From git at ins.uni-bonn.de  Tue Apr 12 21:55:51 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue, 12 Apr 2016 21:55:51 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Remove_CodeMountain created.
	v1.5.1-183-gdb5b62b
Message-ID: <20160412195551.6D9585FD70@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 branch, Remove_CodeMountain has been created
        at  db5b62be350d560359d5ed4c61d5564d0a12f9e9 (commit)

- Log -----------------------------------------------------------------
commit db5b62be350d560359d5ed4c61d5564d0a12f9e9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 21:55:27 2016 +0200

    FIX: Empty row in QtMoleculeList was not deleted.

commit 481d35038d88e8b494c0b15afbcaba23f02318da
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 21:21:00 2016 +0200

    FIX: MoleculeList crashed when selected molecule changed its place.

commit cbb1cd51deb237b9dd73d41feadeced76bacb746
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:37:31 2016 +0200

    GLWorldScene can now reparent atoms and bonds whose molecule is instantiated later.
    
    - parent maps are now bimaps.

commit e4119090a73297fbaa658f30a697186109b2719d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:19:47 2016 +0200

    GLWorldScene's parent maps now store the parent as ObservedValue_Index_t.
    
    - this will allow to change them into a bimap and then browse through them with
      the index of a newly instantiated GLMoleculeObject_molecule in order to
      assign them a proper parent.

commit 37573909b06d90d591605bf3aa04640369b099cd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:17:46 2016 +0200

    FIX: QtMoleculeList should not use getIdtoIndex unnecessarily.
    
    - this function is only meant to be used in interaction with the user, i.e.
      while the GUI does not change.

commit 451927dc065807694556a73a37cc9abe30635fb6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:30 2016 +0200

    QtObservedMolecule uses fixed index which it returns.

commit aa06bbe71817d31a62ac07a6d4446fdca69fe6db
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:22 2016 +0200

    QtObservedBond uses fixed index which it returns.

commit fdb53f7f1ec8a38d0213e18ee37e20fb07388e6b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:13 2016 +0200

    QtObservedAtom uses fixed index which it returns.

commit b87ba04c73d9cf42da6b4bbda37c9b6ab86ce725
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:35:58 2016 +0200

    tempcommit: Merge with 086f051e

commit 825c7ed3596e1d94cc5b4f27102455e4647a6b97
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:32:13 2016 +0200

    FIX: made disconnect() check for NULL pointers.

commit 0dec7b4f1d13295865b51f8d111a13a12f1a19bc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:24:10 2016 +0200

    FIX: GLMoleculeObject_molecule only updates tesselation hull when necessary.

commit 2d19c3f7418a8c13efd4d6e93dddc7db94df5750
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:16:14 2016 +0200

    tempcommit: Merge with 782db0ab

commit eea78c0d7166e3637206212ba13e3f9a6dd47574
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:14:04 2016 +0200

    tempcommit: Merge with 086f051e

commit 17ba709f275827ed7424859e673696da75b6a8e1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:13:25 2016 +0200

    tempcommit: Merge with 5aa9bdc9

commit c82b71e3278112dd2233ce092d1652a395bd03d4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:01:47 2016 +0200

    tempcommit: Merge with 086f051ef

commit 822e7249d092c590282f19171e5416e65781b44b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 15:56:01 2016 +0200

    tempcommit: Merge with d76f20fc

commit 0e0f07fb96d436b48feb009e0e0f7876a4381ef3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 15:19:44 2016 +0200

    tempcommit: FIX: QtMoleculeList's FormulaVisibilityCountMap was not inserted into on new group item. Move below.

commit 074a06efd84ae97695e59ef673291c86ae60a6e5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 15:19:02 2016 +0200

    tempcommit: Merge with 5520c7ce

commit c20b16de10cd11cac879cb42abb2b1bd73691bb8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 14:54:58 2016 +0200

    tempcommit: Merge with 086f051

commit b7f2a1ffd7a93fe656b6b6c874c788bac4904d22
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 14:38:28 2016 +0200

    tempcommit: Merge with 5aa9bdc99

commit 086f051efc730d759ac49dfe9222ce188f6d7f8b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 14:02:45 2016 +0200

    GLWorldScene now properly reassigns parents of GLMoleculeObjects.
    
    - this is important for atoms and bonds such that they disappear when their
      associated molecule is visualized as a tesselated surface.

commit d45a54dfa91ca1517177616966e6f68661b5762e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 13:45:06 2016 +0200

    tempcommit: Merge with 5aa9bdc

commit d76f20fc5f2efb513f20aff1e080aff697b04ad2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 13:29:56 2016 +0200

    QtObservedAtom only offers direct access to associated const QtObservedMolecule ref.
    
    - the molecule index is not part of the atom's state, hence cannot be directly
      observed. The only thing we observe is the association to the molecule. For
      this a O/O-signal is available and we may actively change the ref when
      getting this signal without breaking anything as it occurs in the same
      thread, hence the board can be safely accessed.
    - QtObservedBond now needs to access mol index through the molecule ref.
    - QtInfoBox may now conveniently access atom'smol ref directly.
    - FIX: Removed static QtObservedBond::getMolecule().

commit 5aa9bdc99f175dbcea82acb33fc241a6430a7238
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 13:19:05 2016 +0200

    QtObservedBond also offers direct access to stored QtObservedAtoms as const refs.
    
    - leftatom and rightatom are const throughout the lifetime of the bond. Hence,
      there is no need to update them and we simply store the refs directly. This
      will be different for the atom, where the molecule ref may change over the
      lifetime!

commit 782db0ab8866a1d0638b1c64d9e81af4f30fb401
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 10:51:06 2016 +0200

    Only GLWorldScene creates stuff, GLMoleculeObject_.. are just visual reps.

commit ad2f411c1c7627389c5d337753a48b4a74d054f6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:14:04 2016 +0200

    FIX: QtObservedAtom: getAtomMolecule() -> getMoleculeIndex().
    
