From git at ins.uni-bonn.de  Wed Dec  3 23:17:48 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed,  3 Dec 2014 23:17:48 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	GUI_TesselatedLargeMolecules updated. v1.4.9-17-g174c199
Message-ID: <20141203221748.8439B10000F9@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 updated
       via  174c199165b1533ce15955e80eb49c9a501761eb (commit)
       via  51434cab019b5c476aad17eeaa7c454f7ba1a5f8 (commit)
       via  b0d664acd7255e191d084c1a7308c53818ec56ac (commit)
       via  d9c271d6f3a4c76cd320838b4f400ba74ef20576 (commit)
      from  108652894fc66605c48fd9dc0d85960c03a107eb (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 174c199165b1533ce15955e80eb49c9a501761eb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Dec 3 23:15:42 2014 +0100

    For GLMoleculeObject_atom element and position are only reset..() on hook'ed in draw().
    
    - similarly as with GLMoleculeObject_molecule, we check in draw() when need to
      reset..() and do it before the actual drawing. This speeds up a lot.

commit 51434cab019b5c476aad17eeaa7c454f7ba1a5f8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Dec 3 21:07:53 2014 +0100

    tempcommit: updateTesselationHull() was not called in GLMoleculeObject_molecule::draw().
    
    - this caused no update despite atoms having been moved.

commit b0d664acd7255e191d084c1a7308c53818ec56ac
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Dec 3 20:30:54 2014 +0100

    FIX: In QtMoleculeList group is no longer selectable.

commit d9c271d6f3a4c76cd320838b4f400ba74ef20576
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Dec 3 20:20:31 2014 +0100

    World removes empty molecules.
    
    - on destroyAtom() of molecule's last atom, destroyMolecule() is called.
    - FIX: destroyMolecule(molecule *) did use OBSERVE unncessarily. This caused
      seg'fault.

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

Summary of changes:
 .../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp       |   28 ++++++++++++++++---
 .../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp       |    5 +++
 .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp   |    2 +
 src/UIElements/Views/Qt4/QtMoleculeList.cpp        |    4 +-
 src/World.cpp                                      |    8 +++++-
 5 files changed, 39 insertions(+), 8 deletions(-)


hooks/post-receive
-- 
MoleCuilder


From git at ins.uni-bonn.de  Fri Dec 12 09:00:22 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 12 Dec 2014 09:00:22 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	GUI_TesselatedLargeMolecules updated. v1.4.9-18-g197e264
Message-ID: <20141212080023.7078E10000F9@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 updated
       via  197e264ced646aa6c0bc234550e7c76006790bef (commit)
      from  174c199165b1533ce15955e80eb49c9a501761eb (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 197e264ced646aa6c0bc234550e7c76006790bef
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Dec 6 00:06:53 2014 +0100

    GLWorldView's view may be changed via keyboard (especially zoom).

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

Summary of changes:
 src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp |   27 +++++++++++++++++++++++++
 1 files changed, 27 insertions(+), 0 deletions(-)


hooks/post-receive
-- 
MoleCuilder


From git at ins.uni-bonn.de  Sat Dec 13 09:10:25 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Sat, 13 Dec 2014 09:10:25 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	GUI_TesselatedLargeMolecules updated. v1.4.9-31-g71ec5f1
Message-ID: <20141213081026.1F57F10000F9@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 updated
       via  71ec5f12bad3f9ca07448c022d49cd6cf4cba571 (commit)
       via  94444b5f4bd072f57b46989474a7407caf6a75c4 (commit)
       via  98e539ae2870958646d3af1faf75d84de2de0941 (commit)
       via  475d81cdae13f55cb3ab1a22ec9ea5784cec122d (commit)
       via  655f68de8bef7d0db47490198f9ddcc88ed29267 (commit)
       via  e84c92bda5070ea442b1bbec14dafcf8fc69587f (commit)
       via  5a93de00c8f02283320b822aec6504f20d0822c3 (commit)
       via  3d33f4c3066f85982c6ed23a84bd8e9693f27cdb (commit)
       via  c5a4e7f18f1f16913e26e27f9a919f933ee9e468 (commit)
       via  5df432a62c45c377195b2c1799e3122e1f2a25ee (commit)
       via  50c306d9853a916d7ca381740c48dcd24e72f602 (commit)
       via  f84ff5bcec8b1dfcb0149eae79795d53ffa866ea (commit)
       via  0d1c15e4d7f98048440c8168616f255654632a55 (commit)
      from  197e264ced646aa6c0bc234550e7c76006790bef (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 71ec5f12bad3f9ca07448c022d49cd6cf4cba571
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Dec 13 09:09:40 2014 +0100

    tempcommit: SelectionBox is drawn again when molecule is fully shown.
    
