From git at ins.uni-bonn.de  Tue Aug  4 09:30:50 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue,  4 Aug 2015 09:30:50 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.12 created.
	v1.4.11-80-g3107c8a
Message-ID: <20150804073050.AEC025FD6E@saturn.ins.uni-bonn.de>

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The branch, Candidate_v1.4.12 has been created
        at  3107c8ac84207e4525807b9151d2d08674118a2c (commit)

- Log -----------------------------------------------------------------
commit 3107c8ac84207e4525807b9151d2d08674118a2c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 2 14:05:47 2015 +0200

    Set version to v1.4.12.

commit c0068c29883ab89f29f1ad36a44aa546d131cc6a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 2 14:01:05 2015 +0200

    DOCU: Enhanced description of test policy on version update.

commit 82d111988cb6e74d73ae5383787080b17bf2cce6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 3 11:25:02 2015 +0200

    Cleaned up ActionQueue's interface: Actions are always cloned.
    
    - Action's dstor needs to be public as we have a clone() function.
    - ActionRegistrys' (and AQ's) getActionByName now returns const ref. We must
      not return a ptr as it may not get deleted elsewhere. We are handing out
      prototypes.
    - queueAction(action*,...) is private to prevent leakage, queueAction(string,
      ...) is the public interface.
    - some other small functions are now private, too.
    - MakroActions now need to clone() the prototype on prepare() and delete them
      on unprepare().
    - ActionSequence deletes contained actions.
    - FIX: ActionSequenceUnitTest cannot check on not-called property of removed
      actions anymore as these are gone now (they are deleted on removal and they
      are cloned on insertion).
    - DOCU: Updated documentation on Actions.

commit 5cf61b4ade7303b1c221599fb66ee1076c5c305e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 3 11:20:16 2015 +0200

    Action::isActive() is now const member function.
    
    - also changed TextMenu's items.

commit 725a1da23441218ebfe802d5508feedc1a4a8b46
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 31 19:09:47 2015 +0200

    FIX: Adjacency's operator<<() printed fixed number (3) of entries.
    
    - this caused seg violations and occurred through memcheck run.
    - it was a copy&paste error from trianglematcher's.

commit 3532b77102b83baecdd39fade5a59f5aaf230ed0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 31 12:21:56 2015 +0200

    DISTFIX: adjacencymatcher and trianglematcher are check_PROGRAMS, not bin_...
    
    - as such they are not installed and hence .in files must not use AUTOTEST_PATH
      but topdir (top build directory).
    - also in GuiChecks, regresssion, and Tesselations tests TESTSUITE was made
      dependent on them but target check and installcheck only actually depend
      on the wrapper scripts (molecuilder, ...).

commit 8e790ebd981dac78daa03f5e06560ba8ea84a21a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 31 11:27:06 2015 +0200

    DISTFIX: Additional types.hpp in AdjacencyMatcher/Makefile.am.

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From git at ins.uni-bonn.de  Tue Aug  4 12:41:42 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue,  4 Aug 2015 12:41:42 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue
	deleted. v1.4.11-106-gf4dee7e
Message-ID: <20150804104142.BB1155FD6E@saturn.ins.uni-bonn.de>

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The branch, GUIStates_using_ObservedValue has been deleted
       was  f4dee7e64136fb00c69ffb78887757d27f7e6506

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f4dee7e64136fb00c69ffb78887757d27f7e6506 Revert "TEMP: Removed QtLogBox for the moment."
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From git at ins.uni-bonn.de  Tue Aug  4 12:42:41 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue,  4 Aug 2015 12:42:41 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch AddingConstDescriptors deleted.
	v1.4.11-44-g9ad4d61
Message-ID: <20150804104241.0AFFC5FD6E@saturn.ins.uni-bonn.de>

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The branch, AddingConstDescriptors has been deleted
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9ad4d612899bb1547d6400f43c8330480c78d103 FIX: QtUIFactory copied to wrong argv.
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From git at ins.uni-bonn.de  Tue Aug  4 12:43:22 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue,  4 Aug 2015 12:43:22 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch DebianPackaging deleted.
	v1.4.11-5-g804b7fc
Message-ID: <20150804104322.35B135FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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804b7fc9d8004fcfadf39477d9483baeb8cbc4be Added script for creating debian package.
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From git at ins.uni-bonn.de  Tue Aug  4 12:46:02 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue,  4 Aug 2015 12:46:02 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch SeparatingOutQtThreads deleted.
	v1.4.11-58-g561b945
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561b94558bc3dbfbf79f15bb042f3376517efa4c FIX: tests/regression FragmentationAutomation had a white space after line break.
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From git at ins.uni-bonn.de  Wed Aug  5 09:10:33 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Wed,  5 Aug 2015 09:10:33 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.12 updated.
	v1.4.11-81-g9247f61
Message-ID: <20150805071033.88F685FD6E@saturn.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_v1.4.12 has been updated
       via  9247f6140e2d96abe74afa09ec2b9ab4a9604c10 (commit)
      from  3107c8ac84207e4525807b9151d2d08674118a2c (commit)

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- Log -----------------------------------------------------------------
commit 9247f6140e2d96abe74afa09ec2b9ab4a9604c10
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 5 00:21:02 2015 +0200

    FIX: ActionQueue::isIdle() const nees mutable mutex.

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

Summary of changes:
 src/Actions/ActionQueue.hpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)


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From git at ins.uni-bonn.de  Wed Aug  5 09:12:58 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Wed,  5 Aug 2015 09:12:58 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.12 deleted.
	v1.4.11-81-g9247f61
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9247f6140e2d96abe74afa09ec2b9ab4a9604c10 FIX: ActionQueue::isIdle() const nees mutable mutex.
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From git at ins.uni-bonn.de  Wed Aug  5 09:13:09 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Wed,  5 Aug 2015 09:13:09 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.12 created.
	v1.4.11-80-g0ea4ddb
Message-ID: <20150805071309.3D60D5FD6E@saturn.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_v1.4.12 has been created
        at  0ea4ddbf6833adf1a4a2ada1981935715775879f (commit)

- Log -----------------------------------------------------------------
commit 0ea4ddbf6833adf1a4a2ada1981935715775879f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 2 14:05:47 2015 +0200

    Set version to v1.4.12.

commit c307ba4e4b46954d39964089972d5cb1f29a6f40
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 2 14:01:05 2015 +0200

    DOCU: Enhanced description of test policy on version update.

commit 10aee4386f0c1b8e07b3a74e7d97d99ef2622bc8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 3 11:25:02 2015 +0200

    Cleaned up ActionQueue's interface: Actions are always cloned.
    
    - Action's dstor needs to be public as we have a clone() function.
    - ActionRegistrys' (and AQ's) getActionByName now returns const ref. We must
      not return a ptr as it may not get deleted elsewhere. We are handing out
      prototypes.
    - queueAction(action*,...) is private to prevent leakage, queueAction(string,
      ...) is the public interface.
    - some other small functions are now private, too.
    - MakroActions now need to clone() the prototype on prepare() and delete them
      on unprepare().
    - ActionSequence deletes contained actions.
    - FIX: ActionSequenceUnitTest cannot check on not-called property of removed
      actions anymore as these are gone now (they are deleted on removal and they
      are cloned on insertion).
    - DOCU: Updated documentation on Actions.

commit 94232b82bf9b20300fb870881f38c94ce0857bdd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 3 11:20:16 2015 +0200

    Action::isActive() is now const member function.
    
    - also changed TextMenu's items.
    - mutexes in ActionQueue are now mutable.

commit 725a1da23441218ebfe802d5508feedc1a4a8b46
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 31 19:09:47 2015 +0200

    FIX: Adjacency's operator<<() printed fixed number (3) of entries.
    
    - this caused seg violations and occurred through memcheck run.
    - it was a copy&paste error from trianglematcher's.

commit 3532b77102b83baecdd39fade5a59f5aaf230ed0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 31 12:21:56 2015 +0200

    DISTFIX: adjacencymatcher and trianglematcher are check_PROGRAMS, not bin_...
    
    - as such they are not installed and hence .in files must not use AUTOTEST_PATH
      but topdir (top build directory).
    - also in GuiChecks, regresssion, and Tesselations tests TESTSUITE was made
      dependent on them but target check and installcheck only actually depend
      on the wrapper scripts (molecuilder, ...).

commit 8e790ebd981dac78daa03f5e06560ba8ea84a21a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 31 11:27:06 2015 +0200

    DISTFIX: Additional types.hpp in AdjacencyMatcher/Makefile.am.

commit c66ae6684084ff864820af9b907d9f3b9725530d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 18:36:06 2015 +0200

    TESTFIX: Added AdjacencyMatcher to correctly compare .adj files in save-adjacency regression test.
    
    - GuiChecks sees a different (but still valid) ordering in the .adj file in the
      save-adjacency regression test.

commit f7054cab5c6c0b7c73d7b4866501383e989b50da
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 18:13:44 2015 +0200

    TESTFIX: selection molecule by name had escaped ticks.
    
    - also changed GuiCheck tests.

commit 80f678157992ab9328be5ba384216ae6e1548684
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 12:03:43 2015 +0200

    FIX: Added Parameters Value_Elements to correctly set vector of elements from string.
    
    - this fixes that fit-potential action is not correctly called from python
      scripts. There, we require correct setter of a value from a given string.
      As all arguments to a python command must be given as single string,
      even if it is a vector of arguments, we must correctly decode this string
      again.

commit c569220c375bbffdf838cc2cfd11de122bf57a86
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 8 12:33:49 2015 +0200

    TESTFIX: regression test DepthFirstSearch had extra linebreak.

commit 024c65bc14cdcf98c86fcf1892e8bc3b3c0c6764
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 8 08:47:52 2015 +0200

    TESTFIX: atom selection regression tests with shapes were very noisy and hence very slow.

commit 7a0456949e5c8efe51fc75d2a5902483c296feec
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jul 6 15:07:00 2015 +0200

    TESTFIX: regression test SubgraphDissection Redo was broken.
    
    - also changed derived GuiChecks test.

commit 42b40a4b4a9210b1ed60a0be93acd12541dedde9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 13:45:49 2015 +0200

    Added TriangleMatcher to safely compare tesselation .dat files.
    
    - is used in tests/regression Tesselations, tests/Tesselations, and has its own
      regression test, too. Also added tests/GuiChecks.
    - added trianglematcher to testsuite dependencies.

commit a82f61a466e15715e16f9470a56c3bdadfcb3895
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 14:39:16 2015 +0200

    Added Action::setOptionValue() which allows setting the option via a string.
    
