[Molecuilder-devel] [SCM] branch stable updated. v1.5.3
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Thu Apr 28 20:27:54 CEST 2016
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Those revisions listed above that are new to this repository have
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- Log -----------------------------------------------------------------
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Summary of changes:
configure.ac | 10 +-
doc/userguide/userguide.xml | 13 +-
src/Actions/AtomAction/AddAction.cpp | 73 +-
src/Actions/FillAction/FillRegularGridAction.cpp | 4 +-
src/Actions/FillAction/FillSurfaceAction.cpp | 3 +-
src/Actions/FillAction/FillVolumeAction.cpp | 4 +-
src/Actions/FillAction/SuspendInMoleculeAction.cpp | 1 -
.../AnalyseFragmentationResultsAction.cpp | 57 +-
src/Actions/GlobalListOfActions.hpp | 2 +-
src/Actions/GraphAction/UpdateMoleculesAction.cpp | 17 +-
src/Actions/Makefile.am | 6 +-
src/Actions/MoleculeAction/BondFileAction.def | 2 -
src/Actions/MoleculeAction/ChangeNameAction.def | 2 -
.../LinearInterpolationofTrajectoriesAction.def | 2 -
src/Actions/MoleculeAction/LoadAction.cpp | 20 +-
src/Actions/MoleculeAction/RemoveAction.cpp | 2 +-
.../RotateAroundSelfByAngleAction.def | 1 -
.../RotateToPrincipalAxisSystemAction.def | 2 -
src/Actions/MoleculeAction/SaveAdjacencyAction.def | 2 -
src/Actions/MoleculeAction/SaveBondsAction.def | 2 -
.../MoleculeAction/SaveTemperatureAction.def | 2 -
.../PotentialAction/FitCompoundPotentialAction.cpp | 1 +
.../PotentialAction/FitCompoundPotentialAction.def | 13 +-
...argesAction.cpp => FitPartialChargesAction.cpp} | 16 +-
...argesAction.def => FitPartialChargesAction.def} | 8 +-
...argesAction.hpp => FitPartialChargesAction.hpp} | 4 +-
src/Actions/PotentialAction/FitPotentialAction.cpp | 1 +
src/Actions/PotentialAction/FitPotentialAction.def | 13 +-
src/Actions/UndoRedoHelpers.cpp | 15 +-
src/Actions/WorldAction/InputAction.cpp | 12 +-
src/Actions/WorldAction/RepeatBoxAction.cpp | 4 -
src/Analysis/analysis_bonds.cpp | 15 +-
src/Analysis/analysis_bonds.hpp | 9 +-
src/Analysis/analysis_correlation.cpp | 27 +-
.../AnalysisCorrelationToPointUnitTest.cpp | 1 -
.../AnalysisCorrelationToPointUnitTest.hpp | 1 -
.../AnalysisCorrelationToSurfaceUnitTest.cpp | 1 -
.../AnalysisCorrelationToSurfaceUnitTest.hpp | 1 -
.../unittests/AnalysisPairCorrelationUnitTest.cpp | 1 -
.../unittests/AnalysisPairCorrelationUnitTest.hpp | 1 -
src/Analysis/unittests/CountBondsUnitTest.cpp | 9 +-
src/Analysis/unittests/CountBondsUnitTest.hpp | 3 +-
src/Atom/AtomObserver.cpp | 51 +-
src/Atom/AtomObserver.hpp | 26 +-
src/Atom/AtomicInfo.cpp | 13 +
src/Atom/AtomicInfo.hpp | 1 +
src/Atom/atom.cpp | 59 +-
src/Atom/atom.hpp | 25 +-
src/Atom/atom_observable.hpp | 2 +
src/Atom/unittests/AtomObserverUnitTest.cpp | 47 +-
src/Atom/unittests/AtomObserverUnitTest.hpp | 5 +-
src/Bond/AdjacencyMatcher/Makefile.am | 4 +
src/EntityObserver.hpp | 72 +
src/EntityObserver_impl.hpp | 63 +
src/Filling/Makefile.am | 2 +
...pp => IsCloseEnoughToSurface_FillPredicate.cpp} | 23 +-
.../IsCloseEnoughToSurface_FillPredicate.hpp | 28 +
.../Predicates/IsInsideSurface_FillPredicate.cpp | 3 +-
src/Filling/Preparators/BaseFillerPreparator.cpp | 13 +-
src/Filling/Preparators/BaseFillerPreparator.hpp | 3 +-
src/Fragmentation/Exporters/ExportGraph.cpp | 10 +-
src/Fragmentation/Exporters/ExportGraph.hpp | 5 +-
.../Exporters/ExportGraph_ToFiles.cpp | 5 -
.../Exporters/ExportGraph_ToFiles.hpp | 2 +-
src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp | 1 -
src/Fragmentation/Fragmentation.cpp | 2 +-
.../FunctionApproximation.cpp | 14 +-
.../FunctionApproximation.hpp | 16 +-