    - changed QtInfoBox and QtObservedBond::getMoleculeIndex() which used it.

commit 13fd92f7906e0b5e7a20a8d3e4025ef0523c1392
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:10:42 2016 +0200

    tempcommit: Merge with 40595019

commit 64da96da774da113e4f19083f58694f06376faba
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:10:30 2016 +0200

    tempcommit: Merge with bc661027

commit eed94790c1fa61e71584ef16a562ffae6f9f1340
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:10:12 2016 +0200

    tempcommit: Merge with 40595019

commit ecfa6770a680537135a89bcd3ba760fba2bb5fd9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:09:25 2016 +0200

    tempcommit: Merge with bc661027

commit 3917d2223c179b9e7e42a0f0528c806f5dfe9763
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:08:38 2016 +0200

    tempcommit: Merge with 40595019

commit 2eab9d414c6fa8b6b5dbe020bf1500836880e1ce
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:08:15 2016 +0200

    tempcommit: Merge with e45f9d60

commit c83d065633a9f5e621ef896c2a7af5c8bd906997
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:07:58 2016 +0200

    tempcommit: Merge with bc661027

commit 40595019c19b21f387a2f0d83e6aeed1f5a722a8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Apr 6 19:04:01 2016 +0200

    QtObservedBond now simply gets both QtObservedAtoms on construction.
    
    - they must exist as QtObservedInstanceBoard is in the current update() loop.
    - and we don't need to take care of them and may throw them away when the bonf
      itself is removed. We don't need to care for anything else.

commit c6d729393932901b4f06cab29d8bee8c3fa3c8d8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 29 20:47:16 2016 +0200

    tempcommit: getObserved...() checks whether id is still present.

commit a8de5624542bbab15d7517a95ce0ee3bb66224e7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 29 16:56:56 2016 +0200

    tempcommit: MoleculeList discerns between internal and external name change. Move after 80d5f8c7f

commit 4c7dfb7e02507c01ce3454bb32ecd17da6b700b6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 29 16:54:47 2016 +0200

    tempcommit: Merge with e45f9d60

commit 23e92625c10c58235154c2c8e6e51cd5e59120a2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 29 16:53:56 2016 +0200

    tempcommit: Merge with e45f9d604

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From git at ins.uni-bonn.de  Tue Apr 19 00:43:04 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue, 19 Apr 2016 00:43:04 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Remove_CodeMountain deleted.
	v1.5.1-183-gdb5b62b
Message-ID: <20160418224304.D45405FD70@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 branch, Remove_CodeMountain has been deleted
       was  db5b62be350d560359d5ed4c61d5564d0a12f9e9

- Log -----------------------------------------------------------------
db5b62be350d560359d5ed4c61d5564d0a12f9e9 FIX: Empty row in QtMoleculeList was not deleted.
-----------------------------------------------------------------------


hooks/post-receive
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From git at ins.uni-bonn.de  Tue Apr 19 00:43:12 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue, 19 Apr 2016 00:43:12 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch GLWorldScene_stores_objects
	created. v1.5.1-176-g900613b
Message-ID: <20160418224312.BFF145FD70@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 branch, GLWorldScene_stores_objects has been created
        at  900613bdeac8339019bbb702193d7701d33e9fb7 (commit)

- Log -----------------------------------------------------------------
commit 900613bdeac8339019bbb702193d7701d33e9fb7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Apr 18 22:57:47 2016 +0200

    Protecting access to atom and bond functions in GLWorldScene with mutexes.
    
    - mutex are now for general access to internal maps, not just NodesInSceneMap.

commit 2601f676523a6afb69fee0b7be0fa2a9dcfe0fe9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Apr 18 22:53:43 2016 +0200

    FIX: Exchanged boolean for real mutex in QtMoleculeListView, QtFragmentList, QtHomologyList, QtShapeList.

commit 4ed5d1af4a5592cf81f75c7f09ce62115fc7e915
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Apr 17 23:27:36 2016 +0200

    Revert "GLWorldScene checks that on dstor all internal containers are empty."
    
    This reverts commit b8b7cf664617761e7d4fb3bd97ca0eba8596b029.

commit c34cc982bd74e9a17e8e9b0f7cc348db61dad997
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Apr 17 23:26:58 2016 +0200

    GLWorldScene now holds onto atoms and bonds until ..Removed() signal and parent(s) is reset.

commit 1d92a2c7e6fa9f33825129f67fd49add5f63a174
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Apr 15 13:05:44 2016 +0200

    GLWorldScene checks that on dstor all internal containers are empty.

commit ba93668168af26f09867bc157b221e2a505eaacd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Apr 15 09:38:55 2016 +0200

    GLWorldScene removes stored observed values only after both parent is NULL and atomRemoved() came in.
    
    - this is to ensure that lifetime of the observed value instance is as long as
      required.

commit 7f9e1141c00d489c45032dcabc026c7d72823022
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 14 09:55:41 2016 +0200

    GLWorldScene needs to store observed values to ensure duration of their lifetime.

commit 82a0cecfab903645af724686ca4f3190a3e9cb4f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 14 10:08:36 2016 +0200

    FIX: GLMoleculeObject_atom did not use QtObservedAtom for selected.

commit 8402d7878c8760f716708a337f48655883946d5b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 14 10:01:31 2016 +0200

    QtObservedBond returns ::ptr instead of ptr from left and right atom.
    
    - FIX: GLWorldScene crashed on resolving sender() of a reparent..() signal
      because the object got destroyed in the meantime.

commit 6d5324de098712f778115f1c698241a5c10d5276
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 14 09:47:20 2016 +0200

    QtObserved... signals indexChanged does not transmit ids anymore.
    