    - this is preparatory for allowing the creation of MakroActions inside the
      code. We need to set the options without going through dialogs in some
      way or another and without being completely inside the Actions as is the
      case for the COMMAND variants and the python function calls.

commit 143263bb92532b8d3e50535a2c7cfae698a6ab6d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 08:15:39 2015 +0200

    Added getSelected..Ids() for both atoms and molecules.
    
    - added static function getKey() to _take in Helpers.

commit fe0ddfc870329d8adcaf7269129b4690ddd98db4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 22:58:57 2015 +0200

    FIX: atom_atominfo lacked some notifies or had them wrong.
    
    - ElementChanged only when element actually changes it not helpful
      (QtElementList has then no chance of detecting new atoms with default
      element of hydrogen).
    - TrajectoryChanged was signalled only when current timestep was added or
      removed, rather we signal always and assert that we do not remove or append
      the current time step.

commit f5452477d87da2369a118585276d5b6793a46480
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:34:40 2015 +0200

    FIX: Molecule has new signal IndexChanged.
    
    - this has been overlooked so far, index may be changed similarly as for atoms.

commit c6719db9d555d7c3f1b43c5cd90b1ccc2a8df1c8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 06:45:30 2015 +0200

    FIX: atom_bondedparticle signatures changed to more const versions.
    
    - added getBond() for obtaining bond in const manner.

commit df3f2f34f6c9dbddae6f42d32b7a644c3b756eb8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 20:29:39 2015 +0200

    Group item with atom count of 0 is confusing in QtMoleculeList, creating with empty string.

commit a963cf91fe5fac81f5a6c9c3e2c5d8100868fea3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 12:03:05 2015 +0200

    executePythonScriptFile() calls executePythonScript() now.

commit 883ea068fbdbd4af0bcd8dfb11919f5f24ecb781
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jul 20 00:21:57 2015 +0200

    FIX: QTUIFactory's test-single was not working right.

commit 561b94558bc3dbfbf79f15bb042f3376517efa4c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:35:50 2015 +0200

    FIX: tests/regression FragmentationAutomation had a white space after line break.

commit f27c2c5f268ff6d130b9e9d54bc176a6377242d0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 13:51:08 2015 +0200

    FIX: Added molecuilderguitest to testsuite dependencies.

commit 7d146a387231de6a2198a250dbdbab1f1e9076bd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 13:45:49 2015 +0200

    Added TriangleMatcher to safely compare tesselation .dat files.
    
    - is used in tests/regression Tesselations, tests/Tesselations, and has its own
      regression test, too.
    - added trianglematcher to testsuite dependencies.

commit d4c8694f2cbd423faa6c19ddec88eeb7e5f118a3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:53:26 2015 +0200

    FIX: MakroAction's outputAsPython() uses outputAsPython() not outputAsCLI().

commit 9a48804bc9927b9c662e2653a5f08e7a1b65538b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:32:03 2015 +0200

    FIX: QtMoleculeListView caused Command to be executed when selection changed internally.
    
    - we check via selecting but change is propagated via emit. Now we use
      DirectConnection.

commit a87d1e2e1fdd4b7739a97a917c411937f941852d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:56:26 2015 +0200

    FIX: ActionQueue::isIdle() states whether actions are executed or not.
    
    - QtUIFactory uses this to wait till test running next action.

commit 9ec4b8fd1c0781bcd20ad52c2755ad52ae89d518
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:42:44 2015 +0200

    FIX: Cuboid_impl::getNormal() did not take numerical imprecision into account.

commit bcf0561c44a090831a61ab4b4118c79b38750317
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:42:13 2015 +0200

    FIX: QtTimeLine would cause another WorldSetTime action.
    
    - we did not catch where setValue() was called from, from an obtained
      Observable update() or from changing the slider.
    - QtTimeLine needs DirectConnection for valueChanged.

commit 9fb2137ff4183dfa58b9083f255c8037873fb5ba
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:41:07 2015 +0200

    FIX: QtElementList now uses new updateElement().
    
    - old refill() polls complete list of atoms of specific type in the moment
      an atom is destroyed ... now we only get informed about newly created
      atoms (safe) and changing elements (also safe).

commit 92df042994f7c0a88d2ebb7c6506fd351ed68a39
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:39:28 2015 +0200

    TEMP: Removed QtLogBox for the moment.
    
    - ever and again causes SEGFAULT at QDebugStream::61 (QTextEdit::append()).

commit ea73ce1f1f7bfca1ca449bed235f03c42b10b58b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:09:10 2015 +0200

    Added QMutex to QtElementList for refill().

commit 7d0ddb4a2c0b433b55ce0a432f64c21bde6c9535
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:06:29 2015 +0200

    FIX: QtMoleculeItem would not correctly signOff prior to molecule being destroyed.
    
    - all QtMoleculeItems signOn to molecule::AboutToBeRemoved.
    - getMolecule() may return NULL, is caught at two places.
    - getMoleculeId() for allowing QtMoleculeList to acess molid.

commit 9d4f964574dae09a31c613751f654551f61f308a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 10:50:48 2015 +0200

    FIX: QtHomologyList::refill() is now called via signal/slot.

commit 7d0a4e076689218b5c7275f30d0ca5ee9341af8b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:15:04 2015 +0200

    Storing the id of the main thread in static global variable.
    
    - this is preparatory for thread guard to be used in the context of Qt.

commit 9ad4d612899bb1547d6400f43c8330480c78d103
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jul 20 00:05:41 2015 +0200

    FIX: QtUIFactory copied to wrong argv.

commit 2a4b054470c32d7dfd7235c070c54dcdde1a99a0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:01:13 2015 +0200

    FIX: GLWorldView was signed in to atomInserted and atomRemoved without any need.

commit 9b56f0a18eb8b397e931302e9b49b96672885279
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:00:55 2015 +0200

    FIX: GLWorldScene did not initialize SelectionMode properly.

commit 73b13cdd45329e4acbf0a0ca9dd9b780dac892d7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 18:59:19 2015 +0200

    Extracted signing on to molecule into activateObserver.
    
    - is called by GLWorldScene after all "missed" signals have been emitted.

commit 9737db9c0d2798f3bb61807cda1a59701dc33939
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 18:58:32 2015 +0200

    FIX: QDebugStream is now thread-safe.
    
    - also Fix to QTextCursor not registered.

commit 4965922285cce1bd99002053cab2e8913e7fd819
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 16 20:37:07 2015 +0200

    QtInfoBox updates information on update signal.

commit 2f76d207662ae0c1e550c622a0d53f769646a691
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 15 23:01:19 2015 +0200

    FIX: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted.

commit f759e5f2aa47178e7225d67a127028ed62570fdc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:24:00 2015 +0200

    FIX: GLWorldView must not listen to moleculeRemoved but to its subjectKilled.
    
    - atoms of a molecule a removed after moleculeRemoved which only gives a prior
      note about the removal. Then, we are flooded with atomRemoved for each of
      its atom which go into MoleculeMissedStateMap and pop up when a same-id
      molecule is instantiated, causing assert failures.

commit 9c259e4ccaa1f9c8cabd00d1c1ca8e22e40a8199
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 11 09:33:58 2015 +0200

    FIX: GLWorldScene/View capture all missed signals for each GLMoleculeObject_molecule.
    
    - Taking note of subscribed molecules to sign Off on GLWorldView's destruct.
    - GLWorldView::recieveNotification() is checking for whether molecule actually
      exists still.

commit 8923ad833541d0d5da649e21cb7b6537558a282b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 8 19:05:01 2015 +0200

    Removed GLMoleculeObject_molecule's init() and reinit().
    
    - also removed InitAtomMap and associated code.
    - removed changeAtomId slot/signal in GLWorldScene.

commit 28864c30d2f893d3d3b12899626e0d2defa2da74
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 8 18:26:34 2015 +0200

    UIs are now initialized before any action takes place.
    
    - UIFactory::doneInitializing() is set after mainwindow is instantiated.
    - QTUIFactory::testrun() waits till UI is done initializing.

commit d619338ee65ee4df303696fa8a82dbf27e594f44
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 19:11:15 2015 +0200

    Removed lots of code in GLWorldScene that now resides in GLMoleculeObject_molecule.
    
    - atoms and their bonds are now controlled by the latter.

commit 8d3ee64e6d4d84d033921af0895634eccaec7466
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 19:10:49 2015 +0200

    FIX: GLMoleculeObject_molecule was not informed of atom index change.

commit 084304e6dfbb4c6567df7dac36d3cb925b2a0b8e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 14:45:20 2015 +0200

    FIX: QtElementList does not have a changed() signal.

commit e7341ec2716284e96e58763befbd8fa9e68b27df
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 13:23:35 2015 +0200

    FIX: QtInfoBox now works mostly on ids.
    
    - slots are requested as ..Id_t and not as ptrs anymore for some time.

commit f3b5971ec8cc96538608d12dd2998861f1e187db
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 12:41:40 2015 +0200

    FIX: GLMoleculeObject_molecule() may overlap with atomInserted() signal.
    
    - this is because GLMoleculeObject_molecule takes some time till init() is
      called and its runs in a separate thread (hence, further atoms may be
      loaded into the just created atoms). As we first signOn() and then call
      init(), we may end up initializing atoms whose atomInserted signal then
      also comes in but lateron. This causes the AtomsInSceneMap to have
      double entries and the assertion to fail.
      We now keep book of all atomic ids inserted during init() and these
      are ok to appear doubly and their signal is skipped.

commit fac58f919238a82bc5d6cab2eb5c9621c85c941c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 10:52:11 2015 +0200

    Converted FormatParser::save() to using vector of const atom ptrs.
    
    - required to change all save() functions in all parsers.

commit 99db9baca1782e208fb17d2cc6ace3f4cadb568b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 10:32:10 2015 +0200

    Replaced all World::getSelected...() to const version where possible.
    
    - also added const version of World::getSelectedAtoms().

commit a58c16f47065e9446b7916a407271c6544180022
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:16:02 2015 +0200

    Replaced World::getAllAtoms() by const version where possible.

commit f01769bf04baacedde88443ce16ab2f2dd809f30
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 18:57:36 2015 +0200

    Replaced World::getAtom() wherever possible by const version.
    
    - some AtomSet member functions now have const atom ptr instead of atom ptr.
    - molecule can return const and non-const AtomSet.
    - added FromIdToConstAtom to allow iterate through atoms in molecule (which
      are stored by id, not by ptr) in const fashion.
    - in molecule::isInMolecule() is now const, ::CopyMolecule..() is non-const
      (because copying involves father atom who is stored non-const).

commit 1259df9500410b59c3a56d9cf8d54624b53f97da
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 10:56:36 2015 +0200

    Replaced World::getAllMolecules() wherever possible by const version.

commit 63fb7a963007e0f94b955d96ca949cd435eacb2a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 10:48:35 2015 +0200

    Replaced getMolecule() by const access version where possible.
    
