From git at ins.uni-bonn.de  Mon Feb  2 21:36:27 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon,  2 Feb 2015 21:36:27 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.10
	deleted. v1.4.9-50-g5499fa3
Message-ID: <20150202203627.257CC1000100@jupiter.ins.uni-bonn.de>

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The branch, Candidate_v1.4.10 has been deleted
       was  5499fa3c603f8b0734747fd3e3fbd9fd7bb88e08

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5499fa3c603f8b0734747fd3e3fbd9fd7bb88e08 Set version to 1.4.10.
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From git at ins.uni-bonn.de  Mon Feb  2 21:36:31 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon,  2 Feb 2015 21:36:31 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.10
	created. v1.4.9-47-ga35bd5b
Message-ID: <20150202203631.E42801000100@jupiter.ins.uni-bonn.de>

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The branch, Candidate_v1.4.10 has been created
        at  a35bd5b4fdacf1f588da22703fa0285b100e5e0d (commit)

- Log -----------------------------------------------------------------
commit a35bd5b4fdacf1f588da22703fa0285b100e5e0d
Author: Frederik Heber <heber at 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 "" ()

commit 6e8ef5677fb6f9792ffd7729da8e9504c959816a
Author: Frederik Heber <heber at 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 at ins.uni-bonn.de>
Date:   Mon Feb 2 19:23:36 2015 +0100

    MEMFIX: Mismatched delete[] in SuspendInMoleculeAction.

commit 55feff5ebdb53a41dc5b6013e57eaef1474a08ef
Author: Frederik Heber <heber at 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 at 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 at 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 at ins.uni-bonn.de>
Date:   Thu Jan 29 08:37:57 2015 +0100

    Merge branch 'GUI_TesselatedLargeMolecules' into Candidate_v1.4.10

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From git at ins.uni-bonn.de  Mon Feb  2 22:54:09 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon,  2 Feb 2015 22:54:09 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.10
	deleted. v1.4.9-47-ga35bd5b
Message-ID: <20150202215409.1FA381000100@jupiter.ins.uni-bonn.de>

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a35bd5b4fdacf1f588da22703fa0285b100e5e0d Set version to 1.4.10.
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From git at ins.uni-bonn.de  Mon Feb  2 22:54:13 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon,  2 Feb 2015 22:54:13 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.10
	created. v1.4.9-48-g968ef75
Message-ID: <20150202215413.0D9651000100@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Candidate_v1.4.10 has been created
        at  968ef7574c9d9334e28deed52df74a7c7295f278 (commit)

- Log -----------------------------------------------------------------
commit 968ef7574c9d9334e28deed52df74a7c7295f278
Author: Frederik Heber <heber at 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 8357707c9a5a4bacd22382815857f29750b194ae
Author: Frederik Heber <heber at 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 at 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 at ins.uni-bonn.de>
Date:   Mon Feb 2 19:23:36 2015 +0100

    MEMFIX: Mismatched delete[] in SuspendInMoleculeAction.

commit 55feff5ebdb53a41dc5b6013e57eaef1474a08ef
Author: Frederik Heber <heber at 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 at 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 at 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 at ins.uni-bonn.de>
Date:   Thu Jan 29 08:37:57 2015 +0100

    Merge branch 'GUI_TesselatedLargeMolecules' into Candidate_v1.4.10

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From git at ins.uni-bonn.de  Tue Feb  3 08:32:37 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue,  3 Feb 2015 08:32:37 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.10
	updated. v1.4.9-49-g43c62e0
Message-ID: <20150203073237.A30B71000100@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Candidate_v1.4.10 has been updated
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      from  968ef7574c9d9334e28deed52df74a7c7295f278 (commit)

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- Log -----------------------------------------------------------------
commit 43c62e0c0a62e843f88e55a0a5436829ba300d92
Author: Frederik Heber <heber at 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(-)


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From git at ins.uni-bonn.de  Tue Feb  3 09:02:11 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue,  3 Feb 2015 09:02:11 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.10
	deleted. v1.4.9-49-g43c62e0
Message-ID: <20150203080212.029A71000100@jupiter.ins.uni-bonn.de>

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43c62e0c0a62e843f88e55a0a5436829ba300d92 FIX: We must use --help directly instead of --actionname in checking whether Action is present.
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From git at ins.uni-bonn.de  Tue Feb  3 09:02:15 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue,  3 Feb 2015 09:02:15 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.10
	created. v1.4.9-49-g2e7afe9
Message-ID: <20150203080215.B20821000100@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Candidate_v1.4.10 has been created
        at  2e7afe95e7fc92ca90ef771dbb8089a436d2189a (commit)

- Log -----------------------------------------------------------------
commit 2e7afe95e7fc92ca90ef771dbb8089a436d2189a
Author: Frederik Heber <heber at 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 at 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 at 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 at 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 at ins.uni-bonn.de>
Date:   Mon Feb 2 19:23:36 2015 +0100

    MEMFIX: Mismatched delete[] in SuspendInMoleculeAction.

commit 55feff5ebdb53a41dc5b6013e57eaef1474a08ef
Author: Frederik Heber <heber at 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 at 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 at 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 at ins.uni-bonn.de>
Date:   Thu Jan 29 08:37:57 2015 +0100

    Merge branch 'GUI_TesselatedLargeMolecules' into Candidate_v1.4.10

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Wed Feb  4 20:03:56 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed,  4 Feb 2015 20:03:56 +0100 (CET)
Subject: [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


hooks/post-receive
-- 
MoleCuilder


From git at ins.uni-bonn.de  Wed Feb  4 20:04:03 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed,  4 Feb 2015 20:04:03 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder annotated tag v1.4.10
	created. v1.4.10
Message-ID: <20150204190403.F26991000100@jupiter.ins.uni-bonn.de>

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


From git at ins.uni-bonn.de  Wed Feb  4 20:04:16 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed,  4 Feb 2015 20:04:16 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	GUI_TesselatedLargeMolecules deleted. v1.4.9-25-g4f2895f
Message-ID: <20150204190416.3A0C71000100@jupiter.ins.uni-bonn.de>

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


From git at ins.uni-bonn.de  Wed Feb  4 20:04:33 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed,  4 Feb 2015 20:04:33 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch GUI_smallchanges
	deleted. v1.4.9-2-g7305d52
Message-ID: <20150204190433.344121000100@jupiter.ins.uni-bonn.de>

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


From git at ins.uni-bonn.de  Wed Feb  4 20:04:43 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed,  4 Feb 2015 20:04:43 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.10
	deleted. v1.4.10
Message-ID: <20150204190443.890821000100@jupiter.ins.uni-bonn.de>

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


From git at ins.uni-bonn.de  Wed Feb  4 20:04:51 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed,  4 Feb 2015 20:04:51 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Refactoring_QtMoleculeList_as_QModel deleted. v1.4.9-40-g2050b29
Message-ID: <20150204190451.AA6011000100@jupiter.ins.uni-bonn.de>

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


From git at ins.uni-bonn.de  Wed Feb  4 22:53:30 2015
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed,  4 Feb 2015 22:53:30 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Fix_VMGForces deleted.
	v1.4.9-15-g30bff67
Message-ID: <20150204215330.BC9CA1000100@jupiter.ins.uni-bonn.de>

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
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