February 2015 - Molecuilder-devel

[SCM] MoleCuilder branch Fix_VMGForces deleted. v1.4.9-15-g30bff67
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fix_VMGForces has been deleted was 30bff67aa3428b5502ae8a9a116a176be12a5572 ----------------------------------------------------------------------- 30bff67aa3428b5502ae8a9a116a176be12a5572 tempcommit: Some changes to InterfaceVMGJob on force summation. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Refactoring_QtMoleculeList_as_QModel deleted. v1.4.9-40-g2050b29
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Refactoring_QtMoleculeList_as_QModel has been deleted was 2050b29519e754ad0beb183c35ca29f6a1821f0d ----------------------------------------------------------------------- 2050b29519e754ad0beb183c35ca29f6a1821f0d Commented-out all debugging messages in QtMoleculeList rewrite. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.10 deleted. v1.4.10
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.10 has been deleted was 2e7afe95e7fc92ca90ef771dbb8089a436d2189a ----------------------------------------------------------------------- 2e7afe95e7fc92ca90ef771dbb8089a436d2189a Set version to 1.4.10. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_smallchanges deleted. v1.4.9-2-g7305d52
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_smallchanges has been deleted was 7305d5268402221ff02978b5f2ec39cb12bbd238 ----------------------------------------------------------------------- 7305d5268402221ff02978b5f2ec39cb12bbd238 Removed extra option actionname from HelpAction. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules deleted. v1.4.9-25-g4f2895f
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been deleted was 4f2895fe90439ea317f5f52995da2eaa9bd4aac7 ----------------------------------------------------------------------- 4f2895fe90439ea317f5f52995da2eaa9bd4aac7 FIX: World::SetTime() erased molecules twice. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder annotated tag v1.4.10 created. v1.4.10
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The annotated tag, v1.4.10 has been created at cea2621f22f0473fd56d7e402fb7a500d1946fc8 (tag) tagging 2e7afe95e7fc92ca90ef771dbb8089a436d2189a (commit) replaces v1.4.9 tagged by Frederik Heber on Wed Feb 4 19:58:25 2015 +0100 - Log ----------------------------------------------------------------- Molecules (with many atoms) can now be shown as tesselated surface. Complete rewrite of the GUI's list of molecules tab. No need to add "--actionname" anymore, just supply help with the desired action name. This version contains the following branches: 2e7afe9 Candidate_v1.4.10 (Memfixes, Qt-boost clash fix, and some followup fixes) 55feff5 GUI_smallchanges (no more extra actionname, default value adding) 27e4646 Refactoring_QtMoleculeList_as_QModel (complete and extensive rewrite of thr shown molecule list such that adds and removals are lightweight) 0ac85c3 GUI_TesselatedLargeMolecules (with working tesselation one may switch between molecules shown by their atoms or shown by the tesselated surface) Frederik Heber (49): GLMoleculeObject_atoms and .._bonds are now children of .._molecule. GLMoleculeObject have m_visible, settable in QtMoleculeList. GLMoleculeObject_molecule display tesselated surface in m_visible case. Molecule relays atom's PositionChanged as AtomMoved signal. GLMoleculeObject_molecule listens to AtomMoved signal to update hull only when necessary. Hovering over molecules is working including update of QtInfoBox. Molecules can be (un)selected by clicking on the tesselation hull. Molecule's Visibility can be changed "group-wise". Added MeshFreeType to GLMoleculeObject. World removes empty molecules. For GLMoleculeObject_atom element and position are only reset..