src/Graph/ConnectedSubgraph.cpp | 3 -
src/Graph/DepthFirstSearchAnalysis.cpp | 3 -
src/LinkedCell/LinkedCell.cpp | 4 +-
src/LinkedCell/LinkedCell_View.cpp | 10 +-
src/LinkedCell/types.hpp | 2 +-
src/LinkedCell/unittests/LinkedCellUnitTest.cpp | 2 +-
.../unittests/LinkedCell_ViewUnitTest.cpp | 4 +-
src/LinkedCell/unittests/Makefile.am | 1 -
src/Makefile.am | 6 +-
src/MoleculeListClass.hpp | 62 -
.../AtomObserverStub.cpp => MoleculeObserver.cpp} | 35 +-
src/MoleculeObserver.hpp | 41 +
src/Parser/MpqcParser.cpp | 3 -
src/Parser/PcpParser.cpp | 3 -
src/Parser/PdbParser.cpp | 30 +-
src/Parser/Psi3Parser.cpp | 3 -
src/Parser/TremoloParser.cpp | 3 -
src/Parser/XmlParser.cpp | 3 -
src/Parser/XyzParser.cpp | 3 -
src/Potentials/PotentialTrainer.cpp | 3 +-
src/Potentials/PotentialTrainer.hpp | 1 +
src/Tesselation/TriangleMatcher/Makefile.am | 4 +
src/Tesselation/boundary.cpp | 24 -
src/Tesselation/boundary.hpp | 2 -
src/UIElements/Makefile.am | 24 +-
.../Qt4/InstanceBoard/ObservedValue_types.hpp | 37 +
.../Qt4/InstanceBoard/ObservedValue_wCallback.hpp | 77 +
.../Qt4/InstanceBoard/ObservedValuesContainer.hpp | 169 +
.../InstanceBoard/ObservedValuesContainer_impl.hpp | 208 +
.../Qt4/InstanceBoard/QtObservedAtom.cpp | 457 ++
.../Qt4/InstanceBoard/QtObservedAtom.hpp | 304 +
.../Qt4/InstanceBoard/QtObservedBond.cpp | 388 ++
.../Qt4/InstanceBoard/QtObservedBond.hpp | 328 +
.../Qt4/InstanceBoard/QtObservedInstanceBoard.cpp | 421 ++
.../Qt4/InstanceBoard/QtObservedInstanceBoard.hpp | 177 +
.../Qt4/InstanceBoard/QtObservedMolecule.cpp | 548 ++
.../Qt4/InstanceBoard/QtObservedMolecule.hpp | 327 +
src/UIElements/Qt4/QtMainWindow.cpp | 28 +-
src/UIElements/Qt4/QtMainWindow.hpp | 7 +-
src/UIElements/Qt4/QtUIFactory.cpp | 5 +-
src/UIElements/TextUI/TextWindow.cpp | 48 +-
src/UIElements/TextUI/TextWindow.hpp | 6 +
.../Views/Qt4/{ => ElementList}/QtElementList.cpp | 103 +-
.../Views/Qt4/{ => ElementList}/QtElementList.hpp | 32 +-
.../Qt4/ElementList/QtObservedAtomObserver.cpp | 76 +
.../Qt4/ElementList/QtObservedAtomObserver.hpp | 60 +
.../Views/Qt4/MoleculeList/QtMoleculeItem.cpp | 131 +-
.../Views/Qt4/MoleculeList/QtMoleculeItem.hpp | 88 +-
.../Qt4/MoleculeList/QtMoleculeItemFactory.cpp | 51 +-
.../Qt4/MoleculeList/QtMoleculeItemFactory.hpp | 27 +-
.../Views/Qt4/MoleculeList/QtMoleculeList.cpp | 617 +-
.../Views/Qt4/MoleculeList/QtMoleculeList.hpp | 119 +-
.../Views/Qt4/MoleculeList/QtMoleculeListView.cpp | 122 +-
.../Views/Qt4/MoleculeList/QtMoleculeListView.hpp | 24 +-
.../MoleculeList/QtObservedMoleculeObserver.cpp | 101 +
.../MoleculeList/QtObservedMoleculeObserver.hpp | 66 +
.../SpecificItems/QtMoleculeItem_atomcount.hpp | 49 +-
.../SpecificItems/QtMoleculeItem_formula.hpp | 50 +-
.../SpecificItems/QtMoleculeItem_name.hpp | 56 +-
.../SpecificItems/QtMoleculeItem_occurrence.hpp | 19 +-
.../SpecificItems/QtMoleculeItem_visibility.hpp | 28 +-
.../Views/Qt4/Plotting/QSeisPlotPage.cpp | 10 +-
.../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp | 265 +-
.../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp | 80 +-
.../Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp | 265 +-
.../Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp | 84 +-
.../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 714 +-
.../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp | 127 +-
src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp | 958 ++-
src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp | 136 +-
src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp | 154 +-
src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp | 24 +-
src/UIElements/Views/Qt4/QtInfoBox.cpp | 157 +-
src/UIElements/Views/Qt4/QtInfoBox.hpp | 53 +-