    - so far this is done done via const_casting the World.

commit 795c0fbd35ce4d14a5986636e88a0fe5fcc53381
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 10:30:56 2015 +0200

    World::getAtoms() now has const versions as well.
    
    - this in turn required to adapt all AtomDescriptors and some fixes, e.g.
      predicate is now const member and works on const atom ptr.

commit 97445f1edda30c6d17472c562f9832a49df3e644
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 09:42:00 2015 +0200

    World::getMolecules..() now has const versions as well.
    
    - this required to adapt all MoleculeDescriptors accordingly.

commit 270bdface47b2d970089daba2ed78dc3f90395a7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 09:22:29 2015 +0200

    atom::getMolecule() now returns ptr to const molecule.
    
    - changed some places where getMolecule() was used. Most of them required only
      const access anyway. World is allowed to const'cast the constness away as
      it commands over molecules anyway.

commit 9b3262b2e3b9296a0c5ea340ffa6b8b38a694615
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 12:43:49 2015 +0200

    FIX: molecule's Formula is not changed when atom changes element.

commit d12d818e7c101fa705af778bca10771e52c18690
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 09:42:19 2015 +0200

    DOCU: Corrected userguide.
    
    - this still needs some more work, e.g. w.r.t to code snippets indentation.

commit 599b3232e65ac3b245869d9dd63c45d7e8f162f4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:53:44 2015 +0200

    FIX: createGuiChecks can handle multi-lines.
    
    - also we reduce verbosity by default.
    - redid all GuiCheck test scripts.

commit a4dee7ca90a18a6be133d405f7a0b0f5e8181d6d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 18:00:52 2015 +0200

    tempcommit: Attempt to replace QtElementList::refill() by faster system.
    
    - this is not finished or tested as it is incompatible right now right refill().

commit 6b69594bcabc35afd7ab6ba170e610a1588c1df4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 18:01:34 2015 +0200

    Molecule has new channel FormulaChanged used by specific QtMoleculeItem.

commit 74831898be603d80e0fe28f09943254aee55e893
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 17:59:56 2015 +0200

    FIX: World does not sign on to molecule changes.

commit 6b474e1aa04d153d6d0b68b8cf8de9ed806ef258
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 17:09:31 2015 +0200

    QtElementList now listens to AtomObserver and not MoleculeListClass anymore.

commit 69b434b1d1a5180a87c3d669024542593104c8e0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 22 23:14:50 2015 +0200

    QtMoleculeItem now uses moleculeId_t instead molecule*.

commit 704d59ccf5f2559ab48b197552d1bea827b92ad2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 22 22:18:58 2015 +0200

    Changed hoverChanged() from mol* to moleculeId_t.
    
    - also changed signatures for atom.

commit 34641b910ee6b9ce05b01bd6c5aa2e558ef54466
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 22:56:56 2015 +0200

    FIX: World does not to heed updates from internal MoleculeListClass.
    
    - there is not even an World::update() nor ::recieveNotifications().

commit eac542d5b19b04687918ad9252e1d9cb4adfc4cd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 22:56:40 2015 +0200

    Fixed ObserverLog message in GLWorldView.

commit 2520ccbe1eb2cf5456bd770eedc0656bcef7846f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:57:49 2015 +0200

    FIX: GLWorldScene::changeAtomId() reinserted with oldid instead of newid.
    
    - also fixed assertion message in GLMoleculeObject_molecule::atomInserted().

commit ec6abc5fcbede9d754e9e8267ef3dc93f92ab49a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:05:31 2015 +0200

    FIX: QtMoleculeListView::moleculeSelected() did not check for presence of molitem.

commit 4669341c36fbec6d4f4114ed868a2c6ca3c34085
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:04:49 2015 +0200

    GLWorldScene::atomInserted() also adds NULL object to ..inSceneMap.

commit ef3013cd854f882cf600cfb78dc0c9cd4f78897b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 19:37:52 2015 +0200

    GLWorldScene::moleculeInserted() gets moleculeId_t as param.
    
    - we must not use pointers to instances outside the Qt world as parameters.
    - we add NULL into MoleculesInSceneMap for moleculeRemoved to remove the entry.

commit c13b913f78b416eebfc6ff8ac0031329a4944e78
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue May 19 07:28:36 2015 +0200

    Gui is returning error code of 5 (in test mode) if (last) action failed.
    
    - this allows to take over return code checks in testsuite.

commit 068a852341119fad16f4f312d9ab6289fe0edd65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 14:30:06 2015 +0200

    FIX: print on CommandHelp("help") not required in python regression test.
    
    - also fixed double disclaimer.

commit 7774f7e70f2ae517967d41e9125f5dba0adf1dbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:58:20 2015 +0200

    FIX: parser-parameters in regression tests basis and maxiter contained white spaces.

commit 23110a4092c457be30e89f88181ea2df46c504e5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 10:04:04 2015 +0200

    FIX: Regression test set-parameters-mpqc undo compared against wrong file.
    
    - functionality is actually working and removed XFAIL_IF.
    - regression test set-parameters-mpqc had too many white spaces in
      parser-parameters.

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


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From git at ins.uni-bonn.de  Wed Aug  5 09:14:55 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Wed,  5 Aug 2015 09:14:55 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM]  annotated tag v1.4.12 created. v1.4.12
Message-ID: <20150805071455.CD6225FD6E@saturn.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 "".

The annotated tag, v1.4.12 has been created
        at  8040ff39e1fe7f4360fc961e0654a1734273e821 (tag)
   tagging  0ea4ddbf6833adf1a4a2ada1981935715775879f (commit)
  replaces  v1.4.11
 tagged by  Frederik Heber
        on  Wed Aug 5 09:12:47 2015 +0200

- Log -----------------------------------------------------------------
Preliminary version for working guicheck tests.

This version contains the following branches:
0ea4ddb	Candidate_v1.4.12 (dist fixes, mem fixes and cleaning of Action and
	related interfaces)
c66ae66	GuiCheck_TestFixes (several test fixes such that guicheck regression
	tests are properly constructed via the create script)
561b945 SeparatingOutQtThreads (Adding mutexes in Qt code parts for a start)
9ad4d61 AddingConstDescriptors (descriptors now allow const access, hence they
	don't cause updates via ObservedIterators, many World getters to atoms
	and molecules now have explicit const versions)
a4dee7c	Fixing_MolecuilderGui (Initial GUI fixes)

Frederik Heber (80):
      FIX: Regression test set-parameters-mpqc undo compared against wrong file.
      FIX: parser-parameters in regression tests basis and maxiter contained white spaces.
      FIX: print on CommandHelp("help") not required in python regression test.
      Gui is returning error code of 5 (in test mode) if (last) action failed.
      GLWorldScene::moleculeInserted() gets moleculeId_t as param.
      GLWorldScene::atomInserted() also adds NULL object to ..inSceneMap.
      FIX: QtMoleculeListView::moleculeSelected() did not check for presence of molitem.
      FIX: GLWorldScene::changeAtomId() reinserted with oldid instead of newid.
      Fixed ObserverLog message in GLWorldView.
      FIX: World does not to heed updates from internal MoleculeListClass.
      Changed hoverChanged() from mol* to moleculeId_t.
      QtMoleculeItem now uses moleculeId_t instead molecule*.
      QtElementList now listens to AtomObserver and not MoleculeListClass anymore.
      FIX: World does not sign on to molecule changes.
      Molecule has new channel FormulaChanged used by specific QtMoleculeItem.
      tempcommit: Attempt to replace QtElementList::refill() by faster system.
      FIX: createGuiChecks can handle multi-lines.
      DOCU: Corrected userguide.
      FIX: molecule's Formula is not changed when atom changes element.
      atom::getMolecule() now returns ptr to const molecule.
      World::getMolecules..() now has const versions as well.
      World::getAtoms() now has const versions as well.
      Replaced getMolecule() by const access version where possible.
      Replaced World::getAllMolecules() wherever possible by const version.
      Replaced World::getAtom() wherever possible by const version.
      Replaced World::getAllAtoms() by const version where possible.
      Replaced all World::getSelected...() to const version where possible.
      Converted FormatParser::save() to using vector of const atom ptrs.
      FIX: GLMoleculeObject_molecule() may overlap with atomInserted() signal.
      FIX: QtInfoBox now works mostly on ids.
      FIX: QtElementList does not have a changed() signal.
      FIX: GLMoleculeObject_molecule was not informed of atom index change.
      Removed lots of code in GLWorldScene that now resides in GLMoleculeObject_molecule.
      UIs are now initialized before any action takes place.
      Removed GLMoleculeObject_molecule's init() and reinit().
      FIX: GLWorldScene/View capture all missed signals for each GLMoleculeObject_molecule.
      FIX: GLWorldView must not listen to moleculeRemoved but to its subjectKilled.
      FIX: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted.
      QtInfoBox updates information on update signal.
      FIX: QDebugStream is now thread-safe.
      Extracted signing on to molecule into activateObserver.
      FIX: GLWorldScene did not initialize SelectionMode properly.
      FIX: GLWorldView was signed in to atomInserted and atomRemoved without any need.
      FIX: QtUIFactory copied to wrong argv.
      Storing the id of the main thread in static global variable.
      FIX: QtHomologyList::refill() is now called via signal/slot.
      FIX: QtMoleculeItem would not correctly signOff prior to molecule being destroyed.
      Added QMutex to QtElementList for refill().
      TEMP: Removed QtLogBox for the moment.
      FIX: QtElementList now uses new updateElement().
      FIX: QtTimeLine would cause another WorldSetTime action.
      FIX: Cuboid_impl::getNormal() did not take numerical imprecision into account.
      FIX: ActionQueue::isIdle() states whether actions are executed or not.
      FIX: QtMoleculeListView caused Command to be executed when selection changed internally.
      FIX: MakroAction's outputAsPython() uses outputAsPython() not outputAsCLI().
      Added TriangleMatcher to safely compare tesselation .dat files.
      FIX: Added molecuilderguitest to testsuite dependencies.
      FIX: tests/regression FragmentationAutomation had a white space after line break.
      FIX: QTUIFactory's test-single was not working right.
      executePythonScriptFile() calls executePythonScript() now.
      Group item with atom count of 0 is confusing in QtMoleculeList, creating with empty string.
      FIX: atom_bondedparticle signatures changed to more const versions.
      FIX: Molecule has new signal IndexChanged.
      FIX: atom_atominfo lacked some notifies or had them wrong.
      Added getSelected..Ids() for both atoms and molecules.
      Added Action::setOptionValue() which allows setting the option via a string.
      Added TriangleMatcher to safely compare tesselation .dat files.
      TESTFIX: regression test SubgraphDissection Redo was broken.
      TESTFIX: atom selection regression tests with shapes were very noisy and hence very slow.
      TESTFIX: regression test DepthFirstSearch had extra linebreak.
      FIX: Added Parameters Value_Elements to correctly set vector of elements from string.
      TESTFIX: selection molecule by name had escaped ticks.
      TESTFIX: Added AdjacencyMatcher to correctly compare .adj files in save-adjacency regression test.
      DISTFIX: Additional types.hpp in AdjacencyMatcher/Makefile.am.
      DISTFIX: adjacencymatcher and trianglematcher are check_PROGRAMS, not bin_...
      FIX: Adjacency's operator<<() printed fixed number (3) of entries.
      Action::isActive() is now const member function.
      Cleaned up ActionQueue's interface: Actions are always cloned.
      DOCU: Enhanced description of test policy on version update.
      Set version to v1.4.12.