() on hook'ed in draw(). GLWorldView's view may be changed via keyboard (especially zoom). Extended selection action for Molecule ids to multiple ids. Extended UndoRedoHelpers by AddingMultipleMoleculesfromAtomicInfo. Added new RemoveAction for molecules. Undo/Redobuttons are grayed out when respective Action not possible. FIX: Bonds from new molecules are instantiated, too. FIX: Failing Actions do not clear ActionQueue/History anymore. FIX: ActionQueue is no longer cleared when Action fails. FIX: Changed SuspendInMoleculeAction to catch segfault when rho=1 was given. Added push/pop[Atoms|Molecules]Selection to World. Added Push/PopAtom selection actions. Added Push/PopMolecules selection action. Added TranslateMolecule action. FIX: World::SetTime() erased molecules twice. FIX: On defined LOG_OBSERVER we also enableLogging() in main(). atom::father is now accessible through getter and setter only. FIX: Atom is notified when its father dies and resets father to itself then. Added AboutToBeRemoved channel to molecule. MEMFIX: removeAtomsinMolecule() worked directly with molecule::iterator which accesses invalid memory. Extracted add/removeItem in QtMoleculeList, no more complete refilling on update. First change to convert QtMoleculeList into QStandardItemModel. Header row is correct again in QtMoleculeList. Moved QtMoleculeList files into own subfolder. Added basic QtMoleculeItem and ...Factory. Added a slew of specific QtMoleculeItem for each of the COLUMNs. Modified QtMoleculeList to use QtMoleculeItemFactory. Moved rowsSelected() over to QtMoleculeListView. Visibility checkstate is working for molecule and group item. Commented-out all debugging messages in QtMoleculeList rewrite. Merge branch 'GUI_TesselatedLargeMolecules' into Candidate_v1.4.10 Merge branch 'Refactoring_QtMoleculeList_as_QModel' into Candidate_v1.4.10 CommandLineParser adds Action's default values as implicit. Removed extra option actionname from HelpAction. MEMFIX: Mismatched delete[] in SuspendInMoleculeAction. MEMFIX: LoadAction undo must not use molecule::iterator for atom removal. FIX: Qt and boost crash together in boost::Q_FOREACH. FIX: We must use --help directly instead of --actionname in checking whether Action is present. Set version to 1.4.10. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch stable updated. v1.4.9-49-g2e7afe9
by git＠ins.uni-bonn.de 04 Feb '15

04 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, stable has been updated via 2e7afe95e7fc92ca90ef771dbb8089a436d2189a (commit) via c0db901ecaba08482b2f7f479a62adb649df64dc (commit) via 8357707c9a5a4bacd22382815857f29750b194ae (commit) via 6e8ef5677fb6f9792ffd7729da8e9504c959816a (commit) via ae75d36a3a4541f1839c35edcb3345e6bcb5d42e (commit) via 55feff5ebdb53a41dc5b6013e57eaef1474a08ef (commit) via 7912e9506437aa71ed46d58a27d8f3b9dfc3f45f (commit) via 27e46467b8c07a7572d5e0ff60deede52265f11a (commit) via 0ac85c3bd25e728f48df71f51c7aa94320aa4910 (commit) via 2050b29519e754ad0beb183c35ca29f6a1821f0d (commit) via 2696b18ee037df67c33588e50eedff4bd5d454dd (commit) via d2dbb5d0e44b22b8ce90269637cb0083893cd951 (commit) via 53c1ffef25e1f1a2be3255d54d76e7406c289ab9 (commit) via 6d1e0a20c242ab6c7b0ace4bf93ff53336b9cc26 (commit) via bed759c3580c014ab9c1b68a1a4aac91cd7ea811 (commit) via f62e60b49352956721b98a4106d50c6f681b3f7d (commit) via 1c339020006b5484f510d76a06f91189152fffd5 (commit) via 8ccf3bf66a4ce9f95ab6fdbedd40c087b343c68d 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----------------------------------------------------------------------- Summary of changes: configure.ac | 6 +- doc/userguide/userguide.xml | 46 + src/Actions/Action.cpp | 10 +- src/Actions/ActionQueue.cpp | 92 ++- src/Actions/ActionQueue.hpp | 48 +- src/Actions/ActionRegistry.cpp | 14 + src/Actions/AtomAction/TranslateAction.def | 2 +- src/Actions/CommandAction/HelpAction.def | 2 +- src/Actions/FillAction/SuspendInMoleculeAction.cpp | 72 +- src/Actions/FillAction/SuspendInMoleculeAction.def | 5 +- src/Actions/GlobalListOfActions.hpp | 6 + .../GraphAction/SubgraphDissectionAction.cpp | 26 +- src/Actions/Makefile.am | 30 +- src/Actions/MoleculeAction/LoadAction.cpp | 5 +- src/Actions/MoleculeAction/RemoveAction.cpp | 122 +++ src/Actions/MoleculeAction/RemoveAction.def | 39 + src/Actions/MoleculeAction/RemoveAction.hpp | 22 + src/Actions/MoleculeAction/TranslateAction.cpp | 103 ++ src/Actions/MoleculeAction/TranslateAction.def | 33 + src/Actions/MoleculeAction/TranslateAction.hpp | 22 + .../SelectionAction/Atoms/NotAtomByIdAction.def | 1 - .../SelectionAction/Atoms/PopAtomsAction.cpp | 90 ++ .../SelectionAction/Atoms/PopAtomsAction.def | 35 + .../SelectionAction/Atoms/PopAtomsAction.hpp | 22 + .../SelectionAction/Atoms/PushAtomsAction.cpp | 73 ++ .../SelectionAction/Atoms/PushAtomsAction.def | 33 + .../SelectionAction/Atoms/PushAtomsAction.hpp | 22 + .../Molecules/MoleculeByIdAction.cpp | 65 +- .../Molecules/MoleculeByIdAction.def | 16 +- .../Molecules/NotMoleculeByIdAction.cpp | 64 +- .../Molecules/NotMoleculeByIdAction.def | 16 +- .../Molecules/PopMoleculesAction.cpp | 88 ++ .../Molecules/PopMoleculesAction.def | 35 + .../Molecules/PopMoleculesAction.hpp | 22 + .../Molecules/PushMoleculesAction.cpp | 73 ++ .../Molecules/PushMoleculesAction.def | 33 + .../Molecules/PushMoleculesAction.hpp | 22 + src/Actions/UndoRedoHelpers.cpp | 39 +- src/Actions/UndoRedoHelpers.hpp | 9 +- src/Actions/WorldAction/RepeatBoxAction.cpp | 8 +- src/Atom/AtomicInfo.cpp | 29 +- src/Atom/atom.cpp | 55 +- src/Atom/atom.hpp | 30 +- src/Atom/atom_observable.cpp | 3 + src/Atom/atom_observable.hpp | 4 + src/Fragmentation/Exporters/ExportGraph.cpp | 3 +- src/Fragmentation/Exporters/HydrogenPool.cpp | 2 +- src/Fragmentation/Exporters/SaturatedFragment.cpp | 4 +- src/Graph/BuildInducedSubgraph.cpp | 6 +- src/Graph/DepthFirstSearchAnalysis.cpp | 1 + src/Graph/unittests/AdjacencyListUnitTest.cpp | 3 +- src/MoleculeLeafClass.cpp | 7 +- src/Parser/PdbParser.cpp | 4 +- src/UIElements/CommandLineUI/CommandLineParser.cpp | 49 +- src/UIElements/CommandLineUI/CommandLineParser.hpp | 5 +- src/UIElements/Makefile.am | 19 +- src/UIElements/Qt4/QtDialog.hpp | 1 + src/UIElements/Qt4/QtMainWindow.cpp | 16 +- .../Views/Qt4/MoleculeList/QtMoleculeItem.cpp | 127 +++ .../Views/Qt4/MoleculeList/QtMoleculeItem.hpp | 107 ++ .../Qt4/MoleculeList/QtMoleculeItemFactory.cpp | 128 +++ .../Qt4/MoleculeList/QtMoleculeItemFactory.hpp | 65 ++ .../Views/Qt4/MoleculeList/QtMoleculeList.cpp | 666 +++++++++++++ .../Views/Qt4/MoleculeList/QtMoleculeList.hpp | 131 +++ .../Views/Qt4/MoleculeList/QtMoleculeListView.cpp | 201 ++++ .../Views/Qt4/MoleculeList/QtMoleculeListView.hpp | 48 + .../SpecificItems/QtMoleculeItem_atomcount.hpp | 53 + .../SpecificItems/QtMoleculeItem_formula.hpp | 56 ++ .../SpecificItems/QtMoleculeItem_name.hpp | 52 + .../SpecificItems/QtMoleculeItem_occurrence.hpp | 51 + .../SpecificItems/QtMoleculeItem_visibility.hpp | 51 + src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp | 52 +- src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp | 17 +- .../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp | 28 +- .../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp | 9 +- .../Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp | 4 +- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 538 ++++++++++- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp | 65 ++ .../Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp | 2 +- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp | 407 ++++---- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp | 34 +- src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp | 83 +- src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp | 13 +- src/UIElements/Views/Qt4/QtInfoBox.cpp | 37 +- src/UIElements/Views/Qt4/QtInfoBox.hpp | 6 +- src/UIElements/Views/Qt4/QtMoleculeList.cpp | 209 ---- src/UIElements/Views/Qt4/QtMoleculeList.hpp | 56 -- src/UIElements/Views/Qt4/QtToolBar.cpp | 59 +- src/UIElements/Views/Qt4/QtToolBar.hpp | 19 +- .../Views/Qt4/QtToolBar_QtFavoriteActions.cpp | 1 - src/World.cpp | 47 +- src/World.hpp | 7 + src/builder.cpp | 8 + src/molecule.cpp | 78 ++- src/molecule.hpp | 20 +- src/moleculelist.cpp | 4 +- tests/Python/AllActions/options.dat | 2 +- .../Translation/testsuite-atoms-translation.at | 6 +- .../SuspendInWater/pre/single_molecule.conf | 83 ++ .../Filling/SuspendInWater/pre/test.conf | 46 +- .../SuspendInWater/testsuite-suspend-in-water.at | 42 +- tests/regression/Makefile.am | 5 + .../Molecules/Remove/post/id0_2_missing.pdb | 38 + .../regression/Molecules/Remove/post/water_box.pdb | 44 + .../regression/Molecules/Remove/pre/water_box.pdb | 50 + .../Molecules/Remove/testsuite-molecules-remove.at | 53 + .../testsuite-molecules-translation-periodic.at | 14 +- .../Translation/testsuite-molecules-translation.at | 20 +- tests/regression/Molecules/testsuite-molecules.at | 3 + .../Options/Help/testsuite-options-help.at | 2 +- .../testsuite-options-invalid-commands.at | 1 - .../testsuite-options-load-session-python.at | 8 +- .../testsuite-options-store-session-python.at | 4 +- .../Mpqc/testsuite-parser-mpqc-load-multiply.at | 2 +- .../Pcp/testsuite-parser-pcp-load-multiply.at | 2 +- .../Pdb/testsuite-parser-pdb-load-multiply.at | 2 +- .../Psi3/testsuite-parser-psi3-load-multiply.at | 2 +- .../testsuite-parser-tremolo-load-multiply.at | 2 +- .../Xyz/testsuite-parser-xyz-load-multiply.at | 2 +- .../testsuite-potential-fit-particle-charges.at | 2 +- .../testsuite-potential-fit-potential.at | 12 +- .../{AtomById => PopAtomSelection}/post/empty.xyz | 0 .../post/id01_missing.xyz | 0 .../post/id01_present.xyz | 0 .../post/id0_missing.xyz | 0 .../post/id0_present.xyz | 0 .../post/id1_missing.xyz | 0 .../post/id1_present.xyz | 0 .../post/id2_missing.xyz | 0 .../post/id2_present.xyz | 0 .../post/id3_missing.xyz | 0 .../post/id3_present.xyz | 0 .../post/id4_missing.xyz | 0 .../post/id4_present.xyz | 0 .../post/id5_missing.xyz | 0 .../post/id5_present.xyz | 0 .../post/id6_missing.xyz | 0 .../post/id6_present.xyz | 0 .../post/id7_missing.xyz | 0 .../post/id7_present.xyz | 0 .../post/test-undo.xyz | 0 .../{AtomById => PopAtomSelection}/pre/test.xyz | 0 .../testsuite-selection-pop-atom-selection.at | 65 ++ .../{AtomById => PushAtomSelection}/post/empty.xyz | 0 .../post/id01_missing.xyz | 0 .../post/id01_present.xyz | 0 .../post/id0_missing.xyz | 0 .../post/id0_present.xyz | 0 .../post/id1_missing.xyz | 0 .../post/id1_present.xyz | 0 .../post/id2_missing.xyz | 0 .../post/id2_present.xyz | 0 .../post/id3_missing.xyz | 0 .../post/id3_present.xyz | 0 .../post/id4_missing.xyz | 0 .../post/id4_present.xyz | 0 .../post/id5_missing.xyz | 0 .../post/id5_present.xyz | 0 .../post/id6_missing.xyz | 0 .../post/id6_present.xyz | 0 .../post/id7_missing.xyz | 0 .../post/id7_present.xyz | 0 .../post/test-undo.xyz | 0 .../{AtomById => PushAtomSelection}/pre/test.xyz | 0 .../testsuite-selection-push-atom-selection.at | 65 ++ .../Selection/Atoms/testsuite-selection-atoms.at | 5 + .../Molecules/MoleculeById/post/id2_4_missing.xyz | 1025 +++++++++++++++++++ .../Molecules/MoleculeById/post/id4_missing.xyz | 1028 -------------------- .../Molecules/MoleculeById/post/water_id2_4.xyz | 8 + .../Molecules/MoleculeById/post/water_id4.xyz | 5 - .../testsuite-selection-select-molecule-by-id.at | 10 +- .../testsuite-selection-unselect-molecule-by-id.at | 10 +- .../post/box.xyz | 0 .../post/empty.xyz | 0 .../PopMoleculeSelection/post/id2_4_missing.xyz | 1025 +++++++++++++++++++ .../PopMoleculeSelection/post/water_id2_4.xyz | 8 + .../post => PopMoleculeSelection/pre}/box.xyz | 0 .../testsuite-selection-pop-molecule-selection.at | 61 ++ .../post/box.xyz | 0 .../post/empty.xyz | 0 .../PushMoleculeSelection/post/id2_4_missing.xyz | 1025 +++++++++++++++++++ .../PushMoleculeSelection/post/water_id2_4.xyz | 8 + .../post => PushMoleculeSelection/pre}/box.xyz | 0 .../testsuite-selection-push-molecule-selection.at | 61 ++ .../Molecules/testsuite-selection-molecules.at | 5 + 185 files changed, 8185 insertions(+), 1927 deletions(-) create mode 100644 src/Actions/MoleculeAction/RemoveAction.cpp create mode 100644 src/Actions/MoleculeAction/RemoveAction.def create mode 100644 src/Actions/MoleculeAction/RemoveAction.hpp create mode 100644 src/Actions/MoleculeAction/TranslateAction.cpp create mode 100644 src/Actions/MoleculeAction/TranslateAction.def create mode 100644 src/Actions/MoleculeAction/TranslateAction.hpp create mode 100644 src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp create mode 100644 src/Actions/SelectionAction/Atoms/PopAtomsAction.def create mode 100644 src/Actions/SelectionAction/Atoms/PopAtomsAction.hpp create mode 100644 src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp create mode 100644 src/Actions/SelectionAction/Atoms/PushAtomsAction.def create mode 100644 src/Actions/SelectionAction/Atoms/PushAtomsAction.hpp create mode 100644 src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp create mode 100644 src/Actions/SelectionAction/Molecules/PopMoleculesAction.def create mode 100644 src/Actions/SelectionAction/Molecules/PopMoleculesAction.hpp create mode 100644 src/Actions/SelectionAction/Molecules/PushMoleculesAction.cpp create mode 100644 src/Actions/SelectionAction/Molecules/PushMoleculesAction.def create mode 100644 src/Actions/SelectionAction/Molecules/PushMoleculesAction.