# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 10:57:17 AM Wed, 18 May 2016 22:02:06 GMT Frederik Heber [d713ce] * src/Fragmentation/Homology/AtomFragmentsMap.cpp (moved) * src/Fragmentation/Homology/AtomFragmentsMap.hpp (moved) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) * src/Fragmentation/Makefile.am (modified) AtomFragmentsMap is now a Singleton and part of Homology code. Wed, 18 May 2016 22:02:06 GMT Frederik Heber [bd6e5c] * src/Fragmentation/AtomFragmentsMap.cpp (modified) * src/Fragmentation/AtomFragmentsMap.hpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) Prepared AtomFragmentsMap to work in ids, not instances. - no more ... Wed, 18 May 2016 22:02:06 GMT Frederik Heber [d45ed9] * src/Fragmentation/AtomFragmentsMap.cpp (added) * src/Fragmentation/AtomFragmentsMap.hpp (added) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) * src/Fragmentation/Makefile.am (modified) Abstracted atom -> fragment association out of Interfragmenter. Wed, 18 May 2016 22:02:06 GMT Frederik Heber [b0bc13] * src/Fragmentation/Homology/HomologyGraph.hpp (modified) FIX: HomologyGraph has explicit cstors for KeySet and IndexSet. - ... Wed, 18 May 2016 21:56:59 GMT Frederik Heber [7debff] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) VMGData additionally stores absolute residual. - we check for ... Wed, 18 May 2016 21:55:42 GMT Frederik Heber [f0dea0] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) FragmentationAutomationAction checks FragmentResults for non-zero ... Wed, 18 May 2016 21:55:40 GMT Frederik Heber [9ff818] * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) MPQCJob and VMGJob contain reached and desired accuracy. - both set ... Sat, 07 May 2016 07:05:19 GMT Frederik Heber [a9099d] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.def (modified) * src/Potentials/Particles/Particle.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPartialCharges/post/water.particles (modified) FitPartialChargesAction enforces net charge neutrality on default ... Sat, 07 May 2016 07:05:19 GMT Frederik Heber [666e9e] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * tests/Python/AllActions/options.dat (modified) VMGFragmentController and FragmentationAutomationAction accept ... Sat, 07 May 2016 07:05:19 GMT Frederik Heber [0ba27c9] * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) FragmentationLongRangeResults now takes additional implicit charge ... Sat, 07 May 2016 07:05:19 GMT Frederik Heber [276e2f] * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) ParseHomologiesAction prints parsed homologies on larger verbosity ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [708ec1] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPartialCharges/post/water.particles (added) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (modified) Modified FitPartialChargesAction to register fitted particles with ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [2082637] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/ParseParticleParametersAction.cpp (added) * src/Actions/PotentialAction/ParseParticleParametersAction.def (added) * src/Actions/PotentialAction/ParseParticleParametersAction.hpp (added) * src/Actions/PotentialAction/SaveParticleParametersAction.cpp (added) * src/Actions/PotentialAction/SaveParticleParametersAction.def (added) * src/Actions/PotentialAction/SaveParticleParametersAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/SaveParseParticleParameters/pre/harmonic.particles (added) * tests/regression/Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at (added) * tests/regression/Potential/testsuite-potential.at (modified) Added Parse- and SaveParticleParametersAction to parse/save ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [fde8e7] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/PotentialAction/SavePotentialsAction.cpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialDeserializer.cpp (deleted) * src/Potentials/PotentialDeserializer.hpp (deleted) * src/Potentials/PotentialSerializer.cpp (deleted) * src/Potentials/PotentialSerializer.hpp (deleted) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/RegistryDeserializer.hpp (added) * src/Potentials/RegistryDeserializer_impl.hpp (added) * src/Potentials/RegistrySerializer.hpp (added) * src/Potentials/RegistrySerializer_impl.hpp (added) Refactored PotentialSerializer and -Deserializer into more general ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [f6abb1] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialDeserializer.cpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * src/Potentials/StreamFactory_EmpiricalPotential.cpp (added) * src/Potentials/StreamFactory_EmpiricalPotential.hpp (added) PotentialFactory now also complies to templated StreamFactory. - ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [086e30] * src/Potentials/Makefile.am (modified) * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/Particles/Particle.hpp (modified) * src/Potentials/Particles/ParticleFactory.cpp (added) * src/Potentials/Particles/ParticleFactory.hpp (added) * src/Potentials/Particles/StreamFactory_Particle.cpp (added) * src/Potentials/Particles/StreamFactory_Particle.hpp (added) * src/Potentials/StreamFactory.hpp (added) Added ParticleFactory and general StreamFactory. - StreamFactory ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [fdfc52] * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Potentials/Exceptions.hpp (modified) * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/SerializablePotential.cpp (modified) * src/Potentials/unittests/SerializablePotentialUnitTest.cpp (modified) Renamed all SerializablePotential..Exceptions to ... Sat, 07 May 2016 