    - since the change to ObservedValue_Index_t, the id is not used anymore. Only
      in the GUI for the objectid.

commit 9bc8f12d79aa27b27b866f5f19ae4ec866029f2a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Apr 13 16:10:40 2016 +0200

    Added checks abd verbosity to reparenting in GLWorldScene.

commit a275213219e4fe9704c9dddc8c476c7ef92d42e9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Apr 13 15:43:20 2016 +0200

    FIX: ObservedValue_Index_t is now the memory address of the Observer instance.
    
    - the atom, bond, or molecule may be removed before and reinstantiated at the
      same address. Hence, it is not a good unique index. The only sensible index
      is the memory address of the QtObserved... instance itself.

commit 50b3ff921aa5f0e3c450362baf79ffcdada99776
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 21:55:27 2016 +0200

    FIX: Empty row in QtMoleculeList was not deleted.

commit d4cfdb38ab11676404a3dfca7bf6288936a22bbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 21:21:00 2016 +0200

    FIX: MoleculeList crashed when selected molecule changed its place.

commit 8789e2699574085630badc8849aa083b507dc5d6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:37:31 2016 +0200

    GLWorldScene can now reparent atoms and bonds whose molecule is instantiated later.
    
    - parent maps are now bimaps.

commit fbe3cb26795156b8823d895077b14876e3b2c3f8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:19:47 2016 +0200

    GLWorldScene's parent maps now store the parent as ObservedValue_Index_t.
    
    - this will allow to change them into a bimap and then browse through them with
      the index of a newly instantiated GLMoleculeObject_molecule in order to
      assign them a proper parent.

commit 7251f314288937f6d4693d437b15665ddbe2c23e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:17:46 2016 +0200

    FIX: QtMoleculeList should not use getIdtoIndex unnecessarily.
    
    - this function is only meant to be used in interaction with the user, i.e.
      while the GUI does not change.

commit 9816ce7ab26dd31df4cdf96835a492a6b30dbd63
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:30 2016 +0200

    QtObservedMolecule uses fixed index which it returns.

commit 6541968e65c5fe753173f8f218048ec0c9e6698e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:22 2016 +0200

    QtObservedBond uses fixed index which it returns.

commit f04cbbbae853cced53a3b9a8e5c2c782944ce0aa
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:13 2016 +0200

    QtObservedAtom uses fixed index which it returns.

commit 9d4a2c5bd762f7bed73d0f6bde661c95ab2036c9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:32:13 2016 +0200

    FIX: made disconnect() check for NULL pointers.

commit e7a56576618201aeb9c2d4e831eea508ba18fa53
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:24:10 2016 +0200

    FIX: GLMoleculeObject_molecule only updates tesselation hull when necessary.

commit 490b8ae07ea57c0aa7ef5ad6881f7a454b1d6126
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 14:02:45 2016 +0200

    GLWorldScene now properly reassigns parents of GLMoleculeObjects.
    
    - this is important for atoms and bonds such that they disappear when their
      associated molecule is visualized as a tesselated surface.

commit fd1dd8ad308cb638f6194021321292e5784b2f82
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 13:29:56 2016 +0200

    QtObservedAtom only offers direct access to associated const QtObservedMolecule ref.
    
    - the molecule index is not part of the atom's state, hence cannot be directly
      observed. The only thing we observe is the association to the molecule. For
      this a O/O-signal is available and we may actively change the ref when
      getting this signal without breaking anything as it occurs in the same
      thread, hence the board can be safely accessed.
    - QtObservedBond now needs to access mol index through the molecule ref.
    - QtInfoBox may now conveniently access atom'smol ref directly.
    - FIX: Removed static QtObservedBond::getMolecule().

commit b968a860444fb3652e997e8343d0335d584f58c3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 13:19:05 2016 +0200

    QtObservedBond also offers direct access to stored QtObservedAtoms as const refs.
    
    - leftatom and rightatom are const throughout the lifetime of the bond. Hence,
      there is no need to update them and we simply store the refs directly. This
      will be different for the atom, where the molecule ref may change over the
      lifetime!

commit f608b3e93700e05b3ba2b5bddb9584af2f2da597
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 10:51:06 2016 +0200

    Only GLWorldScene creates stuff, GLMoleculeObject_.. are just visual reps.

commit 160a886ca6f16ae2d51cf41b4dbd8cfcdef4fc64
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:14:04 2016 +0200

    FIX: QtObservedAtom: getAtomMolecule() -> getMoleculeIndex().
    
    - changed QtInfoBox and QtObservedBond::getMoleculeIndex() which used it.

commit 0987c41bb19346d573e028c97685061807335325
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Apr 6 19:04:01 2016 +0200

    QtObservedBond now simply gets both QtObservedAtoms on construction.
    
    - they must exist as QtObservedInstanceBoard is in the current update() loop.
    - and we don't need to take care of them and may throw them away when the bonf
      itself is removed. We don't need to care for anything else.

commit 04c45ddbd3bdbbe381f189c797d32b061b662a5b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 29 20:47:16 2016 +0200

    getObserved...() checks whether id is still present.

commit f68ecbcbf10193a7166999a527a1ed8787b9f405
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Mar 23 11:02:43 2016 +0100

    Removed partial specialization of ObservedValue_wCallback for index.
    
    - we don't need this anymore as ObservedValues now have a unique and permanent
      index, which we can bind right from the start.
    - adapted QtObservedAtom and QtObservedMolecule's initObservedValues().

commit 20a7cda8f82b208fbf128febd45f98ac91b216aa
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 24 14:26:51 2016 +0100

    Modified all GLMoleculeObjects and GLWorldScene to the new QtObservedBond.
    
    - GLWorldScene transmits bondInserted/bondRemoved similarly to those for the
      atoms to the molecule if aLready present and otherwise into the
      MissedStateMap.

commit af593bd3bc9e44ea0b113055d09b2e8506ea0183
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 15 11:10:54 2016 +0100

    Added QtObservedBond, managed by QtObservedInstanceBoard.
    
