/Validators/Specific/AtomIdValidator.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (modified)
	* src/Tesselation/boundary.cpp (modified)
	* src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified)
	* src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified)
	* src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified)
	* src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified)
	* src/UIElements/TextUI/Query/MoleculesTextQuery.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/GLMoleculeObject_molecule.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified)
	* src/UIElements/Views/Qt4/QtFragmentList.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/AtomIdSetUnitTest.cpp (modified)

	Replaced World::getAtom() wherever possible by const version.

	- ...


Wed, 17 Apr 2013 18:56:54 GMT Frederik Heber <heber@…> [378fc6b]
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/Atom/atom_observable.hpp (modified)
	* src/Graph/BondGraph.cpp (modified)
	* src/Graph/BondGraph.hpp (modified)

	Refactored CorrectBondDegree() and resetBondDegree() out of ...


Fri, 22 Mar 2013 00:04:17 GMT Frederik Heber <heber@…> [d948b4]
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)

	atom_bondedparticle::addBond() returns no longer const bond::ptr.

	- ...


Wed, 13 Feb 2013 15:47:38 GMT Frederik Heber <heber@…> [7d82a5]
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/Atom/atom_bondedparticleinfo.hpp (modified)
	* src/Bond/bond.cpp (modified)
	* src/Bond/bond.hpp (modified)
	* src/Fragmentation/BondsPerShortestPath.cpp (modified)
	* src/Fragmentation/BondsPerShortestPath.hpp (modified)
	* src/Fragmentation/PowerSetGenerator.cpp (modified)
	* src/Graph/BreadthFirstSearchAdd.cpp (modified)
	* src/Graph/CyclicStructureAnalysis.cpp (modified)
	* src/Graph/DepthFirstSearchAnalysis.cpp (modified)
	* src/Tesselation/boundary.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified)
	* src/World.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	Changed bond::ptr into boost::shared_ptr.

	Changes:
	- refactored ...


Thu, 17 Jan 2013 22:59:15 GMT Frederik Heber <heber@…> [88c8ec]
	* src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified)
	* src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified)
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/Atom/atom_bondedparticleinfo.hpp (modified)
	* src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified)
	* src/Bond/BondInfo.cpp (modified)
	* src/Bond/BondInfo.hpp (modified)
	* src/Bond/bond.cpp (modified)
	* src/Bond/bond.hpp (modified)
	* src/Fragmentation/BondsPerShortestPath.cpp (modified)
	* src/Fragmentation/PowerSetGenerator.cpp (modified)
	* src/Fragmentation/PowerSetGenerator.hpp (modified)
	* src/Graph/BondGraph.hpp (modified)
	* src/Graph/BreadthFirstSearchAdd.cpp (modified)
	* src/Graph/BreadthFirstSearchAdd.hpp (modified)
	* src/Graph/CyclicStructureAnalysis.cpp (modified)
	* src/Graph/CyclicStructureAnalysis.hpp (modified)
	* src/Graph/DepthFirstSearchAnalysis.cpp (modified)
	* src/Graph/DepthFirstSearchAnalysis.hpp (modified)
	* src/Parser/Psi3Parser.cpp (modified)
	* src/Tesselation/boundary.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.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/GLMoleculeObject_bond.hpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	REFACTOR: Replaced all "bond *" appearances by bond::ptr.

	- this is ...


Fri, 14 Dec 2012 14:30:23 GMT Frederik Heber <heber@…> [f63e41]
	* src/Actions/BondAction/BondAddAction.cpp (added)
	* src/Actions/BondAction/BondAddAction.def (added)
	* src/Actions/BondAction/BondAddAction.hpp (added)
	* src/Actions/BondAction/BondRemoveAction.cpp (added)
	* src/Actions/BondAction/BondRemoveAction.def (added)
	* src/Actions/BondAction/BondRemoveAction.hpp (added)
	* src/Actions/GlobalListOfActions.hpp (modified)
	* src/Actions/Makefile.am (modified)
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/Atom/atom_bondedparticleinfo.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.hpp (modified)
	* src/UIElements/Menu/MenuDescription.cpp (modified)
	* tests/regression/Bond/Add/post/test.pdb (added)
	* tests/regression/Bond/Add/pre/test.pdb (added)
	* tests/regression/Bond/Add/testsuite-bond-add.at (added)
	* tests/regression/Bond/Remove/post/test.pdb (added)
	* tests/regression/Bond/Remove/pre/test.pdb (added)
	* tests/regression/Bond/Remove/testsuite-bond-remove.at (added)
	* tests/regression/Bond/testsuite-bond.at (added)
	* tests/regression/Makefile.am (modified)
	* tests/regression/testsuite.at (modified)

	Added Actions to add and remove a bond in between two atoms.

	- ...


Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber <heber@…> [3aa8a5]
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/fragmentation_helpers.cpp (modified)
	* src/Graph/AdjacencyList.cpp (modified)
	* src/Graph/AdjacencyList.hpp (modified)
	* src/Graph/unittests/AdjacencyListUnitTest.cpp (modified)
	* src/Graph/unittests/AdjacencyListUnitTest.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified)
	* tests/regression/Molecules/SaveAdjacency/post/test.adj (modified)

	REFACTOR: AdjacencyList now just contains a single internal map.

	- ...


Fri, 06 Apr 2012 11:44:50 GMT Frederik Heber <heber@…> [cc9119]
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)

	Refactored BondedParticle::removeAllBonds() into variant with and ...


Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber <heber@…> [05a885]
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)

	FIX: BondedParticle::addBond returns * const not const *.

	- return ...


Wed, 28 Dec 2011 15:30:06 GMT Frederik Heber <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/

	- ...