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


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From git at ins.uni-bonn.de  Sat Aug 15 11:14:56 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Sat, 15 Aug 2015 11:14:56 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM]  annotated tag v1.5.0 created. v1.5.0
Message-ID: <20150815091456.1683B5FD6E@saturn.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 "".

The annotated tag, v1.5.0 has been created
        at  86a5ee025241f95111ddb323821c85944821f2c2 (tag)
   tagging  bff5e273091c20e062b35677796d4f022e572385 (commit)
  replaces  v1.4.12
 tagged by  Frederik Heber
        on  Thu Aug 13 23:53:45 2015 +0200

- Log -----------------------------------------------------------------
GuiChecks regression tests are all fully working (1% crashes tolerated for the moment).

This version contains the following branches:
bff5e27	Candidate_v1.5.0 (Setting version)
66b092e	DebianPackaging (adding debian files for creating a .deb package file)
6fe4f76 GUIStates_using_ObservedValue (ObservedValue cashes a state in the
	World even beyond the instance's destruction, e.g. the position of an
	atom, which allows to have Qt and World run in separate threads)

Frederik Heber (47):
      Using static Observable::..NotificationsChannel() functions.
      Removed init() and signal WorldSelectionChanged() from GLWorldScene.
      GLMoleculeObject_atom uses ObservedValue for internally representing atom's state.
      GLMoleculeObject_bond uses ObservedValue for internally representing atom's state.
      QtMoleculeItem_... use ObservedValue for internally representing atom's state.
      GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state.
      GLWorldScene propagates changed mol id to GLMoleculeObject_molecule.
      Fixing QtElementList::updateElement().
      QtMoleculeList::informDirtyState() does not need to lock refill_mutex anymore.
      Fixing QtMoleculeList with list containing only formulas and ids.
      DOCU: Updated documentation on Qt Gui construct.
      GLWorldView does not emit changed() on each general update() from the World and others.
      GLWorldView no longer listens to WorldTime::TimeChanged.
      Added lastChanged..Id() to both World and molecule.
      Qt4 instance use new lastChanged..Id() in place of lastChanged().
      Removed molecule::lastChanged().
      World now first releases id and then destroys the atom/molecule.
      FIX: Fixing "pure virtual function called" in QtMoleculeItem.
      QtMoleculeItem_.. now shout when they receive subjectKilled().
      Added QtSelectionChangedAgent to transform O/O to S/S system.
      QtMainWindow uses QtSelectionChangedAgent.
      Fixed formula usage in Qt part of code.
      FIX: Setting molecule's name via QtMoleculeList item is again possible.
      GLMoleculeObject_molecule also has ObservedValue for name.
      GLMoleculeObject_molecule does not use getAtomCount() anymore.
      Avoided use of getId() on molecules and atoms in Qt code where possible.
      AddAtomBonds() now uses just id not ptr as param.
      Asserted that GLMoleculeObject_molecule::update() is never called.
      GLWorldScene lacked assert of Walker in atomClicked().
      FIX: Fixing display of shapes in GLWorldView.
      FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more.
      FIX: GLMoleculeObject_bond had both flipped ids and the side.
      TESTFIX: Marked molecule translation guicheck tests as XFAIL.
      FIX: QtLogBox is again included and working thread-safe.
      FIX: updateBoundingBox() must not call molecule::getBoundingBox() on every update.
      FIX: AllPotentialHealder.hpp not excluded from CodeCheck config_h.
      DOCU: Described workaround for missing pyconfig.h.
      FIX: bash_completion was accidentally removed by clean target.
      Added debian/.. files for debian packaging.
      Added script for creating debian package.
      Enabled GUI compilation for debian package.
      Added debugging package molecuilder-dbg and source package molecuilder-dev
      DISTFIX: EXTRA_DIST in tests/../Makefile.ams depended on not yet set variables.
      FIX: Qt can now be found even without --with-Qtbin...
      TESTFIX: for source builds we need to exclude all moc'ed files from codechecks.
      FIX: This prevent crash of molecuildergui in debian package.
      Set version to 1.5.0.

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


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From git at ins.uni-bonn.de  Sat Aug 15 11:15:15 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Sat, 15 Aug 2015 11:15:15 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM]  branch stable updated. v1.5.0
Message-ID: <20150815091516.3BCC05FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, stable has been updated
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- Log -----------------------------------------------------------------
commit bff5e273091c20e062b35677796d4f022e572385
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Jul 25 15:07:28 2015 +0200

    Set version to 1.5.0.
    
    - MoleCuilder library is now 15:0:0.
    - Codename "GUI" (the GUI has tests and is fully working).

commit 5284fffa7f4365151a666b79f37c046f73411a9e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Aug 13 22:31:22 2015 +0200

    FIX: This prevent crash of molecuildergui in debian package.
    
    - somehow QGLView hiccups in the parsed arguments although they should be safe
      to use via QApplication. I have not idea but this solves the issue and does no
      no harm. Hence, we proceed.

commit 57c25368aae2779cf2545bd715d92847c1f853a0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 12 23:11:10 2015 +0200

    TESTFIX: for source builds we need to exclude all moc'ed files from codechecks.

commit 196702d9c311b2871aef6cff534ecf5e37661227
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Aug 13 23:51:14 2015 +0200

    FIX: Qt can now be found even without --with-Qtbin...

commit 65ca735893cc3cd45422991765fad3175ed57b57
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 4 21:51:55 2015 +0200

    DISTFIX: EXTRA_DIST in tests/../Makefile.ams depended on not yet set variables.
    
    - it would use TESTSCRIPT but the variable would be set afterwards.

commit 66b092e089b4fe741dc1a5497ad61222883e30c0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Aug 13 09:31:41 2015 +0200

    Added debugging package molecuilder-dbg and source package molecuilder-dev
    
    - debug information is stripped into extra file. All is handled by CDBS.
    - needed .install files for stating where to install what file in source tree
      in debian/..

commit 8fbd7b3b947194c7f2e32d92bbfeb47a1ca108b0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 12 23:38:07 2015 +0200

    Enabled GUI compilation for debian package.

commit b8b2e63323e4a8a49765e237e34a436191f9a532
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat May 23 21:04:44 2015 +0200

    Added script for creating debian package.

commit d68514266b1d90ca4e9774dc1ebdf195a18c5c02
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat May 23 11:26:47 2015 +0200

    Added debian/.. files for debian packaging.
    
    - added all dependencies (without JobMarket, QtGui, QWT, or vmg).

commit b8f0a8d46d1cb0c1dc07f2d6a783b8cf0fd1f067
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat May 23 20:32:37 2015 +0200

    FIX: bash_completion was accidentally removed by clean target.
    
    - also Python/boxmaker was not contained in EXTRA_DIST.

commit 399571102f903dadaa8e99db9e4f4be3e8d34fb0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat May 23 20:32:01 2015 +0200

    DOCU: Described workaround for missing pyconfig.h.

commit d07a38beef13fba24ae491f74c049ef04179ac35
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat May 23 16:23:14 2015 +0200

    FIX: AllPotentialHealder.hpp not excluded from CodeCheck config_h.
    
    - this only causes an error when not doing an out-of-source bild (which
      debuild does and that's why it came up).

commit 6fe4f7657cee7b53f89f832e3948f7fa4bbbe4ba
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 4 15:53:52 2015 +0200

    FIX: updateBoundingBox() must not call molecule::getBoundingBox() on every update.
    
    - this is O(N^2). We now update by using the current center and radius and
      looking at the last changed atom's position. This diverges with respect to
      the radius after some time. Hence, a true getBoundingBox() should be called
      after a while.

commit ec84716c2318851ba3564aff1286a259ca46df4d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Jul 25 15:06:15 2015 +0200

    FIX: QtLogBox is again included and working thread-safe.
    
    - QDebugStream is now appending text to QtLogBox in a thread-safe manner by
      using signal/slots. This code is taken from qt-forum.de.

commit b9e47e05b980c2d1717a7e44831434a551b3a246
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 23:54:14 2015 +0200

    TESTFIX: Marked molecule translation guicheck tests as XFAIL.
    
    - so far, we cannot use a MakroAction as a python function except if not
      arguments are required. Hence, for the moment we mark it as XFAIL.
    - The problem is with the boost::python::def function. We need to fill its
      arguments during compile-time but that would require some weird preprocessor
      magic going through all Actions contained in the MakroAction's sequence.

commit 7e2adcdacc44d805e377ada69a708f7d564f4498
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 22:47:41 2015 +0200

    FIX: GLMoleculeObject_bond had both flipped ids and the side.
    
    - in essence, both do the same thing. We removed all switches that check the
      sides as flipped ids are actually nice and look good in the observerLog.
      We keep the side variable as it might come handy for checking which one we
      are.

commit a9161db25c69419446f0371e9ca3b69d3d4daac1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 22:22:53 2015 +0200

    FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more.

commit 07136ae14d7826fc7287ec37e92157cd61721c87
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jul 20 11:16:27 2015 +0200

    FIX: Fixing display of shapes in GLWorldView.
    
    - we propagate shape name via S/S system such that we may lookup the name in
      ShapeRegistry and do not have to rely on probably already deallocated
      lastchanged() shape. This affects ShapeAdded() and ShapeRemoved().
    - GLMoleculeObject_shape now copies the shape, ensuring that its present
      while its surface is tesselated.

commit 369cb1be7527ef62fee18c457e912c21b1b698eb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 15:47:57 2015 +0200

    GLWorldScene lacked assert of Walker in atomClicked().

commit 92ee4137bc23814e0da4f5dc268c7ec9f06e392f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 15:47:19 2015 +0200

    Asserted that GLMoleculeObject_molecule::update() is never called.

commit ca4b63bb2e6c328401c4597bf9a2d00d25f055e2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 15:46:41 2015 +0200

    AddAtomBonds() now uses just id not ptr as param.

commit 68989c020a48fae01762aa4040fb603221d5e981
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 15:46:02 2015 +0200

    Avoided use of getId() on molecules and atoms in Qt code where possible.
    