.../Views/Qt4/QtSelectionChangedAgent.cpp | 158 -
.../Views/Qt4/QtSelectionChangedAgent.hpp | 58 -
src/UIElements/Views/Qt4/QtToolBar.hpp | 11 +
.../Views/Qt4/QtToolBar_QtFavoriteActions.cpp | 31 +-
src/World.cpp | 106 +-
src/World.hpp | 58 +-
src/builder_init.cpp | 12 +-
src/cleanUp.cpp | 3 +
src/documentation/constructs/qt-gui.dox | 151 +-
src/molecule.cpp | 197 +-
src/molecule.hpp | 91 +-
src/moleculelist.cpp | 659 --
...egular-grid-with-minimum-distance-to-surface.at | 32 +
tests/GuiChecks/Filling/testsuite-filling.at | 1 +
...suite-fragmentation-analyse-fragment-results.at | 34 +-
tests/GuiChecks/Makefile.am | 349 +-
.../testsuite-molecules-tremolo-dbond-file.at | 6 +-
.../testsuite-potential-fit-partial-charges.at} | 16 +-
.../testsuite-potential-fit-potential.at | 14 +-
tests/GuiChecks/Potential/testsuite-potential.at | 2 +-
tests/GuiChecks/adjacencymatcher.in | 4 +-
tests/GuiChecks/trianglematcher.in | 4 +-
tests/Python/AllActions/options.dat | 1 +
.../RegularGrid/post/amylose_filled_water.pdb | 812 +++
.../RegularGrid/pre/amylose_straightened_more.pdb} | 470 +-
.../regression/Filling/RegularGrid/pre}/water.pdb | 8 +-
...egular-grid-with-minimum-distance-to-surface.at | 31 +
tests/regression/Filling/testsuite-filling.at | 1 +
.../LongRange/OBC/BondFragment_Eigenhistogram.dat | 12 +-
.../LongRange/OBC/BondFragment_Eigenvalues.dat | 10 +-
.../post/LongRange/OBC/BondFragment_Energy.dat | 10 +-
.../post/LongRange/OBC/BondFragment_Forces.dat | 12 +-
.../LongRange/OBC/BondFragment_IndexedEnergy.dat | 42 +-
.../LongRange/OBC/BondFragment_LongRangeEnergy.dat | 12 +-
.../LongRange/OBC/BondFragment_LongRangeForces.dat | 7 +
.../post/LongRange/OBC/BondFragment_Times.dat | 12 +-
.../post/LongRange/OBC/BondFragment_VMGEnergy.dat | 13 +-
.../post/LongRange/OBC/BondFragment_VMGForces.dat | 7 +
.../post/{ => LongRange/OBC}/alkane-3.data | 16 +-
.../LongRange/PBC/BondFragment_Eigenhistogram.dat | 12 +-
.../LongRange/PBC/BondFragment_Eigenvalues.dat | 10 +-
.../post/LongRange/PBC/BondFragment_Energy.dat | 10 +-
.../post/LongRange/PBC/BondFragment_Forces.dat | 12 +-
.../LongRange/PBC/BondFragment_IndexedEnergy.dat | 42 +-
.../LongRange/PBC/BondFragment_LongRangeEnergy.dat | 12 +-
.../LongRange/PBC/BondFragment_LongRangeForces.dat | 7 +
.../post/LongRange/PBC/BondFragment_Times.dat | 12 +-
.../post/LongRange/PBC/BondFragment_VMGEnergy.dat | 13 +-
.../post/LongRange/PBC/BondFragment_VMGForces.dat | 7 +
.../post/{ => LongRange/PBC}/alkane-3.data | 14 +-
.../ShortRange/BondFragment_Eigenhistogram.dat | 12 +-
.../post/ShortRange/BondFragment_Eigenvalues.dat | 10 +-
.../post/ShortRange/BondFragment_Energy.dat | 12 +-
.../post/ShortRange/BondFragment_Forces.dat | 10 +-
.../post/ShortRange/BondFragment_IndexedEnergy.dat | 42 +-
.../post/ShortRange/BondFragment_Times.dat | 12 +-
.../pre/BondFragmentLongRangeResults_OBC.dat | 296 +-
.../pre/BondFragmentLongRangeResults_PBC.dat | 296 +-
.../pre/BondFragmentShortRangeResults.dat | 93 +-
...suite-fragmentation-analyse-fragment-results.at | 30 +-
tests/regression/Makefile.am | 3 +-
.../Molecules/BondFile/pre/silica.dbond.0000 | 17 +-
.../Molecules/BondFile/pre/silica.pov1.0000.pdb | 7164 +-------------------
.../testsuite-molecules-tremolo-dbond-file.at | 6 +-
.../Molecules/Remove/post/id0_2_missing.pdb | 14 +-
.../regression/Molecules/Remove/post/water_box.pdb | 14 +-
.../pre/homology_grid.dat | 0
.../pre/water.pdb | 0
.../testsuite-potential-fit-partial-charges.at} | 12 +-
.../testsuite-potential-fit-potential.at | 22 +-
tests/regression/Potential/testsuite-potential.at | 2 +-
.../Molecules/PopMoleculeSelection/post/box.xyz | 841 +--
.../Molecules/PopMoleculeSelection/post/empty.xyz | 2 +-
