[Molecuilder-devel] [SCM] MoleCuilder branch stable updated. v1.4.9-49-g2e7afe9
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- Log -----------------------------------------------------------------
-----------------------------------------------------------------------
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
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