    - it is ok if we are inside O/O functions or functions called from these
      functions.

commit 25a81dcb5ee7c2436679aa4784523a95b0e90fb6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 15:29:37 2015 +0200

    GLMoleculeObject_molecule does not use getAtomCount() anymore.
    
    - this removes any usage of getAtomCount() apart from ObservedValue's.

commit 5b61e5e3ff8d5a18604de0315358ab7a74c40a48
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 15:25:40 2015 +0200

    GLMoleculeObject_molecule also has ObservedValue for name.
    
    - this removes any (uncached) molecule::getName() from Qt code part.

commit 07b8001035a112557377b6b6205094bc48f53c8e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 14:01:14 2015 +0200

    FIX: Setting molecule's name via QtMoleculeList item is again possible.
    
    - this is similar to checkForVisibilityChange(), only now for the name.
    - we required four Actions, i.e. this cannot be undone in a single step but
      needs four. However, right now it is not easily possible to construct
      MakroActions from inside the code at compile-time as we do not have
      access to modify parameters via their tokens.
    - using constructed MakroAction in QtMoleculeList for name change.

commit a39d72c6d5edf5fa534720d234e4a54c6dcfc17a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 13:35:26 2015 +0200

    Fixed formula usage in Qt part of code.
    
    - formula of a molecule is only access through ObservedValue or directly within
      the World's O/O system.
    - Molecule may disappear before selection event.
    - Atoms may disappear before selection event.

commit 015f8c18d74c335a5af0741c3ff7f82dfcbfa0d1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 09:08:38 2015 +0200

    QtMainWindow uses QtSelectionChangedAgent.
    
    - QtMoleculeListView and GLWorldView receive its signals. The latter passes it
      on to GLWorldScene.
    - QtMoleculeList has new MoleculeIdToIndex to allow QtMoleculeListView to
      (un)select specific rows on a given index.
    - GLWorldScene passes atom and molecule selection to GLMoleculeObject_molecule.
    - GLMoleculeObject_molecule passes atom selection to respective
      GLMoleculeObject_atom.

commit e5a47740179fa6bd45778ad5a4caea81fde92864
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 08:36:38 2015 +0200

    Added QtSelectionChangedAgent to transform O/O to S/S system.
    
    - also this will be far more effective, as e.g. not all
      GLMoleculeOBject_molecule will receive SelectionChanged from World if just a
      single molecule has been selected.
    - Atom might not yet have a molecule, i.e. it is not drawn yet. We do nothing
      then.
    - recieveNotification allows for vanished atom (due to removal). We do nothing
      then.

commit cc297688a2f09a635ccb45323617573684f51f9d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 19 08:30:51 2015 +0200

    QtMoleculeItem_.. now shout when they receive subjectKilled().
    
    - this way we do not have this double system of both QtMoleculeList (in a lazy
      fashion) and each QtMoleculeList listens for moleculeRemoved (one through the
      Observer channel, the other through subjectKilled()).
    - we simply count the number of QtMoleculeItems that received subjectKilled()
      and if max is reached, the row is removed.
    - to prevent molecule id clash, insertion (of same id) after removal is ok.
      This works cause we first remove and then insert new item. Hence, having the
      same id is possible.

commit b9680b48b3c408eb08fa28771d7f329859cf047b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jul 16 10:29:09 2015 +0200

    FIX: Fixing "pure virtual function called" in QtMoleculeItem.
    
    - as a matter of fact this should not be a problem: Inside QtMoleculeItem's
      dstor body while signing off from the channels, it is no problem to receive
      a notification for a channel we have not signed off yet. The vtable has
      not been touched with respect to QtMoleculeItem.
      I really do not understand this issue. I have tried to reproduce it with
      a few mock classes that have the very same inheritance pattern and used
      locks to force the same case of a virtual function being called while
      inside the dstor's body but it does not reproduce the error.
    - the same holds for the cstor and again the vtable is created before the
      code pointer enters the cstor body, hence it should be no problem ...
    - the solution is to signOn..() and signOff..() on the highest level, i.e.
      on the most derived classes. This causes some code duplication but at
      least it works.

commit f02b53a6f30feeb1be573eceaad0edfb9dbcac71
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jul 16 01:26:09 2015 +0200

    World now first releases id and then destroys the atom/molecule.
    
    - this prevents any access to atoms/molecules in the phase of destruction.

commit 5be7988b41312420dd9335d53345f61a79a43f07
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 31 11:20:51 2015 +0200

    Removed molecule::lastChanged().
    
    - we have lastChangedAtomId() and ids are safer to use than ptrs.

commit 54bdaae692392765ace3b38c8635806888d0c8b5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jul 16 01:25:22 2015 +0200

    Qt4 instance use new lastChanged..Id() in place of lastChanged().
    
    - also changed in FormatParser_common.

commit fb95a5645025c4f145cfcbf9ef41a1f12c86a506
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jul 16 01:23:30 2015 +0200

    Added lastChanged..Id() to both World and molecule.

commit f714763c1502a8d2a462b4e01ad3c708f9fa17cf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 15 17:22:04 2015 +0200

    GLWorldView no longer listens to WorldTime::TimeChanged.
    
    - molecules are re-created when the time changes anyway so the world view is
      informed about the change.
    - removed all commented-out lines.

commit 3d5b5bdeb158f9612295a4adbb43add240c21bd9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 15 16:01:41 2015 +0200

    GLWorldView does not emit changed() on each general update() from the World and others.

commit 52c5d4c7c4ecce1343353bae76e18959dd8d2d1a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 15 15:56:58 2015 +0200

    DOCU: Updated documentation on Qt Gui construct.

commit fcdf0553321b79c267b07b0d50decd2bd4fd4a2d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jul 14 15:55:47 2015 +0200

    Fixing QtMoleculeList with list containing only formulas and ids.
    
    - COLUMNTYPE now belongs to QtMoleculeItem not QtMoleculeItemFactory.
    - callback function in QtMoleculeItem signature changed to molid and column.
    - QtMoleculeItem::getType() for obtaining the type to be used as argument in
      the callback.

commit 95f49f80844c3103ded5d5940874d5342ce246a6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jul 7 03:10:10 2015 +0200

    QtMoleculeList::informDirtyState() does not need to lock refill_mutex anymore.
    
    - we simply write the QtMoleculeItem to the ToBeMoved list and convert it to
      the very first item in the row in updateItemStates().

commit 88846bef6d3c0a61836ca4125b1bd6c2ee80ef95
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jul 7 03:08:58 2015 +0200

    Fixing QtElementList::updateElement().

commit 20f9b5ca3d0b9027b2885d6239e5b48b8dea45a5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jul 20 10:35:41 2015 +0200

    GLWorldScene propagates changed mol id to GLMoleculeObject_molecule.
    
    - GLWorldScene must emit MoleculeRemoved on last subjectKlled().
    - GLWorldScene has internal RemovalMolecule in case moleculeRemoved comes prior
      to moleculeInserted.

commit 6c16a02ecd71315045f7522510b3807789050e4b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:19 2015 +0200

    GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state.

commit 3e52834b600d16813f5a1e262cafdbdc7586571d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 06:49:13 2015 +0200

    QtMoleculeItem_... use ObservedValue for internally representing atom's state.
    
    - this affects atomcount, formula, and name. visibility depends on clicked
      state and occurrence is changed elsewhere.

commit 009e2e2d372810a555a452769338209c68591479
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 06:46:32 2015 +0200

    GLMoleculeObject_bond uses ObservedValue for internally representing atom's state.

commit 53437425e2d51ca59e9a3ab458b6f636927987ee
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:37:50 2015 +0200

    GLMoleculeObject_atom uses ObservedValue for internally representing atom's state.
    
    - we use internal owner as ref to Observable.

commit b3a33d2dc647c629f4efa8e07674f19b1af1740f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:57 2015 +0200

    Removed init() and signal WorldSelectionChanged() from GLWorldScene.

commit 574d377d6df9c61b2d15b880404e8bb7d6d2fff0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jul 5 09:55:15 2015 +0200

    Using static Observable::..NotificationsChannel() functions.
    
    - requiring now CodePatterns 1.3.0 due to ObservedValue.
    - also we purge the GlobalObservablesInfo in cleanUp().