    - QtObservedBond is special because it observes not only a bond, but also two
      atoms and a molecule in total.
    - but the general idea is to rather have information duplicate, i.e. the left
      atom's position is also available via the QtObservedAtom. But in this way
      QtObservedBond does not depend on the QtObservedAtom being still or already
      present.

commit 9dafcd80a67ad8c8777de34fae935aaa89ede55e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 24 14:13:31 2016 +0100

    FIX: Removed GLMoleculeObject_molecule's molref.

commit 2bfb97a5e35a695b5b35463b22b68133414da618
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Mar 23 10:56:51 2016 +0100

    QtObservedMolecule also uses new index internally.

commit 4de3573335967314e96416c284ba3e35359f4462
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 22 12:58:35 2016 +0100

    QtObservedAtom uses new index internally.
    
    - thus we don't have to jump through the loops with constructing prior an
      IndexGetter in initObservedValues().

commit 6dfe0960939bf4c37bc57267d6672d3f02f86a48
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Mar 23 10:58:26 2016 +0100

    FIX: QtObservedMolecule::initObservedValues was still static.

commit 9a9a92cb72926a3e4c818017c9a478c1333fa95b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Mar 23 11:06:23 2016 +0100

    Removed unneeded specialization ObservedValue_UpdateAtoms.

commit a2fa3a6d5e9791e5a5dfe63ae43abdde9c300d18
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 22 00:38:09 2016 +0100

    Changed atomRemoved slot of GLMoleculeObject_molecule.
    
    - this required AtomsInSceneMap to use new Index.

commit 15dac91b9762acbbeb2b64d6924e4ebc4a756e81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 22 00:32:47 2016 +0100

    Removed GLMoleculeObject_molecule::getPresentAtoms().

commit 037f27579e88833f5a762818716c3265a293d12a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 22 00:12:07 2016 +0100

    FIX: Removed some unnecessary observer code from GLWorldView.

commit cf2bd632ed1b18798095d54cf453f4412752be65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 23:36:39 2016 +0100

    Changed slots of GLWorldScene and GLWorldView.

commit 31fedf84e71e028fd6f4265aea62af210c4fa69d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 29 16:56:56 2016 +0200

    MoleculeList discerns between internal and external name change.

commit 76ea826df7e55bea3fd8193fc9b51824625791cb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 23:02:31 2016 +0100

    Changed slots of QtElementList, QtMoleculeList, and QtMoleculeListView.
    
    - this is not all of them, but they now all used ObservedValue_Index_t.

commit 5b370456f75d78a273af10a14d5c775aaccc2665
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 22:13:43 2016 +0100

    QtObserved...Observed now get index on ...Removed() signal.

commit 9b7ac059fd9058736a876f0c035e058c8723bf9d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 22:42:14 2016 +0100

    Added convenience function to return current id for given index.
    
    - this is mainly for printing in asserts and logs.
    - required to convert IdtoIndex to bimap.
    - ...Observed wire through getIdtoIndex() function.

commit c7c6d21a861eb2aa5200c32485360da0d4b0de81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 21:42:05 2016 +0100

    Introduced unique and permanent ObservedValue_Index_t.
    
    - this is currently the address of the observable which is not perfectly
      secure but might work for the moment.
    - QtObservedInstanceBoard uses the index internally and only has an additional
      map to serve instances on request for the their atomId_t, moleculeId_t, ....
      However, this id should nowhere else be used because it may change during
      the lifetime of the object.
    - this should prevent the hazzle with the possibly changing atomId_t,
      moleculeId_t, ... in all classes that work with QtObserved... instances.

commit bff202c6e3d0515447a54bacfa6e9ed5ffca83cf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 15:19:44 2016 +0200

    FIX: QtMoleculeList's FormulaVisibilityCountMap was not inserted into on new group item.

commit 743eabedffa61ec5ac67780d49badf443f6daef9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 20:56:27 2016 +0100

    Added missing updateState() to QtMoleculeList.
    
    - As QtMoleculeItem no longer recieve notifications, QtMoleculeList must
      update each item itself.

commit b6587939d0431dec255b436d437b2c3d64d32c2c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 20:44:17 2016 +0100

    QtMoleculeItems do not store ObservedMolecule::ptr any longer.
    
    - it is given as parameter in updateState().
    - in the cstor they only get it to initiate the item text properly.

commit 55443e28a0241b365a47745e7933c4c58a27e0d2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 20:43:25 2016 +0100

    FIX: QtMoleculeList::moveItem() does not need to search for groupitem.

commit ea26633a5a6e22128ba0fcc52a60bb13aed31710
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 11:27:58 2016 +0100

    QtMoleculeItemFactory is pure static.
    
    - QtMoleculeItemFactory was never needed as singleton as it has now state,
      contains now purely static variables and functions.

commit 5771e66594e586dad5518921119581034d3235d2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Mar 18 11:17:01 2016 +0100

    Removed all mutexes and updateDirtyStates() in QtMoleculeList, replaced by simpler slots.
    
    - thanks to events we don't need this humonguous system of lists, update
      timers, and mutexes. We simply need to take action whenever an event comes
      in.

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


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From git at ins.uni-bonn.de  Mon Apr 25 09:18:15 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Mon, 25 Apr 2016 09:18:15 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.5.3 created.
	v1.5.1-181-ga95f5d3
Message-ID: <20160425071815.755045FD70@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
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The branch, Candidate_v1.5.3 has been created
        at  a95f5d33525f59abab6d0c6c038124f19f3dce8f (commit)

- Log -----------------------------------------------------------------
commit a95f5d33525f59abab6d0c6c038124f19f3dce8f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Apr 25 09:11:24 2016 +0200

    Set version to 1.5.3.
    