.../PopMoleculeSelection/post/id2_4_missing.xyz | 1025 ---
.../PopMoleculeSelection/post/water_id2_4.xyz | 8 +-
.../Molecules/PopMoleculeSelection/pre/box.xyz | 841 +--
218 files changed, 8578 insertions(+), 15368 deletions(-)
rename src/Actions/PotentialAction/{FitParticleChargesAction.cpp => FitPartialChargesAction.cpp} (93%)
rename src/Actions/PotentialAction/{FitParticleChargesAction.def => FitPartialChargesAction.def} (91%)
rename src/Actions/PotentialAction/{FitParticleChargesAction.hpp => FitPartialChargesAction.hpp} (81%)
create mode 100644 src/EntityObserver.hpp
create mode 100644 src/EntityObserver_impl.hpp
copy src/Filling/Predicates/{IsInsideSurface_FillPredicate.cpp => IsCloseEnoughToSurface_FillPredicate.cpp} (66%)
create mode 100644 src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.hpp
delete mode 100644 src/MoleculeListClass.hpp
rename src/{LinkedCell/unittests/stubs/AtomObserverStub.cpp => MoleculeObserver.cpp} (59%)
create mode 100644 src/MoleculeObserver.hpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/ObservedValue_types.hpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/ObservedValue_wCallback.hpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp
create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp
rename src/UIElements/Views/Qt4/{ => ElementList}/QtElementList.cpp (67%)
rename src/UIElements/Views/Qt4/{ => ElementList}/QtElementList.hpp (52%)
create mode 100644 src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp
create mode 100644 src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.hpp
create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp
create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.hpp
delete mode 100644 src/UIElements/Views/Qt4/QtSelectionChangedAgent.cpp
delete mode 100644 src/UIElements/Views/Qt4/QtSelectionChangedAgent.hpp
delete mode 100755 src/moleculelist.cpp
create mode 100644 tests/GuiChecks/Filling/RegularGrid/testsuite-fill-regular-grid-with-minimum-distance-to-surface.at
rename tests/GuiChecks/Potential/{FitParticleCharges/testsuite-potential-fit-particle-charges.at => FitPartialCharges/testsuite-potential-fit-partial-charges.at} (69%)
create mode 100644 tests/regression/Filling/RegularGrid/post/amylose_filled_water.pdb
copy tests/{Tesselations/Convex/amylose/pre/amylose.pdb => regression/Filling/RegularGrid/pre/amylose_straightened_more.pdb} (60%)
copy {data/molecules => tests/regression/Filling/RegularGrid/pre}/water.pdb (54%)
create mode 100644 tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid-with-minimum-distance-to-surface.at
create mode 100644 tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_LongRangeForces.dat
create mode 100644 tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_VMGForces.dat
copy tests/regression/Fragmentation/AnalyseFragmentationResults/post/{ => LongRange/OBC}/alkane-3.data (61%)
create mode 100644 tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_LongRangeForces.dat
create mode 100644 tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_VMGForces.dat
copy tests/regression/Fragmentation/AnalyseFragmentationResults/post/{ => LongRange/PBC}/alkane-3.data (66%)
rename tests/regression/Potential/{FitParticleCharges => FitPartialCharges}/pre/homology_grid.dat (100%)
rename tests/regression/Potential/{FitParticleCharges => FitPartialCharges}/pre/water.pdb (100%)
rename tests/regression/Potential/{FitParticleCharges/testsuite-potential-fit-particle-charges.at => FitPartialCharges/testsuite-potential-fit-partial-charges.at} (83%)
delete mode 100644 tests/regression/Selection/Molecules/PopMoleculeSelection/post/id2_4_missing.xyz
hooks/post-receive
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