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

Summary of changes:
 Makefile.am                                        |   10 +-
 configure.ac                                       |   65 +-
 debian/changelog                                   |    6 +
 debian/compat                                      |    1 +
 debian/control                                     |   53 +
 debian/copyright                                   |   29 +
 debian/molecuilder-dev.install                     |    2 +
 debian/molecuilder.install                         |    6 +
 debian/rules                                       |   12 +
 debian/source/format                               |    1 +
 doc/userguide/userguide.xml                        | 5439 +++++++++-----------
 makeDebianPackage.sh                               |   46 +
 src/Actions/Action.cpp                             |    2 +-
 src/Actions/Action.hpp                             |   19 +-
 src/Actions/ActionQueue.cpp                        |   42 +-
 src/Actions/ActionQueue.hpp                        |   37 +-
 src/Actions/ActionRegistry.cpp                     |   85 +-
 src/Actions/ActionRegistry.hpp                     |    3 +-
 src/Actions/ActionSequence.cpp                     |   47 +-
 src/Actions/ActionSequence.hpp                     |    3 +-
 src/Actions/ActionStatusList.cpp                   |    2 +-
 src/Actions/Action_impl_header.hpp                 |    2 +
 src/Actions/Action_impl_pre.hpp                    |   23 +-
 .../DipoleAngularCorrelationAction.cpp             |   16 +-
 .../AnalysisAction/DipoleCorrelationAction.cpp     |    3 +-
 .../AnalysisAction/PairCorrelationAction.cpp       |    6 +-
 .../AnalysisAction/PointCorrelationAction.cpp      |    3 +-
 .../AnalysisAction/SurfaceCorrelationAction.cpp    |    3 +-
 src/Actions/AtomAction/ChangeElementAction.cpp     |   23 +-
 .../AtomAction/RotateAroundOriginByAngleAction.cpp |    2 +-
 src/Actions/AtomAction/SaturateAction.cpp          |    8 +-
 src/Actions/Calculation.hpp                        |    2 +
 src/Actions/Calculation_impl.hpp                   |    4 +
 src/Actions/CommandAction/HelpAction.cpp           |    4 +-
 src/Actions/FillAction/FillRegularGridAction.cpp   |    3 +-
 src/Actions/FillAction/FillSurfaceAction.cpp       |    6 +-
 src/Actions/FillAction/FillVolumeAction.cpp        |    4 +-
 src/Actions/FillAction/SuspendInMoleculeAction.cpp |    7 +-
 .../AnalyseFragmentationResultsAction.cpp          |    4 +-
 .../FragmentationAction/FragmentationAction.cpp    |   10 +-
 .../FragmentationAutomationAction.cpp              |    2 +-
 .../MolecularDynamicsAction.cpp                    |   24 +-
 .../StructuralOptimizationAction.cpp               |   24 +-
 .../GraphAction/CorrectBondDegreeAction.cpp        |   12 +-
 src/Actions/GraphAction/CreateAdjacencyAction.cpp  |   17 +-
 src/Actions/GraphAction/DestroyAdjacencyAction.cpp |   12 +-
 .../GraphAction/SubgraphDissectionAction.cpp       |   16 +-
 src/Actions/GraphAction/UpdateMoleculesAction.cpp  |   24 +-
 src/Actions/MakroAction.cpp                        |   11 +-
 src/Actions/MakroAction.hpp                        |    5 +-
 src/Actions/MakroAction_impl_pre.hpp               |    6 +-
 src/Actions/ManipulateAtomsProcess.cpp             |    3 +
 src/Actions/ManipulateAtomsProcess.hpp             |    2 +
 src/Actions/MethodAction.cpp                       |    3 +
 src/Actions/MethodAction.hpp                       |    1 +
 src/Actions/MoleculeAction/RemoveAction.cpp        |    4 +-
 .../MoleculeAction/SaveTemperatureAction.cpp       |    5 +-
 src/Actions/MoleculeAction/StretchBondAction.cpp   |   15 +-
 src/Actions/MoleculeAction/TranslateAction.cpp     |   12 +-
 .../SaveSelectedAtomsAsExtTypesAction.cpp          |    5 +-
 .../SelectionAction/Atoms/AllAtomsAction.cpp       |    5 +-
 .../SelectionAction/Atoms/AllAtomsAction.def       |    2 +-
 .../Atoms/AllAtomsInsideVolumeAction.cpp           |    5 +-
 .../Atoms/AllAtomsInsideVolumeAction.def           |    2 +-
 .../Atoms/AllAtomsOfMoleculeAction.cpp             |    5 +-
 .../Atoms/AllAtomsOfMoleculeAction.def             |    2 +-
 .../SelectionAction/Atoms/AtomByElementAction.cpp  |    5 +-
 .../SelectionAction/Atoms/AtomByElementAction.def  |    2 +-
 .../SelectionAction/Atoms/AtomByIdAction.cpp       |   15 +-
 .../SelectionAction/Atoms/AtomByOrderAction.cpp    |    9 +-
 .../SelectionAction/Atoms/ClearAllAtomsAction.cpp  |    5 +-
 .../SelectionAction/Atoms/ClearAllAtomsAction.def  |    2 +-
 .../SelectionAction/Atoms/NotAllAtomsAction.cpp    |    5 +-
 .../SelectionAction/Atoms/NotAllAtomsAction.def    |    2 +-
 .../Atoms/NotAllAtomsInsideVolumeAction.cpp        |    5 +-
 .../Atoms/NotAllAtomsInsideVolumeAction.def        |    2 +-
 .../Atoms/NotAllAtomsOfMoleculeAction.cpp          |    5 +-
 .../Atoms/NotAllAtomsOfMoleculeAction.def          |    2 +-
 .../Atoms/NotAtomByElementAction.cpp               |    5 +-
 .../Atoms/NotAtomByElementAction.def               |    2 +-
 .../SelectionAction/Atoms/NotAtomByIdAction.cpp    |   15 +-
 .../SelectionAction/Atoms/NotAtomByOrderAction.cpp |    9 +-
 .../SelectionAction/Atoms/PopAtomsAction.cpp       |   16 +-
 .../SelectionAction/Atoms/PopAtomsAction.def       |    4 +-
 .../Molecules/AllMoleculesAction.cpp               |    5 +-
 .../Molecules/AllMoleculesAction.def               |    2 +-
 .../Molecules/ClearAllMoleculesAction.cpp          |    5 +-
 .../Molecules/ClearAllMoleculesAction.def          |    2 +-
 .../Molecules/MoleculeByFormulaAction.cpp          |    8 +-
 .../Molecules/MoleculeByFormulaAction.def          |    2 +-
 .../Molecules/MoleculeByIdAction.cpp               |    9 +-
 .../Molecules/MoleculeByNameAction.cpp             |    7 +-
 .../Molecules/MoleculeByNameAction.def             |    2 +-
 .../Molecules/MoleculeByOrderAction.cpp            |    3 +-
 .../Molecules/MoleculeOfAtomAction.cpp             |    5 +-
 .../Molecules/MoleculeOfAtomAction.def             |    2 +-
 .../Molecules/NotAllMoleculesAction.cpp            |    5 +-
 .../Molecules/NotAllMoleculesAction.def            |    4 +-
 .../Molecules/NotMoleculeByFormulaAction.cpp       |   10 +-
 .../Molecules/NotMoleculeByFormulaAction.def       |    2 +-
 .../Molecules/NotMoleculeByIdAction.cpp            |    9 +-
 .../Molecules/NotMoleculeByNameAction.cpp          |    7 +-
 .../Molecules/NotMoleculeByNameAction.def          |    2 +-
 .../Molecules/NotMoleculeByOrderAction.cpp         |    3 +-
 .../Molecules/NotMoleculeOfAtomAction.cpp          |    7 +-
 .../Molecules/NotMoleculeOfAtomAction.def          |    4 +-
 .../Molecules/PopMoleculesAction.cpp               |   16 +-
 .../Molecules/PopMoleculesAction.def               |    4 +-
 .../TesselationAction/ConvexEnvelopeAction.cpp     |    3 +-
 src/Actions/WorldAction/BoundInBoxAction.cpp       |   28 +-
 src/Actions/WorldAction/CenterInBoxAction.cpp      |   28 +-
 src/Actions/WorldAction/RepeatBoxAction.cpp        |    7 +-
 src/Actions/unittests/ActionSequenceUnitTest.cpp   |   56 +-
 src/Analysis/analysis_bonds.cpp                    |    4 +-
 src/Analysis/analysis_correlation.cpp              |   73 +-
 src/Analysis/analysis_correlation.hpp              |   89 +-
 .../AnalysisCorrelationToPointUnitTest.cpp         |    2 +-
 .../AnalysisCorrelationToPointUnitTest.hpp         |    2 +-
 .../AnalysisCorrelationToSurfaceUnitTest.cpp       |    2 +-
 .../AnalysisCorrelationToSurfaceUnitTest.hpp       |    2 +-
 .../unittests/AnalysisPairCorrelationUnitTest.cpp  |    3 +-
 src/Atom/AtomObserver.cpp                          |    2 +-
 src/Atom/AtomSet.hpp                               |   12 +-
 src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp         |    6 +-
 src/Atom/atom.cpp                                  |    5 +-
 src/Atom/atom.hpp                                  |    2 +-
 src/Atom/atom_atominfo.cpp                         |   18 +-
 src/Atom/atom_bondedparticle.cpp                   |   40 +-
 src/Atom/atom_bondedparticle.hpp                   |   14 +-
 src/Atom/atom_observable.cpp                       |    2 +-
 src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp  |    8 +-
 src/AtomIdSet.cpp                                  |   16 +-
 src/AtomIdSet.hpp                                  |    8 +-
 src/Bond/AdjacencyMatcher/Adjacency.hpp            |  149 +
 src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp     |  193 +
 src/Bond/AdjacencyMatcher/Makefile.am              |   33 +
 src/Bond/BondInfo.cpp                              |    4 +-
 src/Bond/bond_observable.cpp                       |    2 +-
 src/Box.cpp                                        |    6 +-
 src/Descriptors/AtomDescriptor.cpp                 |   53 +-
 src/Descriptors/AtomDescriptor.hpp                 |   15 +-
 src/Descriptors/AtomDescriptor_impl.hpp            |   37 +-
 src/Descriptors/AtomIdDescriptor.cpp               |   13 +-
 src/Descriptors/AtomIdDescriptor_impl.hpp          |    4 +-
 ...ulePtrDescriptor.cpp => AtomNameDescriptor.cpp} |   31 +-
 src/Descriptors/AtomNameDescriptor.hpp             |   22 +
 src/Descriptors/AtomNameDescriptor_impl.hpp        |   25 +
 src/Descriptors/AtomOfMoleculeDescriptor.cpp       |    2 +-
 src/Descriptors/AtomOfMoleculeDescriptor_impl.hpp  |    2 +-
 .../AtomOfMoleculeSelectionDescriptor.cpp          |   28 +-
 .../AtomOfMoleculeSelectionDescriptor_impl.hpp     |    7 +-
 src/Descriptors/AtomOrderDescriptor.cpp            |   43 +-
 src/Descriptors/AtomOrderDescriptor_impl.hpp       |    5 +-
 src/Descriptors/AtomSelectionDescriptor.cpp        |   22 +-
 src/Descriptors/AtomSelectionDescriptor_impl.hpp   |    7 +-
 src/Descriptors/AtomShapeDescriptor.cpp            |   24 +-
 src/Descriptors/AtomShapeDescriptor_impl.hpp       |    6 +-
 src/Descriptors/AtomTypeDescriptor.cpp             |    2 +-
 src/Descriptors/AtomTypeDescriptor_impl.hpp        |    2 +-
 .../AtomsWithinDistanceOfDescriptor.cpp            |   17 +-
