# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 10:32:08 AM Tue, 13 Oct 2015 20:13:12 GMT Frederik Heber [00d815] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: Need to divide by global number of particles, when summing ... Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [6e73f5] * src/Jobs/InterfaceVMGJob.cpp (modified) Added debugging changes to InterfaceVMGJob on force summation. Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [ff347f] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) Added gathering of full and longrange forces into extra file. - ... Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [20bb3b] * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) MPQCData now also uses FragmentForces (instead of typedef ... Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [94db13] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) Again changes to obtain correct longrange forces, also forces are ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [83a425] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) Split off sampled_potential im VMGDataMap_t into separate fusion ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [ce9874] * src/Jobs/InterfaceVMGJob.cpp (modified) Added extraction of long-range forces from VMGData's array f. Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [d200ae] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/SetValues/FragmentForces.cpp (added) * src/Fragmentation/Summation/SetValues/FragmentForces.hpp (added) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) Added new SetValues FragmentForces. - struct is particle_forces ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [057c8a] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) FIX: When there's just a single fragment, don't remove the ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [9593d1] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob. ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [c20839] * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) FIX: Shared libraries's Makefile.am rules are now consistent. - ... Thu, 13 Aug 2015 21:52:27 GMT Frederik Heber [5284ff] * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: This prevent crash of molecuildergui in debian package. - ... Fri, 07 Aug 2015 22:38:46 GMT Frederik Heber [3995711] * src/documentation/install.dox (modified) DOCU: Described workaround for missing pyconfig.h. Wed, 05 Aug 2015 17:32:13 GMT Frederik Heber [6fe4f7] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) FIX: updateBoundingBox() must not call molecule::getBoundingBox() on ... Wed, 05 Aug 2015 17:32:13 GMT Frederik Heber [ec8471] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/QDebugStream.hpp (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) * src/UIElements/Views/Qt4/QtLogBox.hpp (modified) FIX: QtLogBox is again included and working thread-safe. - ... Wed, 05 Aug 2015 17:32:13 GMT Frederik Heber [7e2adc] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) FIX: GLMoleculeObject_bond had both flipped ids and the side. - in ... Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [a9161d] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtShapeList.cpp (modified) FIX: GLWorldView and QtShapeList do not assert single source in ... Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [07136a] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) FIX: Fixing display of shapes in GLWorldView. - we propagate shape ... Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [369cb1] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) GLWorldScene lacked assert of Walker in atomClicked(). Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [92ee41] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) Asserted that GLMoleculeObject_molecule::update() is never called. Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [ca4b63b] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) AddAtomBonds() now uses just id not ptr as param. Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [68989c] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) Avoided use of getId() on molecules and atoms in Qt code where ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [25a81d] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) GLMoleculeObject_molecule does not use getAtomCount() anymore. - ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [5b61e5] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) GLMoleculeObject_molecule also has ObservedValue for name. - this ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [07b800] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) FIX: Setting molecule's name via QtMoleculeList item is again ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [a39d72] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Fixed formula usage in Qt part of code. - formula of a molecule is ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [015f8c] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.hpp (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_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) QtMainWindow uses QtSelectionChangedAgent. - QtMoleculeListView and ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [e5a477] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/QtSelectionChangedAgent.cpp (added) * src/UIElements/Views/Qt4/QtSelectionChangedAgent.hpp (added) Added QtSelectionChangedAgent to transform O/O to S/S system. - ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [cc2976] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) QtMoleculeItem_.. now shout when they receive subjectKilled(). - ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [b9680b] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) FIX: Fixing "pure virtual function called" in QtMoleculeItem. - as ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [f02b53] * src/World.cpp (modified) World now first releases id and then destroys the atom/molecule. - ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [5be798] * src/molecule.cpp (modified) * src/molecule.hpp (modified) Removed molecule::lastChanged(). - we have lastChangedAtomId() and ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [54bdaa] * src/Parser/FormatParser_common.