    - MoleCuilder library is now 16:0:0.
    - Codename "" ().

commit 9d1a7852dfe99a1cb296f633da73d5db75927b7d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Apr 24 16:19:38 2016 +0200

    FIX: GLWorldScene used iterator also in NDEBUG, connect still outside mutex.

commit abb1154e536baa00480c16bd3f03a86d8c3b1827
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Apr 24 16:16:40 2016 +0200

    FIX: QtMoleculeListView::rowsSelected() checks for illegal id from get..ToIndex().
    
    - also check was faulty before and we still tried getting the mol from the
      world before.

commit 097da78c5ee5df3259577e1b98ad9c5dfba1f859
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Apr 24 16:15:37 2016 +0200

    FIX: QtMoleculeList has flag to tell when nameChanged came from outside.
    
    - this causes irregular calls to getMoleculeIdToIndex() which could crash the
      code due to the present assertion.

commit 006f6a88499dfff7622fae1a1ebbbebf94c10e25
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Apr 24 16:15:11 2016 +0200

    QtObservedInstanceBoard::get..ToIndex() now serve -1 as illegal id when index not found

commit ffa69c3a5430f43a2fcff8f8332be2d5df161bcd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Apr 24 16:14:09 2016 +0200

    FIX: PdbParser scanned through all present atoms once per ATOM line.
    
    - this was the cause of a O(N^2) scaling issue.

commit 30b134008ab63ad98ce7dfb5bee4983ddc68169d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Apr 22 10:50:56 2016 +0200

    FIX: GLWorldScene::removeBond() needs to check whether molecule changed already.
    
    - there are two possibilities for bonds to be removed: Either the molecule is
      removed (with its atoms) and this one we got so far. Or the bond is simply
      removed (because auf adjacency recreation) and this we did not check so far.
    - If the simply the bond is removed, then we receive removeBond() but no
      moleculeChanged() signals. Hence, the QtObservedBond is never removed.
      We need to check in removeBonds() whether the associated molecules are
      not NULL and then reset the parent entries ourselves.

commit 67c4ea8af8af5680e462a6c86512e875859b1852
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Apr 22 10:29:28 2016 +0200

    FIX: molecule returned BondCount twice as large.

commit 0bddd1ed82f44fe38f41c7b31c9a974b63b4a862
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Apr 22 09:30:12 2016 +0200

    Made GLWorldScene::resetParent() safe for multiple threads.

commit ea79260c69a50c8b23e40674182e6bd828d52ff6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Apr 20 07:45:11 2016 +0200

    Split ObservedValueIndexLookup such that it is protected under atom or bond mutex.

commit 1eba7cfbf78368fcfda41c0aafd0173295c50739
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Apr 18 22:57:47 2016 +0200

    Protecting access to atom and bond functions in GLWorldScene with mutexes.
    
    - mutex are now for general access to internal maps, not just NodesInSceneMap.

commit efeeb77d0498bbfe882b8473da74a31a8d40277f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Apr 17 23:26:58 2016 +0200

    GLWorldScene now holds onto atoms and bonds until ..Removed() signal and parent(s) is reset.

commit 649f59a7ea5ca2db2837dd54e016436f34564ec3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Apr 15 09:38:55 2016 +0200

    GLWorldScene removes stored observed values only after both parent is NULL and atomRemoved() came in.
    
    - this is to ensure that lifetime of the observed value instance is as long as
      required.

commit 13684213eddb4d1e92250a7618e5af0715cd87e9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 14 09:55:41 2016 +0200

    GLWorldScene needs to store observed values to ensure duration of their lifetime.

commit d16a06ce12b228789f8b4bbb0b922c6d57fd9d2a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 14 10:08:36 2016 +0200

    FIX: GLMoleculeObject_atom did not use QtObservedAtom for selected.

commit 507f3ce7e91faebcd1012d9752b9561db91064ff
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 14 10:01:31 2016 +0200

    QtObservedBond returns ::ptr instead of ptr from left and right atom.
    
    - FIX: GLWorldScene crashed on resolving sender() of a reparent..() signal
      because the object got destroyed in the meantime.

commit 522c456e53a0b038cad5c4e43564052c0e06d8c8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 14 09:47:20 2016 +0200

    QtObserved... signals indexChanged does not transmit ids anymore.
    
    - since the change to ObservedValue_Index_t, the id is not used anymore. Only
      in the GUI for the objectid.

commit 6c4b69d116a458152c8f6d55ce5f08afa7882f7a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Apr 13 16:10:40 2016 +0200

    Added checks abd verbosity to reparenting in GLWorldScene.

commit 08a7eccd3406971777d82560ee81d569921045ec
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Apr 13 15:43:20 2016 +0200

    FIX: ObservedValue_Index_t is now the memory address of the Observer instance.
    
    - the atom, bond, or molecule may be removed before and reinstantiated at the
      same address. Hence, it is not a good unique index. The only sensible index
      is the memory address of the QtObserved... instance itself.

commit 375bc3f1ea4847031faded1937b326d122ce6ce3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 21:55:27 2016 +0200

    FIX: Empty row in QtMoleculeList was not deleted.

commit b2eeafa325f99ae34f45cf7e6aff1c93efa6eaa9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 21:21:00 2016 +0200

    FIX: MoleculeList crashed when selected molecule changed its place.

commit a13f2bb2167e2b7f751acdd3c12df751bb03a105
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:37:31 2016 +0200

    GLWorldScene can now reparent atoms and bonds whose molecule is instantiated later.
    
    - parent maps are now bimaps.

commit 5026148ed739f29b2229d07be76ad31aca20fe30
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:19:47 2016 +0200

    GLWorldScene's parent maps now store the parent as ObservedValue_Index_t.
    
    - this will allow to change them into a bimap and then browse through them with
      the index of a newly instantiated GLMoleculeObject_molecule in order to
      assign them a proper parent.

commit 6e1628b7373c59c6545f88f455af8d047506193e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:17:46 2016 +0200

    FIX: QtMoleculeList should not use getIdtoIndex unnecessarily.
    