07:03:56 GMT Frederik Heber [fd5440] * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/Particles/Particle.hpp (modified) FIX: Particle's member variables are now public and fixes to stream ... Mon, 25 Apr 2016 07:06:12 GMT Frederik Heber [9d1a78] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene used iterator also in NDEBUG, connect still outside ... Mon, 25 Apr 2016 07:06:12 GMT Frederik Heber [abb115] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) FIX: QtMoleculeListView::rowsSelected() checks for illegal id from ... Mon, 25 Apr 2016 07:06:12 GMT Frederik Heber [097da7] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) FIX: QtMoleculeList has flag to tell when nameChanged came from ... Mon, 25 Apr 2016 07:06:11 GMT Frederik Heber [006f6a] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) QtObservedInstanceBoard::get..ToIndex() now serve -1 as illegal id ... Mon, 25 Apr 2016 07:06:11 GMT Frederik Heber [ffa69c] * src/Parser/PdbParser.cpp (modified) FIX: PdbParser scanned through all present atoms once per ATOM line. ... Mon, 25 Apr 2016 07:06:10 GMT Frederik Heber [30b134] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene::removeBond() needs to check whether molecule ... Mon, 25 Apr 2016 07:06:10 GMT Frederik Heber [67c4ea] * src/molecule.hpp (modified) FIX: molecule returned BondCount twice as large. Mon, 25 Apr 2016 07:06:10 GMT Frederik Heber [0bddd1e] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Made GLWorldScene::resetParent() safe for multiple threads. Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [ea7926] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) Split ObservedValueIndexLookup such that it is protected under atom ... Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [1eba7c] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) Protecting access to atom and bond functions in GLWorldScene with ... Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [efeeb7] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene now holds onto atoms and bonds until ..Removed() signal ... Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [649f59] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene removes stored observed values only after both parent is ... Mon, 25 Apr 2016 07:05:31 GMT Frederik Heber [136842] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene needs to store observed values to ensure duration of ... Mon, 25 Apr 2016 07:02:56 GMT Frederik Heber [d16a06] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) FIX: GLMoleculeObject_atom did not use QtObservedAtom for selected. Mon, 25 Apr 2016 07:02:56 GMT Frederik Heber [507f3c] * src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) QtObservedBond returns ::ptr instead of ptr from left and right atom. ... Mon, 25 Apr 2016 07:02:56 GMT Frederik Heber [522c45] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.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) QtObserved... signals indexChanged does not transmit ids anymore. - ... Mon, 25 Apr 2016 07:02:56 GMT Frederik Heber [6c4b69] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Added checks abd verbosity to reparenting in GLWorldScene. Mon, 25 Apr 2016 07:02:56 GMT Frederik Heber [08a7ecc] * src/UIElements/Qt4/InstanceBoard/ObservedValue_types.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) FIX: ObservedValue_Index_t is now the memory address of the Observer ... Mon, 25 Apr 2016 07:02:56 GMT Frederik Heber [375bc3f] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) FIX: Empty row in QtMoleculeList was not deleted. Mon, 25 Apr 2016 07:02:56 GMT Frederik Heber [b2eeaf] * 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) FIX: MoleculeList crashed when selected molecule changed its place. Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [a13f2b] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene can now reparent atoms and bonds whose molecule is ... Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [502614] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene's parent maps now store the parent as ... Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [6e1628] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) FIX: QtMoleculeList should not use getIdtoIndex unnecessarily. - ... Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [2560f1] * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) QtObservedMolecule uses fixed index which it returns. Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [205389] * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp (modified) QtObservedBond uses fixed index which it returns. Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [498c678] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) QtObservedAtom uses fixed index which it returns. Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [50246c] * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) FIX: made disconnect() check for NULL pointers. Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [691533] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) FIX: GLMoleculeObject_molecule only updates tesselation hull when ... Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [bd6768] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene now properly reassigns parents of GLMoleculeObjects. - ... Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [273c8a] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) QtObservedAtom only offers direct access to associated const ... Wed, 20 Apr 2016 23:07:47 GMT Frederik Heber [7f185f9] * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp (modified) QtObservedBond also offers direct access to stored QtObservedAtoms as ... Wed, 20 Apr 2016 23:07:46 GMT Frederik Heber [f1b5ca] * 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) Only GLWorldScene creates stuff, GLMoleculeObject_.. are just visual ... Wed, 20 Apr 2016 23:06:59 GMT Frederik Heber [785d89] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) FIX: QtObservedAtom: getAtomMolecule() -> getMoleculeIndex(). - ... Wed, 20 Apr 2016 23:06:55 GMT Frederik Heber [4112691] * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) QtObservedBond now simply gets both QtObservedAtoms on construction. ... Wed, 20 Apr 2016 23:04:54 GMT Frederik Heber [e4b13a] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) getObserved...() checks whether id is still present. Wed, 20 Apr 2016 23:04:53 GMT Frederik Heber [d48a16] * src/UIElements/Qt4/InstanceBoard/ObservedValue_wCallback.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) Removed partial specialization of ObservedValue_wCallback for index. ... Wed, 20 Apr 2016 22:58:43 GMT Frederik Heber [96f14a] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/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) Modified all GLMoleculeObjects and GLWorldScene to the new ... Wed, 20 Apr 2016 22:58:42 GMT Frederik Heber [b4bd0e] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp (added) * src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp (added) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) Added QtObservedBond, managed by QtObservedInstanceBoard. - ... Wed, 20 Apr 2016 20:36:11 GMT Frederik Heber [6af6a62] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) FIX: Removed GLMoleculeObject_molecule's molref. Wed, 20 Apr 2016 08:53:33 GMT Frederik Heber [bf6245] * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) QtObservedMolecule also uses new index internally. Wed, 20 Apr 2016 08:53:33 GMT Frederik Heber [ee3fb8] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) QtObservedAtom uses new index internally. - thus we don't have to ... Wed, 20 Apr 2016 08:53:33 GMT Frederik Heber [62a127] * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) FIX: QtObservedMolecule::initObservedValues was still static. Wed, 20 Apr 2016 08:53:33 GMT Frederik Heber [4690a7] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValue_UpdateAtoms.hpp (deleted) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) Removed unneeded specialization ObservedValue_UpdateAtoms. Wed, 20 Apr 2016 08:52:04 GMT Frederik Heber [76c238] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) Removed GLMoleculeObject_molecule::getPresentAtoms() and changed ... Wed, 20 Apr 2016 08:52:04 GMT Frederik Heber [1d9b6dd] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: Removed some unnecessary observer code from GLWorldView. Wed, 20 Apr 2016 08:52:03 GMT Frederik Heber [f91ef6] * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) * src/UIElements/Qt4/QtMainWindow.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) Changed slots of GLWorldScene and GLWorldView. Wed, 20 Apr 2016 08:52:03 GMT Frederik Heber [0a558d] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) MoleculeList discerns between internal and external name change. Wed, 20 Apr 2016 08:51:51 GMT Frederik Heber [3054f4a] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Views/Qt4/ElementList/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtElementList.hpp (modified) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.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/MoleculeList/QtObservedMoleculeObserver.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) QtObserved...Observed now get index on ...Removed() signal. - ... Wed, 20 Apr 2016 07:17:43 GMT Frederik Heber [1a58ce] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.hpp (modified) Added convenience function to return current id for given index. - ... Wed, 20 Apr 2016 07:17:41 GMT Frederik Heber [59eabc] * src/UIElements/Qt4/InstanceBoard/ObservedValue_types.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) Introduced unique and permanent ObservedValue_Index_t. - this is ... Mon, 18 Apr 2016 22:33:41 GMT Frederik Heber [bff202] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) FIX: QtMoleculeList's FormulaVisibilityCountMap was not inserted into ... Mon, 18 Apr 2016 22:33:41 GMT Frederik Heber [743eab] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.hpp (modified) Added missing updateState() to QtMoleculeList. - As QtMoleculeItem ... Mon, 18 Apr 2016 22:33:41 GMT Frederik Heber [b65879] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (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/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) QtMoleculeItems do not store ObservedMolecule::ptr any longer. - it ... Mon, 18 Apr 2016 22:33:41 GMT Frederik Heber [55443e] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) FIX: QtMoleculeList::moveItem() does not need to search for groupitem. Mon, 18 Apr 2016 22:33:41 GMT Frederik Heber [ea2663] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) QtMoleculeItemFactory is pure static. - QtMoleculeItemFactory was ... Mon, 18 Apr 2016 22:33:41 GMT Frederik Heber [5771e6] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) Removed all mutexes and updateDirtyStates() in QtMoleculeList, ... Thu, 24 Mar 2016 14:58:04 GMT Frederik Heber [24eb6b] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.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) Removed QtMoleculeList::informDirtyState(), callback is not needed ... Thu, 24 Mar 2016 14:58:04 GMT Frederik Heber [7993fe] * 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/QtObservedMoleculeObserver.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.