    - SelectionBox is not correctly updated.

commit 94444b5f4bd072f57b46989474a7407caf6a75c4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 21:38:29 2014 +0100

    FIX: Bonds from new molecules are instantiated, too.
    
    - when filling in molecules, initially empty molecules are created and atoms
      added lateron. Added atoms would not add their already present atoms but
      only new ones via an Observer update. Now when an atom is inserted, all
      bonds if any are added.

commit 98e539ae2870958646d3af1faf75d84de2de0941
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 21:05:41 2014 +0100

    tempcommit: New update scheme for QtMoleculeList requires changing flag to prevent VisibilityChanged() trigger.

commit 475d81cdae13f55cb3ab1a22ec9ea5784cec122d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 20:43:05 2014 +0100

    tempcommit: Extracted add/removeItem in QtMoleculeList, no more complete refilling on update.
    
    - this is unfinished as we can't find the item to a molecule that is about to
      be removed.

commit 655f68de8bef7d0db47490198f9ddcc88ed29267
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 19:41:27 2014 +0100

    Undo/Redobuttons are grayed out when respective Action not possible.

commit e84c92bda5070ea442b1bbec14dafcf8fc69587f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 19:22:55 2014 +0100

    Extracted removeAtomsinMolecule from molecule class.
    
    - this is necessary since World will automatically remove empty molecules.

commit 5a93de00c8f02283320b822aec6504f20d0822c3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 19:13:18 2014 +0100

    tempcommit: Fixes due to molecules being automatically removed.

commit 3d33f4c3066f85982c6ed23a84bd8e9693f27cdb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 19:03:06 2014 +0100

    tempcommit: Fixes to RemoveAction.

commit c5a4e7f18f1f16913e26e27f9a919f933ee9e468
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 18:50:58 2014 +0100

    tempcommit: Fixes to World destroying empty molecules.

commit 5df432a62c45c377195b2c1799e3122e1f2a25ee
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 18:43:03 2014 +0100

    tempcommit: Fixes to extension of MoleculeIdAction.

commit 50c306d9853a916d7ca381740c48dcd24e72f602
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 18:29:46 2014 +0100

    Added new RemoveAction for molecules.
    
    - also add regression test.

commit f84ff5bcec8b1dfcb0149eae79795d53ffa866ea
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 09:28:58 2014 +0100

    Extended UndoRedoHelpers by AddingMultipleMoleculesfromAtomicInfo.

commit 0d1c15e4d7f98048440c8168616f255654632a55
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 09:28:30 2014 +0100

    Extended selection action for Molecule ids to multiple ids.