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) Qt4 instance use new lastChanged..Id() in place of lastChanged(). - ... Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [fb95a5] * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Added lastChanged..Id() to both World and molecule. Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [f714763] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) GLWorldView no longer listens to WorldTime::TimeChanged. - ... Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [3d5b5b] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) GLWorldView does not emit changed() on each general update() from the ... Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [52c5d4] * src/documentation/constructs/qt-gui.dox (modified) DOCU: Updated documentation on Qt Gui construct. Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [fcdf05] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) * src/UIElements/Views/Qt4/QtElementList.hpp (modified) Fixing QtMoleculeList with list containing only formulas and ids. - ... Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [95f49f] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) QtMoleculeList::informDirtyState() does not need to lock refill_mutex ... Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [88846b] * src/UIElements/Views/Qt4/QtElementList.cpp (modified) Fixing QtElementList::updateElement(). Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [20f9b5] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) GLWorldScene propagates changed mol id to GLMoleculeObject_molecule. ... Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [6c16a0] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) GLMoleculeObject_molecule uses ObservedValue for internally ... Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [3e52834] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) QtMoleculeItem_... use ObservedValue for internally representing ... Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [009e2e2] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) GLMoleculeObject_bond uses ObservedValue for internally representing ... Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [534374] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) GLMoleculeObject_atom uses ObservedValue for internally representing ... Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [b3a33d] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) Removed init() and signal WorldSelectionChanged() from GLWorldScene. Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [574d377] * configure.ac (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionStatusList.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/molecule.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) Using static Observable::..NotificationsChannel() functions. - ... Wed, 05 Aug 2015 07:12:24 GMT Frederik Heber [c307ba] * src/documentation/tests/tests.dox (modified) DOCU: Enhanced description of test policy on version update. Wed, 05 Aug 2015 07:12:24 GMT Frederik Heber [10aee4] * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/documentation/constructs/actions.dox (modified) Cleaned up ActionQueue's interface: Actions are always cloned. - ... Wed, 05 Aug 2015 07:12:09 GMT Frederik Heber [94232b] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.hpp (modified) Action::isActive() is now const member function. - also changed ... Mon, 03 Aug 2015 15:03:34 GMT Frederik Heber [725a1d] * src/Bond/AdjacencyMatcher/Adjacency.hpp (modified) FIX: Adjacency's operator<<() printed fixed number (3) of entries. ... Mon, 03 Aug 2015 15:03:34 GMT Frederik Heber [3532b7] * src/Bond/AdjacencyMatcher/Makefile.am (modified) * src/Tesselation/TriangleMatcher/Makefile.am (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/adjacencymatcher.in (modified) * tests/GuiChecks/trianglematcher.in (modified) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/trianglematcher.in (modified) * tests/regression/Makefile.am (modified) * tests/regression/adjacencymatcher.in (modified) * tests/regression/trianglematcher.in (modified) DISTFIX: adjacencymatcher and trianglematcher are check_PROGRAMS, not ... Fri, 31 Jul 2015 09:27:06 GMT Frederik Heber [8e790eb] * src/Bond/AdjacencyMatcher/Makefile.am (modified) DISTFIX: Additional types.hpp in AdjacencyMatcher/Makefile.am. Wed, 29 Jul 2015 18:15:49 GMT Frederik Heber [c66ae6] * Makefile.am (modified) * configure.ac (modified) * src/Bond/AdjacencyMatcher/Adjacency.hpp (added) * src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp (added) * src/Bond/AdjacencyMatcher/Makefile.am (added) * src/Tesselation/TriangleMatcher/TriangleMatcher.cpp (modified) * tests/GuiChecks/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at (added) * tests/GuiChecks/Bond/testsuite-bond.at (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/GuiChecks/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at (modified) * tests/GuiChecks/adjacencymatcher.in (added) * tests/regression/Bond/AdjacencyMatcher/pre/notequal.adj (added) * tests/regression/Bond/AdjacencyMatcher/pre/notequal2.adj (added) * tests/regression/Bond/AdjacencyMatcher/pre/test.adj (added) * tests/regression/Bond/AdjacencyMatcher/pre/test2.adj (added) * tests/regression/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/regression/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at (modified) * tests/regression/adjacencymatcher.in (added) TESTFIX: Added AdjacencyMatcher to correctly compare .adj files in ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [80f678] * src/Parameters/Makefile.am (modified) * src/Parameters/Specifics/Value_elements.cpp (added) * src/Parameters/Specifics/Value_elements.hpp (added) FIX: Added Parameters Value_Elements to correctly set vector of ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [a82f61] * src/Actions/Action.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) Added Action::setOptionValue() which allows setting the option via a ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [143263] * src/Helpers/helpers.