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp create mode 100644 src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp delete mode 100644 src/UIElements/Views/Qt4/QtMoleculeList.cpp delete mode 100644 src/UIElements/Views/Qt4/QtMoleculeList.hpp create mode 100644 tests/regression/Filling/SuspendInWater/pre/single_molecule.conf create mode 100644 tests/regression/Molecules/Remove/post/id0_2_missing.pdb create mode 100644 tests/regression/Molecules/Remove/post/water_box.pdb create mode 100644 tests/regression/Molecules/Remove/pre/water_box.pdb create mode 100644 tests/regression/Molecules/Remove/testsuite-molecules-remove.at copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/empty.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id01_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id01_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id0_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id0_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id1_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id1_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id2_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id2_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id3_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id3_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id4_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id4_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id5_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id5_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id6_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id6_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id7_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/id7_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/post/test-undo.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PopAtomSelection}/pre/test.xyz (100%) create mode 100644 tests/regression/Selection/Atoms/PopAtomSelection/testsuite-selection-pop-atom-selection.at copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/empty.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id01_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id01_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id0_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id0_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id1_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id1_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id2_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id2_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id3_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id3_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id4_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id4_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id5_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id5_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id6_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id6_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id7_missing.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/id7_present.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/post/test-undo.xyz (100%) copy tests/regression/Selection/Atoms/{AtomById => PushAtomSelection}/pre/test.xyz (100%) create mode 100644 tests/regression/Selection/Atoms/PushAtomSelection/testsuite-selection-push-atom-selection.at create mode 100644 tests/regression/Selection/Molecules/MoleculeById/post/id2_4_missing.xyz delete mode 100644 tests/regression/Selection/Molecules/MoleculeById/post/id4_missing.xyz create mode 100644 tests/regression/Selection/Molecules/MoleculeById/post/water_id2_4.xyz delete mode 100644 tests/regression/Selection/Molecules/MoleculeById/post/water_id4.xyz copy tests/regression/Selection/Molecules/{MoleculeById => PopMoleculeSelection}/post/box.xyz (100%) copy tests/regression/Selection/Molecules/{MoleculeById => PopMoleculeSelection}/post/empty.xyz (100%) create mode 100644 tests/regression/Selection/Molecules/PopMoleculeSelection/post/id2_4_missing.xyz create mode 100644 tests/regression/Selection/Molecules/PopMoleculeSelection/post/water_id2_4.xyz copy tests/regression/Selection/Molecules/{MoleculeById/post => PopMoleculeSelection/pre}/box.xyz (100%) create mode 100644 tests/regression/Selection/Molecules/PopMoleculeSelection/testsuite-selection-pop-molecule-selection.at copy tests/regression/Selection/Molecules/{MoleculeById => PushMoleculeSelection}/post/box.xyz (100%) copy tests/regression/Selection/Molecules/{MoleculeById => PushMoleculeSelection}/post/empty.xyz (100%) create mode 100644 tests/regression/Selection/Molecules/PushMoleculeSelection/post/id2_4_missing.xyz create mode 100644 tests/regression/Selection/Molecules/PushMoleculeSelection/post/water_id2_4.xyz copy tests/regression/Selection/Molecules/{MoleculeById/post => PushMoleculeSelection/pre}/box.xyz (100%) create mode 100644 tests/regression/Selection/Molecules/PushMoleculeSelection/testsuite-selection-push-molecule-selection.at hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.10 created. v1.4.9-49-g2e7afe9