    - this function is only meant to be used in interaction with the user, i.e.
      while the GUI does not change.

commit 2560f1b24789baa35df95165f384b1b4741ed2d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:30 2016 +0200

    QtObservedMolecule uses fixed index which it returns.

commit 20538962d2829639cd69cee58b8ff49473984aec
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:22 2016 +0200

    QtObservedBond uses fixed index which it returns.

commit 498c678babf7da7e93da5832726a8c44043533d3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:13 2016 +0200

    QtObservedAtom uses fixed index which it returns.

commit 50246c63f842a77b7c479453a59b17092c472339
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:32:13 2016 +0200

    FIX: made disconnect() check for NULL pointers.

commit 691533f57d4b19acfb8ebfa5dd9096e4754f42c1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 16:24:10 2016 +0200

    FIX: GLMoleculeObject_molecule only updates tesselation hull when necessary.

commit bd676856deb95da62852a3d3d0a1bfdd7e404f1b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 14:02:45 2016 +0200

    GLWorldScene now properly reassigns parents of GLMoleculeObjects.
    
    - this is important for atoms and bonds such that they disappear when their
      associated molecule is visualized as a tesselated surface.

commit 273c8a207d79d5a69b073ffc4c58dd18220aa90b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 13:29:56 2016 +0200

    QtObservedAtom only offers direct access to associated const QtObservedMolecule ref.
    
    - the molecule index is not part of the atom's state, hence cannot be directly
      observed. The only thing we observe is the association to the molecule. For
      this a O/O-signal is available and we may actively change the ref when
      getting this signal without breaking anything as it occurs in the same
      thread, hence the board can be safely accessed.
    - QtObservedBond now needs to access mol index through the molecule ref.
    - QtInfoBox may now conveniently access atom'smol ref directly.
    - FIX: Removed static QtObservedBond::getMolecule().

commit 7f185f928e77138d9f68a9af929ddf86c7ed5bf1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 13:19:05 2016 +0200

    QtObservedBond also offers direct access to stored QtObservedAtoms as const refs.
    
    - leftatom and rightatom are const throughout the lifetime of the bond. Hence,
      there is no need to update them and we simply store the refs directly. This
      will be different for the atom, where the molecule ref may change over the
      lifetime!

commit f1b5ca904ef2ca5bf64048122b7d6dc1ed4716e3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Apr 12 10:51:06 2016 +0200

    Only GLWorldScene creates stuff, GLMoleculeObject_.. are just visual reps.

commit 785d89098de752b05e69ab46e0145f0a07a87128
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Apr 7 18:14:04 2016 +0200

    FIX: QtObservedAtom: getAtomMolecule() -> getMoleculeIndex().
    
    - changed QtInfoBox and QtObservedBond::getMoleculeIndex() which used it.

commit 411269194c0e399da21c636ada2ea31c72975d31
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Apr 6 19:04:01 2016 +0200

    QtObservedBond now simply gets both QtObservedAtoms on construction.
    
    - they must exist as QtObservedInstanceBoard is in the current update() loop.
    - and we don't need to take care of them and may throw them away when the bonf
      itself is removed. We don't need to care for anything else.

commit e4b13a04aa3b6fa93fd0438be7cb89dd9ad312cc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 29 20:47:16 2016 +0200

    getObserved...() checks whether id is still present.

commit d48a1666332f282b0853f2214a842d9d2da6b67c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Mar 23 11:02:43 2016 +0100

    Removed partial specialization of ObservedValue_wCallback for index.
    
    - we don't need this anymore as ObservedValues now have a unique and permanent
      index, which we can bind right from the start.
    - adapted QtObservedAtom and QtObservedMolecule's initObservedValues().

commit 96f14ae4f021b1976486ad5658a68c30645c7467
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 24 14:26:51 2016 +0100

    Modified all GLMoleculeObjects and GLWorldScene to the new QtObservedBond.
    
    - GLWorldScene transmits bondInserted/bondRemoved similarly to those for the
      atoms to the molecule if aLready present and otherwise into the
      MissedStateMap.

commit b4bd0ec170830621ec3bcc64a4a1a99403399bd9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 15 11:10:54 2016 +0100

    Added QtObservedBond, managed by QtObservedInstanceBoard.
    
    - QtObservedBond is special because it observes not only a bond, but also two
      atoms and a molecule in total.
    - but the general idea is to rather have information duplicate, i.e. the left
      atom's position is also available via the QtObservedAtom. But in this way
      QtObservedBond does not depend on the QtObservedAtom being still or already
      present.

commit 6af6a62fa039882142c48e7ac4a0e1d2c5364715
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 24 14:13:31 2016 +0100

    FIX: Removed GLMoleculeObject_molecule's molref.

commit bf6245259c76b4be2e6085db24148e21e1844c8f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Mar 23 10:56:51 2016 +0100

    QtObservedMolecule also uses new index internally.

commit ee3fb8349db0a97b7274dd3ae8a157fc0387a363
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 22 12:58:35 2016 +0100

    QtObservedAtom uses new index internally.
    
    - thus we don't have to jump through the loops with constructing prior an
      IndexGetter in initObservedValues().

commit 62a127cb29522511523a9fc2274cd27e608670b2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Mar 23 10:58:26 2016 +0100

    FIX: QtObservedMolecule::initObservedValues was still static.

commit 4690a7201ee4bd9d43ddb96d1a3d9c79f986b917
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Mar 23 11:06:23 2016 +0100

    Removed unneeded specialization ObservedValue_UpdateAtoms.

commit 76c238dfdd440371633103e91a848b5dcc8838ee
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 22 00:32:47 2016 +0100

    Removed GLMoleculeObject_molecule::getPresentAtoms() and changed atomRemoved slot of GLMoleculeObject_molecule.
    