 .../AtomsWithinDistanceOfDescriptor_impl.hpp       |    6 +-
 src/Descriptors/DescriptorBase.hpp                 |   11 +
 src/Descriptors/DescriptorBase_impl.hpp            |   34 +-
 src/Descriptors/MoleculeDescriptor.cpp             |   67 +-
 src/Descriptors/MoleculeDescriptor.hpp             |   12 +
 src/Descriptors/MoleculeDescriptor_impl.hpp        |   37 +-
 src/Descriptors/MoleculeFormulaDescriptor.cpp      |    2 +-
 src/Descriptors/MoleculeFormulaDescriptor_impl.hpp |    2 +-
 src/Descriptors/MoleculeIdDescriptor.cpp           |   14 +-
 src/Descriptors/MoleculeIdDescriptor_impl.hpp      |    4 +-
 src/Descriptors/MoleculeNameDescriptor.cpp         |    2 +-
 src/Descriptors/MoleculeNameDescriptor_impl.hpp    |    2 +-
 .../MoleculeOfAtomSelectionDescriptor.cpp          |   47 +-
 .../MoleculeOfAtomSelectionDescriptor_impl.hpp     |    7 +-
 src/Descriptors/MoleculeOrderDescriptor.cpp        |   45 +-
 src/Descriptors/MoleculeOrderDescriptor_impl.hpp   |    5 +-
 src/Descriptors/MoleculePtrDescriptor.cpp          |    6 +-
 src/Descriptors/MoleculePtrDescriptor.hpp          |    2 +-
 src/Descriptors/MoleculePtrDescriptor_impl.hpp     |    6 +-
 src/Descriptors/MoleculeSelectionDescriptor.cpp    |   22 +-
 .../MoleculeSelectionDescriptor_impl.hpp           |    7 +-
 .../unittests/AtomDescriptorUnitTest.cpp           |   94 +-
 .../unittests/MoleculeDescriptorUnitTest.cpp       |   78 +-
 src/Filling/unittests/ClusterUnitTest.cpp          |   15 +-
 src/Filling/unittests/FillerUnitTest.cpp           |    4 +-
 .../Automation/VMGFragmentController.cpp           |    5 +-
 src/Fragmentation/Exporters/SaturatedFragment.cpp  |    7 +-
 src/Fragmentation/Fragmentation.cpp                |   20 +-
 src/Fragmentation/Graph.cpp                        |    3 +-
 .../Homology/HomologyGraph_getFromKeyset.cpp       |   10 +-
 src/Fragmentation/Interfragmenter.cpp              |    2 +-
 src/Graph/AdjacencyList.cpp                        |    3 +-
 src/Graph/BuildInducedSubgraph.cpp                 |    2 +-
 src/Graph/BuildInducedSubgraph.hpp                 |    4 +-
 src/Graph/DepthFirstSearchAnalysis.cpp             |   13 +-
 src/Helpers/helpers.hpp                            |    9 +-
 .../unittests/stubs/AtomObserverStub.cpp           |    2 +-
 src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp |    2 +-
 src/LinkedCell/unittests/stubs/WorldTimeStub.cpp   |    2 +-
 src/Makefile.am                                    |    8 +-
 src/Parameters/Makefile.am                         |    2 +
 src/Parameters/Specifics/Value_atom.cpp            |   20 +-
 src/Parameters/Specifics/Value_elements.cpp        |   99 +
 .../{Value_element.hpp => Value_elements.hpp}      |    0
 src/Parameters/Specifics/Value_molecule.cpp        |   21 +-
 src/Parameters/StreamOperators.hpp                 |   14 +-
 .../Validators/Specific/AtomIdValidator.cpp        |    2 +-
 .../Validators/Specific/MoleculeIdValidator.cpp    |    2 +-
 .../Specific/TimeStepPresentValidator.cpp          |    8 +-
 src/Parser/FormatParser.hpp                        |    2 +-
 src/Parser/FormatParserInterface.hpp               |    2 +-
 src/Parser/FormatParserStorage.cpp                 |   24 +-
 src/Parser/FormatParserStorage.hpp                 |    2 +-
 src/Parser/FormatParser_common.cpp                 |    7 +-
 src/Parser/MpqcParser.cpp                          |    7 +-
 src/Parser/MpqcParser.hpp                          |    2 +-
 src/Parser/PcpParser.cpp                           |   22 +-
 src/Parser/PcpParser.hpp                           |   15 +-
 src/Parser/PdbParser.cpp                           |   32 +-
 src/Parser/PdbParser.hpp                           |    8 +-
 src/Parser/Psi3Parser.cpp                          |   11 +-
 src/Parser/Psi3Parser.hpp                          |    4 +-
 src/Parser/TremoloParser.cpp                       |   39 +-
 src/Parser/TremoloParser.hpp                       |   13 +-
 src/Parser/XmlParser.cpp                           |   13 +-
 src/Parser/XmlParser.hpp                           |    2 +-
 src/Parser/XyzParser.cpp                           |   12 +-
 src/Parser/XyzParser.hpp                           |    2 +-
 src/Parser/unittests/ParserMpqcUnitTest.cpp        |    3 +-
 src/Parser/unittests/ParserPcpUnitTest.cpp         |    5 +-
 src/Parser/unittests/ParserPdbUnitTest.cpp         |    5 +-
 src/Parser/unittests/ParserPsi3UnitTest.cpp        |    8 +-
 src/Parser/unittests/ParserTremoloUnitTest.cpp     |   27 +-
 src/Parser/unittests/ParserXmlUnitTest.cpp         |    5 +-
 src/Parser/unittests/ParserXyzUnitTest.cpp         |   23 +-
 src/Python/PythonScripting.cpp                     |   37 +-
 src/Shapes/BaseShapes.cpp                          |    6 +-
 src/Shapes/ShapeFactory.cpp                        |    3 +-
 src/Shapes/ShapeRegistry.cpp                       |    2 +-
 .../unittests/stubs/WorldSelectedMoleculesStub.cpp |    6 +-
 src/Tesselation/TriangleMatcher/Makefile.am        |   34 +
 src/Tesselation/TriangleMatcher/Triangle.hpp       |  145 +
 .../TriangleMatcher/TriangleMatcher.cpp            |  203 +
 src/Tesselation/TriangleMatcher/types.hpp          |   30 +
 src/Tesselation/boundary.cpp                       |   12 +-
 src/ThreadGuard.hpp                                |   34 +
 .../CommandLineUI/CommandLineUIFactory.cpp         |    4 +-
 .../CommandLineUI/Query/AtomCommandLineQuery.cpp   |    2 +-
 .../CommandLineUI/Query/AtomsCommandLineQuery.cpp  |    2 +-
 .../Query/MoleculeCommandLineQuery.cpp             |    2 +-
 .../Query/MoleculesCommandLineQuery.cpp            |    3 +-
 src/UIElements/Makefile.am                         |    8 +-
 src/UIElements/Menu/TextMenu/ActionMenuItem.cpp    |    6 +-
 src/UIElements/Menu/TextMenu/ActionMenuItem.hpp    |    2 +-
 src/UIElements/Menu/TextMenu/MenuItem.cpp          |    2 +-
 src/UIElements/Menu/TextMenu/MenuItem.hpp          |    2 +-
 src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp |    3 +
 src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp |    1 +
 src/UIElements/Qt4/QtMainWindow.cpp                |   14 +-
 src/UIElements/Qt4/QtMainWindow.hpp                |    2 +
 src/UIElements/Qt4/QtUIFactory.cpp                 |   22 +-
 src/UIElements/Qt4/Query/AtomQtQuery.cpp           |    7 +-
 src/UIElements/Qt4/Query/MoleculeQtQuery.cpp       |    7 +-
 src/UIElements/TextUI/Query/AtomTextQuery.cpp      |    2 +-
 src/UIElements/TextUI/Query/AtomsTextQuery.cpp     |    4 +-
 src/UIElements/TextUI/Query/MoleculeTextQuery.cpp  |    2 +-
 src/UIElements/TextUI/Query/MoleculesTextQuery.cpp |    4 +-
 src/UIElements/TextUI/TextUIFactory.cpp            |    4 +-
 src/UIElements/TextUI/TextWindow.cpp               |    2 +-
 src/UIElements/UIFactory.cpp                       |    2 +
 src/UIElements/UIFactory.hpp                       |    4 +
 .../Views/Qt4/MoleculeList/QtMoleculeItem.cpp      |   86 +-
 .../Views/Qt4/MoleculeList/QtMoleculeItem.hpp      |   48 +-
 .../Qt4/MoleculeList/QtMoleculeItemFactory.cpp     |   34 +-
 .../Qt4/MoleculeList/QtMoleculeItemFactory.hpp     |    9 +-
 .../Views/Qt4/MoleculeList/QtMoleculeList.cpp      |  727 ++-
 .../Views/Qt4/MoleculeList/QtMoleculeList.hpp      |   94 +-
 .../Views/Qt4/MoleculeList/QtMoleculeListView.cpp  |  106 +-
 .../Views/Qt4/MoleculeList/QtMoleculeListView.hpp  |    8 +
 .../SpecificItems/QtMoleculeItem_atomcount.hpp     |   44 +-
 .../SpecificItems/QtMoleculeItem_formula.hpp       |   44 +-
 .../SpecificItems/QtMoleculeItem_name.hpp          |   44 +-
 .../SpecificItems/QtMoleculeItem_occurrence.hpp    |   16 +-
 .../SpecificItems/QtMoleculeItem_visibility.hpp    |   16 +-
 src/UIElements/Views/Qt4/QDebugStream.hpp          |  139 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp       |  347 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp       |   69 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp       |  363 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp       |   77 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp   |  726 ++-
 .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp   |  131 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp      |    1 -
 .../Views/Qt4/Qt3D/GLMoleculeObject_shape.hpp      |    4 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp     |  532 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp     |   55 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp      |  148 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp      |   26 +-
 src/UIElements/Views/Qt4/QtElementList.cpp         |  160 +-
 src/UIElements/Views/Qt4/QtElementList.hpp         |   29 +-
 src/UIElements/Views/Qt4/QtFragmentList.cpp        |    3 +-
 src/UIElements/Views/Qt4/QtHomologyList.cpp        |    4 +-
 src/UIElements/Views/Qt4/QtHomologyList.hpp        |    3 +-
 src/UIElements/Views/Qt4/QtInfoBox.cpp             |   70 +-
 src/UIElements/Views/Qt4/QtInfoBox.hpp             |   25 +-
 src/UIElements/Views/Qt4/QtLogBox.cpp              |    5 +-
 src/UIElements/Views/Qt4/QtLogBox.hpp              |    4 +-
 .../Views/Qt4/QtSelectionChangedAgent.cpp          |  158 +
 .../Views/Qt4/QtSelectionChangedAgent.hpp          |   58 +
 src/UIElements/Views/Qt4/QtShapeList.cpp           |    3 +-
 src/UIElements/Views/Qt4/QtTimeLine.cpp            |   12 +-
 src/UIElements/Views/Qt4/QtTimeLine.hpp            |    2 +
 src/World.cpp                                      |  112 +-
 src/World.hpp                                      |   60 +-
 src/WorldTime.cpp                                  |    2 +-
 src/builder.cpp                                    |    6 +
 src/builder_init.cpp                               |   18 +
 src/builder_init.hpp                               |    1 -
 src/cleanUp.cpp                                    |    2 +
 src/documentation/constructs/actions.dox           |   49 +-
 src/documentation/constructs/qt-gui.dox            |  275 +-
 src/documentation/install.dox                      |   11 +
 src/documentation/tests/tests.dox                  |   36 +-