by git＠ins.uni-bonn.de 03 Feb '15

03 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.10 has been created at 2e7afe95e7fc92ca90ef771dbb8089a436d2189a (commit) - Log ----------------------------------------------------------------- commit 2e7afe95e7fc92ca90ef771dbb8089a436d2189a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 08:44:17 2015 +0100 Set version to 1.4.10. - MoleCuilder library is now 14:3:0. - Codename "One for ten" (In the states since 1976 for every ten people executed one has been exonerated. Online series of films.) commit c0db901ecaba08482b2f7f479a62adb649df64dc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 3 08:32:02 2015 +0100 FIX: We must use --help directly instead of --actionname in checking whether Action is present. commit 8357707c9a5a4bacd22382815857f29750b194ae Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 2 22:52:28 2015 +0100 FIX: Qt and boost crash together in boost::Q_FOREACH. - added QObject include in QtDialog.hpp as very first one. commit 6e8ef5677fb6f9792ffd7729da8e9504c959816a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 2 19:24:06 2015 +0100 MEMFIX: LoadAction undo must not use molecule::iterator for atom removal. commit ae75d36a3a4541f1839c35edcb3345e6bcb5d42e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 2 19:23:36 2015 +0100 MEMFIX: Mismatched delete[] in SuspendInMoleculeAction. commit 55feff5ebdb53a41dc5b6013e57eaef1474a08ef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 17 18:04:58 2014 +0200 Removed extra option actionname from HelpAction. - this shortens the way to getting help a lot. - TESTFIX: regression potentials fixed due to removed actionname. commit 7912e9506437aa71ed46d58a27d8f3b9dfc3f45f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 17 18:50:10 2014 +0200 CommandLineParser adds Action's default values as implicit. - this allows to have action's token as option with both empty (then default is used) and some given argument. commit 27e46467b8c07a7572d5e0ff60deede52265f11a Merge: 0ac85c3 2050b29 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 08:38:10 2015 +0100 Merge branch 'Refactoring_QtMoleculeList_as_QModel' into Candidate_v1.4.10 commit 0ac85c3bd25e728f48df71f51c7aa94320aa4910 Merge: 7b38d3c 4f2895f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 08:37:57 2015 +0100 Merge branch 'GUI_TesselatedLargeMolecules' into Candidate_v1.4.10 ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.10 deleted. v1.4.9-49-g43c62e0
by git＠ins.uni-bonn.de 03 Feb '15

03 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.10 has been deleted was 43c62e0c0a62e843f88e55a0a5436829ba300d92 ----------------------------------------------------------------------- 43c62e0c0a62e843f88e55a0a5436829ba300d92 FIX: We must use --help directly instead of --actionname in checking whether Action is present. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.10 updated. v1.4.9-49-g43c62e0
by git＠ins.uni-bonn.de 03 Feb '15

03 Feb '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.10 has been updated via 43c62e0c0a62e843f88e55a0a5436829ba300d92 (commit) from 968ef7574c9d9334e28deed52df74a7c7295f278 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 43c62e0c0a62e843f88e55a0a5436829ba300d92 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 3 08:32:02 2015 +0100 FIX: We must use --help directly instead of --actionname in checking whether Action is present. ----------------------------------------------------------------------- Summary of changes: .../testsuite-options-load-session-python.at | 8 ++++---- .../testsuite-options-store-session-python.at | 4 ++-- .../testsuite-potential-fit-particle-charges.at | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) hooks/post-receive -- MoleCuilder

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