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

Summary of changes:
 src/Actions/ActionQueue.cpp                        |   10 +
 src/Actions/ActionQueue.hpp                        |   12 +
 src/Actions/GlobalListOfActions.hpp                |    1 +
 src/Actions/Makefile.am                            |    3 +
 src/Actions/MoleculeAction/RemoveAction.cpp        |  122 +++++++++++
 .../RemoveAction.def}                              |   24 ++-
 .../RemoveAction.hpp                               |    8 +-
 .../SelectionAction/Atoms/NotAtomByIdAction.def    |    1 -
 .../Molecules/MoleculeByIdAction.cpp               |   65 +++++--
 .../Molecules/MoleculeByIdAction.def               |   16 +-
 .../Molecules/NotMoleculeByIdAction.cpp            |   64 +++++--
 .../Molecules/NotMoleculeByIdAction.def            |   16 +-
 src/Actions/UndoRedoHelpers.cpp                    |   39 ++++-
 src/Actions/UndoRedoHelpers.hpp                    |    9 +-
 src/Actions/WorldAction/RepeatBoxAction.cpp        |    8 +-
 src/Fragmentation/Exporters/ExportGraph.cpp        |    3 +-
 src/Graph/unittests/AdjacencyListUnitTest.cpp      |    3 +-
 src/MoleculeLeafClass.cpp                          |    7 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp   |   77 +++++---
 .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp   |    6 +
 src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp     |   10 +-
 src/UIElements/Views/Qt4/QtMoleculeList.cpp        |  216 +++++++++++++-------
 src/UIElements/Views/Qt4/QtMoleculeList.hpp        |    6 +
 src/UIElements/Views/Qt4/QtToolBar.cpp             |   59 +++++-
 src/UIElements/Views/Qt4/QtToolBar.hpp             |   19 ++-
 .../Views/Qt4/QtToolBar_QtFavoriteActions.cpp      |    1 -
 src/World.cpp                                      |    1 +
 src/molecule.cpp                                   |    6 +-
 src/molecule.hpp                                   |    7 +-
 tests/regression/Makefile.am                       |    1 +
 .../Molecules/Remove/post/id0_2_missing.pdb        |   38 ++++
 .../regression/Molecules/Remove/post/water_box.pdb |   44 ++++
 .../regression/Molecules/Remove/pre/water_box.pdb  |   50 +++++
 .../testsuite-molecules-remove.at}                 |   48 +++--
 tests/regression/Molecules/testsuite-molecules.at  |    3 +
 .../post/{id4_missing.xyz => id2_4_missing.xyz}    |    5 +-
 .../post/{water_id4.xyz => water_id2_4.xyz}        |    5 +-
 .../testsuite-selection-select-molecule-by-id.at   |   10 +-
 .../testsuite-selection-unselect-molecule-by-id.at |   10 +-
 39 files changed, 812 insertions(+), 221 deletions(-)
 create mode 100644 src/Actions/MoleculeAction/RemoveAction.cpp
 copy src/Actions/{GraphAction/DestroyAdjacencyAction.def => MoleculeAction/RemoveAction.def} (59%)
 copy src/Actions/{AtomAction => MoleculeAction}/RemoveAction.hpp (61%)
 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
 copy tests/regression/Molecules/{ChangeBondAngle/testsuite-molecules-change-bond-angle.at => Remove/testsuite-molecules-remove.at} (53%)
 rename tests/regression/Selection/Molecules/MoleculeById/post/{id4_missing.xyz => id2_4_missing.xyz} (99%)
 rename tests/regression/Selection/Molecules/MoleculeById/post/{water_id4.xyz => water_id2_4.xyz} (65%)


hooks/post-receive
-- 
MoleCuilder


From git at ins.uni-bonn.de  Fri Dec 19 22:54:21 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 19 Dec 2014 22:54:21 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	GUI_TesselatedLargeMolecules updated. v1.4.9-43-g99b1759
Message-ID: <20141219215422.5850810000F9@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 updated
       via  99b1759cc8e41e6df7fbdf41b40c5c6ff40ad5b1 (commit)
       via  0f2e30633c636c0cccb1e31b38bfa7bc743ce630 (commit)
       via  0bda4554bfa598ae892d665e5afa95d7a682393b (commit)
       via  2122ad01dba5a4567eafce075beb89f7d50d61a6 (commit)
       via  5d9b8641f43b319ff2a5b7453d5ff9bb2f3555ee (commit)
       via  7315986e2f2bd37ded044dd495b6d2b890696080 (commit)
       via  f7ffa9816725f66a38e9311eae206b41ea09145f (commit)
       via  2c21102b9c991c3977d061f7eab6bf4c195cab78 (commit)
       via  9c602744180737b258d8a92605021afb88cdc500 (commit)
       via  f763f34ab6077c50b53ca2d1df19de17bd7b9d77 (commit)
       via  6c74c06c3ba093a18bcbd07a1282da2b3edc6e7d (commit)
       via  94c17043166ec2d8b4cf369029351dedcbda86f9 (commit)
      from  71ec5f12bad3f9ca07448c022d49cd6cf4cba571 (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 99b1759cc8e41e6df7fbdf41b40c5c6ff40ad5b1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 19 17:45:44 2014 +0100

    Added Push/PopMolecules selection action.

commit 0f2e30633c636c0cccb1e31b38bfa7bc743ce630
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 19 17:37:33 2014 +0100

    Added TranslateMolecule action.

commit 0bda4554bfa598ae892d665e5afa95d7a682393b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 19 17:37:06 2014 +0100

    Added Push/PopAtom selection actions.

commit 2122ad01dba5a4567eafce075beb89f7d50d61a6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 19 17:36:38 2014 +0100

    tempcommit: World Queue fixes.

commit 5d9b8641f43b319ff2a5b7453d5ff9bb2f3555ee
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 19 17:36:18 2014 +0100

    tempcommit: clearTempQueue() fixes.

commit 7315986e2f2bd37ded044dd495b6d2b890696080
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Dec 14 20:32:31 2014 +0100

    Added push/pop[Atoms|Molecules]Selection to World.
    