 src/molecule.cpp                                   |   70 +-
 src/molecule.hpp                                   |   27 +-
 src/molecule_geometry.cpp                          |   16 +-
 src/moleculelist.cpp                               |   46 +-
 src/unittests/AtomIdSetUnitTest.cpp                |   16 +-
 src/unittests/stubs/WorldStub.cpp                  |    2 +-
 tests/CodeChecks/testsuite-config_h.at             |    9 +-
 tests/CodeChecks/testsuite-memdebug.at             |    7 +
 tests/CodeChecks/testsuite-project-disclaimer.at   |    7 +
 tests/Fragmentations/Makefile.am                   |    4 +-
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 tests/GuiChecks/Bond/testsuite-bond.at             |    3 +
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 .../testsuite-fill-surface-everywhere.at           |   16 +-
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 .../FillSurface/testsuite-fill-surface-nowhere.at  |   16 +-
 .../FillSurface/testsuite-fill-surface-sphere.at   |   51 +-
 .../FillVolume/testsuite-fill-volume-cube.at       |   14 +-
 .../FillVolume/testsuite-fill-volume-cylinder.at   |   45 +-
 .../FillVolume/testsuite-fill-volume-everywhere.at |   14 +-
 .../FillVolume/testsuite-fill-volume-nowhere.at    |   14 +-
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 tests/GuiChecks/Makefile.am                        |    7 +-
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 ...ite-parser-set-parameters-mpqc-maxiterations.at |    9 +-
 .../Mpqc/testsuite-parser-set-parameters-mpqc.at   |    9 +-
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 ...ion-select-atoms-inside-cuboid-with-defaults.at |    6 +-
 ...stsuite-selection-select-atoms-inside-cuboid.at |    6 +-
 ...suite-selection-unselect-atoms-inside-cuboid.at |    6 +-
 ...stsuite-selection-select-atoms-inside-sphere.at |    6 +-
 ...te-selection-select-atoms-inside-tiny-sphere.at |    6 +-
 ...suite-selection-unselect-atoms-inside-sphere.at |    6 +-
 ...-selection-unselect-atoms-inside-tiny-sphere.at |    6 +-
 ...testsuite-selection-select-molecules-by-name.at |    6 +-
 ...stsuite-selection-unselect-molecules-by-name.at |    6 +-
 .../testsuite-tesselation-big-convex-envelope.at   |    4 +-
 ...estsuite-tesselation-big-non-convex-envelope.at |    4 +-
 .../testsuite-tesselation-convex-envelope.at       |    4 +-
 .../testsuite-tesselation-non-convex-envelope.at   |    4 +-
 .../testsuite-tesselation-trianglematcher.at       |   35 +
 .../GuiChecks/Tesselation/testsuite-tesselation.at |    3 +
 .../{molecuilder.in => adjacencymatcher.in}        |    6 +-
 .../{molecuilder.in => trianglematcher.in}         |    6 +-
 tests/JobMarket/Makefile.am                        |   24 +-
 .../CommandHelp/testsuite-python-commandhelp.at    |   18 +-
 tests/Python/Makefile.am                           |    8 +-
 .../testsuite-1_2-dimethoxyethane.at               |    4 +-
 .../testsuite-1_2-dimethylbenzene.at               |    4 +-
 .../testsuite-2-methylcyclohexanone.at             |    4 +-
 .../testsuite-N_N-dimethylacetamide.at             |    4 +-
 .../Convex/amylose/testsuite-amylose.at            |    4 +-
 .../Convex/benzene/testsuite-benzene.at            |    4 +-
 .../Convex/cholesterol/testsuite-cholesterol.at    |    4 +-
 .../Convex/cycloheptane/testsuite-cycloheptane.at  |    4 +-
 .../testsuite-dimethyl_bromomalonate.at            |    4 +-
 .../Convex/glucose/testsuite-glucose.at            |    4 +-
 .../Tesselations/Convex/heptan/testsuite-heptan.at |    4 +-
 .../Convex/isoleucine/testsuite-isoleucine.at      |    4 +-
 .../Convex/neohexane/testsuite-neohexane.at        |    4 +-
 .../Convex/proline/testsuite-proline.at            |    4 +-
 .../Convex/putrescine/testsuite-putrescine.at      |    4 +-
 .../tartaric_acid/testsuite-tartaric_acid.at       |    4 +-
 tests/Tesselations/Makefile.am                     |    9 +-
 .../testsuite-1_2-dimethoxyethane.at               |    4 +-
 .../testsuite-1_2-dimethylbenzene.at               |    4 +-
 .../testsuite-2-methylcyclohexanone.at             |    4 +-
 .../testsuite-N_N-dimethylacetamide.at             |    4 +-
 .../NonConvex/benzene/testsuite-benzene.at         |    4 +-
 .../NonConvex/cholesterol/testsuite-cholesterol.at |    4 +-
 .../cycloheptane/testsuite-cycloheptane.at         |    4 +-
 .../testsuite-dimethyl_bromomalonate.at            |    4 +-
 .../NonConvex/glucose/testsuite-glucose.at         |    4 +-
 .../NonConvex/heptan/testsuite-heptan.at           |    4 +-
 .../NonConvex/isoleucine/testsuite-isoleucine.at   |    4 +-
 .../NonConvex/neohexane/testsuite-neohexane.at     |    4 +-
 .../NonConvex/proline/testsuite-proline.at         |    4 +-
 .../NonConvex/putrescine/testsuite-putrescine.at   |    4 +-
 .../tartaric_acid/testsuite-tartaric_acid.at       |    4 +-
 .../trianglematcher.in}                            |    6 +-
 .../AdjacencyMatcher/pre/notequal.adj}             |    6 +-
 .../AdjacencyMatcher/pre/notequal2.adj}            |    6 +-
 .../post => Bond/AdjacencyMatcher/pre}/test.adj    |    4 +-
 .../AdjacencyMatcher/pre/test2.adj}                |    1 +
 .../testsuite-bond-adjacencymatcher.at             |   34 +
 tests/regression/Bond/testsuite-bond.at            |    3 +
 ...suite-fragmentation-fragmentation-automation.at |    8 +-
 .../testsuite-graph-depth-first-search.at          |    3 +-
 .../testsuite-graph-subgraph-dissection.at         |    3 +-
 tests/regression/Makefile.am                       |   13 +-
 .../testsuite-molecules-save-adjacency.at          |    2 +-
 .../testsuite-parser-set-parameters-mpqc-basis.at  |    9 +-
 ...ite-parser-set-parameters-mpqc-maxiterations.at |    9 +-
 .../Mpqc/testsuite-parser-set-parameters-mpqc.at   |    9 +-
 ...ion-select-atoms-inside-cuboid-with-defaults.at |    6 +-
 ...stsuite-selection-select-atoms-inside-cuboid.at |    6 +-
 ...suite-selection-unselect-atoms-inside-cuboid.at |    6 +-
 ...stsuite-selection-select-atoms-inside-sphere.at |    6 +-
 ...te-selection-select-atoms-inside-tiny-sphere.at |    6 +-
 ...suite-selection-unselect-atoms-inside-sphere.at |    6 +-
 ...-selection-unselect-atoms-inside-tiny-sphere.at |    6 +-
 ...testsuite-selection-select-molecules-by-name.at |    6 +-
 ...stsuite-selection-unselect-molecules-by-name.at |    6 +-
 .../testsuite-tesselation-big-convex-envelope.at   |    4 +-
 ...estsuite-tesselation-big-non-convex-envelope.at |    4 +-
 .../testsuite-tesselation-convex-envelope.at       |    4 +-
 .../testsuite-tesselation-non-convex-envelope.at   |    4 +-
 .../Tesselation/TriangleMatcher/pre/convex.dat     |    5 +
 .../TriangleMatcher/pre/convex_none.dat            |    5 +
 .../TriangleMatcher/pre/convex_other.dat           |    5 +
 .../testsuite-tesselation-trianglematcher.at       |   35 +
 .../Tesselation/testsuite-tesselation.at           |    3 +
 .../adjacencymatcher.in}                           |    6 +-
 .../trianglematcher.in}                            |    6 +-
 utils/Bash/Makefile.am                             |    3 +-
 utils/Python/Makefile.am                           |    4 +-
 utils/developer/createGuiChecks.sh                 |   14 +-
 446 files changed, 9387 insertions(+), 6334 deletions(-)
 create mode 100644 debian/changelog
 create mode 100644 debian/compat
 create mode 100644 debian/control
 create mode 100644 debian/copyright
 create mode 100644 debian/molecuilder-dev.install
 create mode 100644 debian/molecuilder.install
 create mode 100755 debian/rules
 create mode 100644 debian/source/format
 create mode 100755 makeDebianPackage.sh
 create mode 100644 src/Bond/AdjacencyMatcher/Adjacency.hpp
 create mode 100644 src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp
 create mode 100644 src/Bond/AdjacencyMatcher/Makefile.am
 copy src/Descriptors/{MoleculePtrDescriptor.cpp => AtomNameDescriptor.cpp} (60%)
 create mode 100644 src/Descriptors/AtomNameDescriptor.hpp
 create mode 100644 src/Descriptors/AtomNameDescriptor_impl.hpp
 create mode 100644 src/Parameters/Specifics/Value_elements.cpp
 copy src/Parameters/Specifics/{Value_element.hpp => Value_elements.hpp} (100%)
 create mode 100644 src/Tesselation/TriangleMatcher/Makefile.am
 create mode 100644 src/Tesselation/TriangleMatcher/Triangle.hpp
 create mode 100644 src/Tesselation/TriangleMatcher/TriangleMatcher.cpp
 create mode 100644 src/Tesselation/TriangleMatcher/types.hpp
 create mode 100644 src/ThreadGuard.hpp
 create mode 100644 src/UIElements/Views/Qt4/QtSelectionChangedAgent.cpp
 create mode 100644 src/UIElements/Views/Qt4/QtSelectionChangedAgent.hpp
 create mode 100644 tests/GuiChecks/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at
 create mode 100644 tests/GuiChecks/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at
 copy tests/GuiChecks/{molecuilder.in => adjacencymatcher.in} (72%)
 copy tests/GuiChecks/{molecuilder.in => trianglematcher.in} (71%)
 copy tests/{GuiChecks/molecuilder.in => Tesselations/trianglematcher.in} (71%)
 copy tests/regression/{Molecules/SaveAdjacency/post/test.adj => Bond/AdjacencyMatcher/pre/notequal.adj} (52%)
 copy tests/regression/{Molecules/SaveAdjacency/post/test.adj => Bond/AdjacencyMatcher/pre/notequal2.adj} (51%)
 copy tests/regression/{Molecules/SaveAdjacency/post => Bond/AdjacencyMatcher/pre}/test.adj (66%)
 copy tests/regression/{Molecules/SaveAdjacency/post/test.adj => Bond/AdjacencyMatcher/pre/test2.adj} (98%)
 create mode 100644 tests/regression/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at
 create mode 100644 tests/regression/Tesselation/TriangleMatcher/pre/convex.dat
 create mode 100644 tests/regression/Tesselation/TriangleMatcher/pre/convex_none.dat
 create mode 100644 tests/regression/Tesselation/TriangleMatcher/pre/convex_other.dat
 create mode 100644 tests/regression/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at
 copy tests/{GuiChecks/molecuilder.in => regression/adjacencymatcher.in} (72%)
 copy tests/{GuiChecks/molecuilder.in => regression/trianglematcher.in} (71%)


hooks/post-receive
--