    - this required AtomsInSceneMap to use new Index.

commit 1d9b6dd666010d66bb843c17134d6df49aa030df
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 22 00:12:07 2016 +0100

    FIX: Removed some unnecessary observer code from GLWorldView.

commit f91ef6007a43260154696025a6213300e1067126
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 23:36:39 2016 +0100

    Changed slots of GLWorldScene and GLWorldView.

commit 0a558d693706673fef514adf5851afe6aed5661e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Mar 29 16:56:56 2016 +0200

    MoleculeList discerns between internal and external name change.

commit 3054f4a837e9cb89d591549c873572989e548c33
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 22:13:43 2016 +0100

    QtObserved...Observed now get index on ...Removed() signal.
    
    - Changed slots of QtElementList, QtMoleculeList, and QtMoleculeListView. This
      is not all of them, but they now all used ObservedValue_Index_t.

commit 1a58ce8105d4937e5093f614ba56c6d4688852bc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 22:42:14 2016 +0100

    Added convenience function to return current id for given index.
    
    - this is mainly for printing in asserts and logs.
    - required to convert IdtoIndex to bimap.
    - ...Observed wire through getIdtoIndex() function.

commit 59eabc83f7f01a0f2797b83aea97182aa3c14b71
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Mar 21 21:42:05 2016 +0100

    Introduced unique and permanent ObservedValue_Index_t.
    
    - this is currently the address of the observable which is not perfectly
      secure but might work for the moment.
    - QtObservedInstanceBoard uses the index internally and only has an additional
      map to serve instances on request for the their atomId_t, moleculeId_t, ....
      However, this id should nowhere else be used because it may change during
      the lifetime of the object.
    - this should prevent the hazzle with the possibly changing atomId_t,
      moleculeId_t, ... in all classes that work with QtObserved... instances.

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


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From git at ins.uni-bonn.de  Thu Apr 28 20:26:14 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 28 Apr 2016 20:26:14 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch GLWorldScene_stores_objects
	deleted. v1.5.1-176-g900613b
Message-ID: <20160428182614.A1C965FD70@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
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The branch, GLWorldScene_stores_objects has been deleted
       was  900613bdeac8339019bbb702193d7701d33e9fb7

- Log -----------------------------------------------------------------
900613bdeac8339019bbb702193d7701d33e9fb7 Protecting access to atom and bond functions in GLWorldScene with mutexes.
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From git at ins.uni-bonn.de  Thu Apr 28 20:27:26 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 28 Apr 2016 20:27:26 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch
	NoPartialSpecialization_ObservedValue_wCallback deleted.
	v1.5.1-145-g6edc017
Message-ID: <20160428182726.8AFBA5FD70@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, NoPartialSpecialization_ObservedValue_wCallback has been deleted
       was  6edc017981e57df23f15b819c4092694ba7617a8

- Log -----------------------------------------------------------------
6edc017981e57df23f15b819c4092694ba7617a8 Removed partial specialization of ObservedValue_wCallback for index.
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From git at ins.uni-bonn.de  Thu Apr 28 20:27:56 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 28 Apr 2016 20:27:56 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM]  annotated tag v1.5.3 created. v1.5.3
Message-ID: <20160428182756.1F4145FD70@saturn.ins.uni-bonn.de>

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The annotated tag, v1.5.3 has been created
        at  b2fc1c7ae9ab022737fedf97e0205a4a23952928 (tag)
   tagging  a95f5d33525f59abab6d0c6c038124f19f3dce8f (commit)
  replaces  v1.5.1
 tagged by  Frederik Heber
        on  Thu Apr 28 20:09:46 2016 +0200

- Log -----------------------------------------------------------------
- QtGui now crashes only in 1-2% of all regression tests (new record).
- we copy all information regarding visual entities and regaring the displayed
  lists via QtObserved... instances or via central ..Observer entities.

This version contains the following branches:
a95f5d3	Candidate_v1.5.3
9d1a785	QtGUI_lastfixes (and more final fixes).
30b1340	GLWorldScene_lastfixes (some final fixes)
ea79260	GLWorldScene_stores_objects (All GLMoleculeObjects now are created by
	and belong to GLWorldScene)
d16a06c	Changes_due_to_changes (some subsequent changes)
a13f2bb	GLWorldScene_notes_parents (great GUI simplification: GLWorldScene just
	changes GLMoleculeObject_..'s parents when necessary)
785d890	NoPartialSpecialization_ObservedValue_wCallback (simplified
	ObservedValue)
96f14ae	Adding_QtObservedBond (QtObservedBond to copy info on bonds)
bf62452	QtObservedInstances_use_index_internally (QtObserved.. instances also
	use the new index for all its contained ObservedValues)
76c238d	QtObservedInstanceBoard_introducing_index (unique index of same type
	for all QtObserved.. instances)
bff202c	QtMoleculeList_MoleculeObserver (central MoleculeObserver that
	registers all changes to molecules)
bfd520c	QtElementList_AtomObserver (central AtomObserver that registers all
	changes to atom's elements)
14de9a4	Fix_BondsNotShowing (bonds were not shown in QtGUI)