    - this is mostly convenience for MakroActions to use selections and still keep
      the selection from the user.

commit f7ffa9816725f66a38e9311eae206b41ea09145f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Dec 14 20:32:19 2014 +0100

    tempcommit: Fixing clearTempQueue().

commit 2c21102b9c991c3977d061f7eab6bf4c195cab78
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Dec 14 20:27:35 2014 +0100

    tempcommit: Fixing SelectionBox drawing, was not scaled nor translated. Merge with ...

commit 9c602744180737b258d8a92605021afb88cdc500
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Dec 14 20:10:19 2014 +0100

    EDITME: FIX: ActionQueue is no longer cleared when Action fails.
    
    - we only remove the present and all following Actions.
    - also cleaned up threaded/non-threaded parts of ActionQueue: CurrentAction,
      tempQueue is solely used in threaded part.
    
    - EDITME: clearTempQueue() should be in threaded only but I did not want to
      recompile the whole thing (due to header change).

commit f763f34ab6077c50b53ca2d1df19de17bd7b9d77
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Dec 14 19:17:01 2014 +0100

    tempcommit: Merge with 94c1704

commit 6c74c06c3ba093a18bcbd07a1282da2b3edc6e7d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Dec 14 19:15:47 2014 +0100

    FIX: Failing Actions do not clear ActionQueue/History anymore.

commit 94c17043166ec2d8b4cf369029351dedcbda86f9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Dec 14 19:11:47 2014 +0100

    tempcommit: Zoom and keys distance change scaled by eye-center distance. Merge with ...

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

Summary of changes:
 src/Actions/Action.cpp                             |   10 +-
 src/Actions/ActionQueue.cpp                        |   82 +++++++++-------
 src/Actions/ActionQueue.hpp                        |   36 +++++--
 src/Actions/ActionRegistry.cpp                     |   14 +++
 src/Actions/GlobalListOfActions.hpp                |    5 +
 .../GraphAction/SubgraphDissectionAction.cpp       |   26 +----
 src/Actions/Makefile.am                            |   27 ++++-
 src/Actions/MoleculeAction/TranslateAction.cpp     |  103 ++++++++++++++++++++
 src/Actions/MoleculeAction/TranslateAction.def     |   33 ++++++
 src/Actions/MoleculeAction/TranslateAction.hpp     |   22 ++++
 .../SelectionAction/Atoms/PopAtomsAction.cpp       |   72 ++++++++++++++
 .../SelectionAction/Atoms/PopAtomsAction.def       |   33 ++++++
 .../SelectionAction/Atoms/PopAtomsAction.hpp       |   22 ++++
 .../SelectionAction/Atoms/PushAtomsAction.cpp      |   73 ++++++++++++++
 .../SelectionAction/Atoms/PushAtomsAction.def      |   33 ++++++
 .../SelectionAction/Atoms/PushAtomsAction.hpp      |   22 ++++
 .../Molecules/PopMoleculesAction.cpp               |   72 ++++++++++++++
 .../Molecules/PopMoleculesAction.def               |   33 ++++++
 .../Molecules/PopMoleculesAction.hpp               |   22 ++++
 .../Molecules/PushMoleculesAction.cpp              |   73 ++++++++++++++
 .../Molecules/PushMoleculesAction.def              |   33 ++++++
 .../Molecules/PushMoleculesAction.hpp              |   22 ++++
 src/UIElements/CommandLineUI/CommandLineParser.cpp |    1 +
 src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp |    3 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp   |   17 +++-
 src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp      |   10 ++-
 src/World.cpp                                      |   30 ++++++-
 src/World.hpp                                      |    7 ++
 28 files changed, 849 insertions(+), 87 deletions(-)
 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


hooks/post-receive
-- 
MoleCuilder