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) Removed emitDirtyState callback from QtMoleculeItem. - this does ... Thu, 24 Mar 2016 14:58:04 GMT Frederik Heber [924259] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp (added) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.hpp (added) Added QtObservedMoleculeObserver that relays signals on all ... Thu, 24 Mar 2016 14:58:04 GMT Frederik Heber [1c9eb8] * src/molecule.cpp (modified) FIX: molecule::SetNameFromFilename did not notify about ... Thu, 24 Mar 2016 14:24:02 GMT Frederik Heber [d316ad] * src/molecule.cpp (modified) FIX: molecule did not notify about FormulaChanged at the right ... Thu, 24 Mar 2016 14:23:20 GMT Frederik Heber [bfd520c] * src/UIElements/Views/Qt4/ElementList/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtElementList.hpp (modified) QtElementList uses QtObservedAtomObserver and is no longer Observer ... Thu, 24 Mar 2016 14:23:19 GMT Frederik Heber [6a7353] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp (added) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.hpp (added) Added QtObservedAtomObserver to ElementList subfolder. Thu, 24 Mar 2016 14:23:19 GMT Frederik Heber [bfd5d5f] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) QtObservedAtom and ..Molecule now have internal selfref. - this can ... Wed, 16 Mar 2016 10:02:23 GMT Frederik Heber [1e1893] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtElementList.cpp (moved) * src/UIElements/Views/Qt4/ElementList/QtElementList.hpp (moved) Moved QtElementList into own subfolder. Wed, 16 Mar 2016 09:12:28 GMT Frederik Heber [7f1c00] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) Added getObserved..() functions to QtObservedInstanceBoard that take ... Mon, 14 Mar 2016 09:53:43 GMT Frederik Heber [f35f7e] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) All QtObserved..::update..() now use the atom or molecule ref instead ... Mon, 14 Mar 2016 09:51:15 GMT Frederik Heber [d845bd] * src/UIElements/Qt4/QtUIFactory.cpp (modified) GUITESTS: Decreased waiting times in QtGUI's test mode. Mon, 14 Mar 2016 09:51:00 GMT Frederik Heber [c44763] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) FIX: QtObserved... did not destroyObservedValues() so far. Thu, 03 Mar 2016 20:46:55 GMT Frederik Heber [14de9a4] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) FIX: GLMoleculeObject_atom did reset position not bonds on bondsChanged. Thu, 03 Mar 2016 18:38:19 GMT Frederik Heber [35ab62] * 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) Half of the bonds are showing up again. - but the other half is ... Thu, 03 Mar 2016 12:48:14 GMT Frederik Heber [2edf77] * src/Bond/AdjacencyMatcher/Makefile.am (modified) * src/Tesselation/TriangleMatcher/Makefile.am (modified) * tests/regression/adjacencymatcher.in (modified) * tests/regression/trianglematcher.in (modified) DISTFIX: Added AdjacencyMatcher and TriangleMatcher noinst targets. ... Sun, 28 Feb 2016 18:00:02 GMT Frederik Heber [df0c80] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Filling/Makefile.am (modified) * src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.cpp (added) * src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.hpp (added) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (modified) * src/Filling/Preparators/BaseFillerPreparator.cpp (modified) * src/Filling/Preparators/BaseFillerPreparator.hpp (modified) * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid-with-minimum-distance-to-surface.at (modified) FIX: Filling actions did not use minimum distance for tesselated ... Sun, 28 Feb 2016 17:59:42 GMT Frederik Heber [50d49d] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (moved) * src/Actions/PotentialAction/FitPartialChargesAction.def (moved) * src/Actions/PotentialAction/FitPartialChargesAction.hpp (moved) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Potential/FitParticleCharges/testsuite-potential-fit-partial-charges.at (moved) * tests/GuiChecks/Potential/testsuite-potential.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/FitPartialCharges/pre/homology_grid.dat (moved) * tests/regression/Potential/FitPartialCharges/pre/water.pdb (moved) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (moved) * tests/regression/Potential/testsuite-potential.at (modified) FIX: Renamed FitParticleCharges -> FitPartialCharges. - fitting ... Fri, 26 Feb 2016 09:54:40 GMT Frederik Heber [0824dd] * src/documentation/constructs/qt-gui.dox (modified) Enhanced documentation for Qt constructs. Fri, 26 Feb 2016 09:54:40 GMT Frederik Heber [4a187d] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene also takes note of empty molecule. - this is for the ... Fri, 26 Feb 2016 09:54:40 GMT Frederik Heber [1187c5] * src/Atom/atom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) FIX: QtObservedAtom's AtomMoleculeIndex was not informed of molecule ... Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [640cbd] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: emit changed signal before moleculeEmptied. Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [e29427] * 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) GLWorldScene RemovedMolecules now uses QtObservedMolecule* as key. ... Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [805fdc] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene's moleculesAtomRemoved was checking ... Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [5c9604] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) SignedOn_t in QtObservedInstanceBoard is again just a set. - we do ... Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [8b59dd] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) Removed last...removed in QtObservedInstanceBoard. - this does not ...