# # ChangeLog for src/Graph # # Generated by Trac 1.6 # Aug 13, 2025, 11:37:06 AM 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.