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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