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added getSelected..Ids() for both atoms and molecules. - added ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [fe0ddf] * src/Atom/atom_atominfo.cpp (modified) FIX: atom_atominfo lacked some notifies or had them wrong. - ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [f54524] * src/molecule.cpp (modified) * src/molecule.hpp (modified) FIX: Molecule has new signal IndexChanged. - this has been ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [c6719d] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) FIX: atom_bondedparticle signatures changed to more const versions. ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [df3f2f] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) Group item with atom count of 0 is confusing in QtMoleculeList, ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [a963cf] * src/Python/PythonScripting.cpp (modified) executePythonScriptFile() calls executePythonScript() now. Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [883ea0] * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: QTUIFactory's test-single was not working right. Tue, 28 Jul 2015 13:42:43 GMT Frederik Heber [7d146a] * Makefile.am (modified) * configure.ac (modified) * src/Tesselation/TriangleMatcher/Makefile.am (added) * src/Tesselation/TriangleMatcher/Triangle.hpp (added) * src/Tesselation/TriangleMatcher/TriangleMatcher.cpp (added) * src/Tesselation/TriangleMatcher/types.hpp (added) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/testsuite-tesselation.at (modified) * tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/Convex/amylose/testsuite-amylose.at (modified) * tests/Tesselations/Convex/benzene/testsuite-benzene.at (modified) * tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/Convex/glucose/testsuite-glucose.at (modified) * tests/Tesselations/Convex/heptan/testsuite-heptan.at (modified) * tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/Convex/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/Convex/proline/testsuite-proline.at (modified) * tests/Tesselations/Convex/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at (modified) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/NonConvex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/NonConvex/benzene/testsuite-benzene.at (modified) * tests/Tesselations/NonConvex/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/NonConvex/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/NonConvex/glucose/testsuite-glucose.at (modified) * tests/Tesselations/NonConvex/heptan/testsuite-heptan.at (modified) * tests/Tesselations/NonConvex/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/NonConvex/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/NonConvex/proline/testsuite-proline.at (modified) * tests/Tesselations/NonConvex/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/NonConvex/tartaric_acid/testsuite-tartaric_acid.at (modified) * tests/Tesselations/trianglematcher.in (added) * tests/regression/Makefile.am (modified) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) * tests/regression/Tesselation/TriangleMatcher/pre/convex.dat (added) * tests/regression/Tesselation/TriangleMatcher/pre/convex_none.dat (added) * tests/regression/Tesselation/TriangleMatcher/pre/convex_other.dat (added) * tests/regression/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at (added) * tests/regression/Tesselation/testsuite-tesselation.at (modified) * tests/regression/trianglematcher.in (added) Added TriangleMatcher to safely compare tesselation .dat files. - ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [d4c869] * src/Actions/MakroAction_impl_pre.hpp (modified) FIX: MakroAction's outputAsPython() uses outputAsPython() not ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [9a4880] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) FIX: QtMoleculeListView caused Command to be executed when selection ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [a87d1e2] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: ActionQueue::isIdle() states whether actions are executed or ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [9ec4b8] * src/Shapes/BaseShapes.cpp (modified) FIX: Cuboid_impl::getNormal() did not take numerical imprecision into ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [bcf056] * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.hpp (modified) FIX: QtTimeLine would cause another WorldSetTime action. - we did ... Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [9fb213] * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.hpp (modified) FIX: QtElementList now uses new updateElement(). - old refill() ... Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [92df04] * src/UIElements/Qt4/QtMainWindow.cpp (modified) TEMP: Removed QtLogBox for the moment. - ever and again causes ... Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [ea73ce] * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.hpp (modified) Added QMutex to QtElementList for refill(). Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [7d0ddb] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) FIX: QtMoleculeItem would not correctly signOff prior to molecule ... Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [9d4f964] * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.hpp (modified) FIX: QtHomologyList::refill() is now called via signal/slot. Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [7d0a4e] * configure.ac (modified) * src/Makefile.am (modified) * src/ThreadGuard.hpp (added) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) Storing the id of the main thread in static global variable. - this ... Sat, 25 Jul 2015 13:01:45 GMT Frederik Heber [9ad4d6] * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: QtUIFactory copied to wrong argv. Sat, 25 Jul 2015 13:01:45 GMT Frederik Heber [2a4b05] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: GLWorldView was signed in to atomInserted and atomRemoved ... Sat, 25 Jul 2015 13:01:45 GMT Frederik Heber [9b56f0a] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene did not initialize SelectionMode properly. Sat, 25 Jul 2015 13:01:44 GMT Frederik Heber [73b13c] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) Extracted signing on to molecule into activateObserver. - is called ... Sat, 25 Jul 2015 13:01:21 GMT Frederik Heber [9737db] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/QDebugStream.hpp (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) FIX: QDebugStream is now thread-safe. - also Fix to QTextCursor not ... Sat, 25 Jul 2015 13:01:21 GMT Frederik Heber [4965922] * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.hpp (modified) QtInfoBox updates information on update signal. Sat, 25 Jul 2015 13:01:21 GMT Frederik Heber [2f76d2] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) FIX: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted. Sat, 25 Jul 2015 13:01:21 GMT Frederik Heber [f759e5] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: GLWorldView must not listen to moleculeRemoved but to its ... Sat, 25 Jul 2015 13:01:20 GMT Frederik Heber [9c259e] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) FIX: GLWorldScene/View capture all missed signals for each ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [8923ad8] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Removed GLMoleculeObject_molecule's init() and reinit(). - also ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [28864c] * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/builder_init.cpp (modified) UIs are now initialized before any action takes place. - ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [d619338] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) Removed lots of code in GLWorldScene that now resides in ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [8d3ee6] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) FIX: GLMoleculeObject_molecule was not informed of atom index change. Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [084304] * src/UIElements/Views/Qt4/QtElementList.cpp (modified) FIX: QtElementList does not have a changed() signal. Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [e7341e] * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.hpp (modified) FIX: QtInfoBox now works mostly on ids. - slots are requested as ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [f3b597] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLMoleculeObject_molecule() may overlap with atomInserted() ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [fac58f] * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserInterface.hpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XmlParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (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/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/moleculelist.cpp (modified) Converted FormatParser::save() to using vector of const atom ptrs. ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [99db9b] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.def (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.def (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Shapes/ShapeFactory.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Replaced all World::getSelected...() to const version where possible. ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [a58c16] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.def (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.def (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/Descriptors/AtomNameDescriptor.cpp (added) * src/Descriptors/AtomNameDescriptor.hpp (added) * src/Descriptors/AtomNameDescriptor_impl.hpp (added) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Filling/unittests/ClusterUnitTest.cpp (modified) * src/Filling/unittests/FillerUnitTest.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Makefile.am (modified) * src/Parameters/Specifics/Value_atom.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.cpp (modified) Replaced World::getAllAtoms() by const version where possible. Fri, 24 Jul 2015 16:44:34 GMT Frederik 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. - ... Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [1259df] * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.def (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Parameters/Specifics/Value_molecule.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Replaced World::getAllMolecules() wherever possible by const version. Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [63fb7a] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Parameters/StreamOperators.hpp (modified) * src/Parameters/Validators/Specific/MoleculeIdValidator.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Replaced getMolecule() by const access version where possible. - so ... Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [795c0f] * src/Atom/AtomSet.hpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor_impl.hpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp (modified) * src/Descriptors/AtomOrderDescriptor.cpp (modified) * src/Descriptors/AtomOrderDescriptor_impl.hpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor_impl.hpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor_impl.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor_impl.hpp (modified) * src/Descriptors/DescriptorBase.hpp (modified) * src/Descriptors/DescriptorBase_impl.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World::getAtoms() now has const versions as well. - this in turn ... Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [97445f] * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.hpp (modified) * src/Descriptors/MoleculeDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor_impl.hpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.hpp (modified) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor_impl.hpp (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) World::getMolecules..() now has const versions as well. - this ... Fri, 24 Jul 2015 16:44:34 GMT Frederik Heber [270bdf] * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/World.cpp (modified) atom::getMolecule() now returns ptr to const molecule. - changed ...