[Molecuilder-devel] [SCM] branch stable updated. v1.5.3

28 Apr 2016

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The branch, stable has been updated
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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

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[Molecuilder-devel] [SCM] branch stable updated. v1.5.3

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