Frederik Heber (181):
      World's ObservedContainer no longer observe.
      FIX: Fitting domain to window on QtMainWindow's init.
      FIX: World::destroy..() did not emit SelectionChanged signal.
      FIX: World needs to first destroy the molecule, then release its ids.
      FIX: not using const ref in binding updateBoundingBox() for molecule.
      Added recreateAtom() and recreateMolecule() to World.
      AddAction and UndoRedoHelpers' AddAtomsFromAtomicInfo use recreate..().
      Added extra signal MoleculeChanged to AtomObservable.
      FIX: Added copy cstor for AtomicInfo.
      FIX: PotentialTrainer did not use user-specified threshold so far.
      Fit..PotentialAction now allow setting maximum number of optimization iteration.
      TESTS: Trimmed down PopMoleculesSelection regression test.
      TESTS: Trimmed down TREMOLO dbond regression test.
      LinkedCell's LinkedList is now a vector and no longer a set.
      FIX: PdbParser would calculate trajectors over all atoms, not just given set.
      FIX: Long-range forces were not added onto atom's forces.
      Added Cacheable MoleculeCenter to molecule which is cleverly updated.
      FIX: molecuilder.py is now loaded after GUI is done initializing.
      FIX: Fixed wrong paths for adjacency and trianglematcher in regression and GuiChecks tests.
      Added select() and unselect() functions to atom and molecule, also SelectionChanged channel.
      Added template functions to (un)set vector of instances in a row.
      FIX: AtomObserver was not up-to-date with respect to atom's channels.
      Added MoleculeObserver as pendant to AtomObserver for molecules.
      Extracted common code out of Molecule/AtomObserver into EntityObserver.
      Removed FindEmbeddingHole which lacked implementation so far.
      Replaced MoleculeListClass in analysis_bonds by vector of molecules.
      Replaced MoleculeListClass in ExportGraph by vector of molecules.
      Removed molecules_deprecated from World and unnecessary includes of MoleculeListClass and all insert/erase.
      Deleted MoleculeListClass.
      atom now uses associate... and disassociatedAtomWithMolecule().
      Molecule now has maps with old values for bond counts and element number per atom.
      Removed molecule's resetFormula() and doCountBonds() and doCountNoNonHydrogen().
      FIX: molecule's BoundingBoxSweepingAxis used unordered set of atomids.
      QtFavoriteActions uses ObservedValue for checking last queued action's name.
      FIX: GLMoleculeObject_molecule still contained hack to get upper bound on molecule's bounding box.
      FIX: GLWorldScene has additional moleculePrepared... slots and signals.
      FIX: GLMoleculeObject_molecule::subjectKilled() should not call deactivateObserver().
      FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule wrapped into vector.
      FIX: QtInfoBox only updatePage() when ref still present (no subjectKilled() yet).
      FIX: GLMoleculeObject_molecule::updateAtoms() used DisplayAtoms directly.
      GLMoleculeObject_molecule's ObservedValues is now all static.
      GLMoleculeObject_atom's ObservedValues is now all static.
      GLMoleculeObject_bond's ObservedValues is now all static.
      Changed GLMoleculeObject_...:countSubjectKilled() to taking id parameter.
      Added QtInstanceInformationBoard that handles ObservedValues through the QtGui interface.
      FIX: QtMoleculeItem not signing off after subjectKilled().
      GLMoleculeObject_atom, _bond, _molecule all use QtInstanceInformationBoard passed via GLWorldScene.
      Changed connections between GLWorldScene, GLWorldView and GLMoleculeObject_molecule.
      Moved and renamed QtInstanceInformationBoard -> QtObservedInstanceBoard.
      Added QtObservedAtom and ..Molecule() instances.
      Added rudimentary getter and returner for ObservedAtom/..Molecule() to InstanceBoard.
      Extracted functions handling refcounting of ObservedValues into ObservedValuesContainer.
      Extracted all ObservedValue functionality out of GLMoleculeObject_atom.
      Extracted all ObservedValue functionality out of GLMoleculeObject_molecule.
      Moved countSubjectKilled related code from QtObservedInstanceBoard into ObservedValuesContainer.
      ObservedValuesContainer now stores QtObserved.. instances directly.
      FIX: ObservedValue_wCallback needs to call callback() only on last channel's signOff().
      Added AtomCount and FormulaChanged to QtObservedMolecule.
      All QtMoleculeItem now heed QtObservedMolecule and QtMoleculeList takes InstanceBoard.
      Removed molecule's AboutToBeRemoved channel.
      Extended QtObservedAtom by Name and Molecule.
      Extended QtObservedMolecule by Center, NonHydrogenCount, and BondCount.
      QtInfoBox now obtains information completely from QtObservedInstanceBoard and ObservedValues.
      FIX: All ObservedValue getters now return const references.
      Equipped QtInfoBox with mutex and split clearTabs().
      FIX: Qt's parent properly set from QtMainWindow's point of view.
      QtObservedAtom, ..Molecule, and ObservedValue_wCallback have flag to indicate invalid callback.
      FIX: ObservedValue need to be removed with a bit of delay.
      QtInfoBox disconnects signals.
      FIX: QtObservedInstanceBoard needs to allow delayed atomInserted from World.
      Added ObservedValue for selection status of atoms and molecules to QtObserved...
      Removed QtSelectionUsage in GLWorldView and related.
      Removed QtSelectionAgent usage in QtMoleculeListView.
      Removed QtSelectionChangedAgent.
      FIX: ObservedValuesContainer uses deque for internal observed values.
      FIX: ObservesValuesContainer uses internal struct for two iterators for observedvalues.
      ObservedValuesContainer now asserts that observedinstance has been requested at least once before deletion.
      QtMoleculeList must not use QtObservedMolecules in lists but only request them on need.
      CHECK: tempcommit: Removed Cacheable of TesselationHull for GLMoleculeObject_molecule.
      GLMoleculeObject_atom and .._molecule don't get QtObserved... right away.
      CHECK: Don't admonish empty missed states in GLWorldScene?
      QtElementList must not use atom but only QtObservedAtom.
      FIX: Added mutex to ObservedValuesContainer to ensure atomic access.
      Combined checks into checkRemoval() in ObservedValuesContainer.
      QtObservedInstanceBoard now sends QtObserved..::ptr around in signals.
      QtObserved... now count the subjectKilled() from the containes values.
      FIX: indexChanged from QtObserved... transmit both old and new id.
      FIX: Making sure that atomInserted is received from same source in GLWorldScene and GLMoleculeObject_molecule.
      FIX: GLMoleculeObject_.. does not care whether selection state did not change.
      All ..Inserted/..Removed signals now go through GLWorldScene.
      Removed RefCounted... again.
      GLWorldScene places GLMoleculeObject_molecule into extra list before removal.
      AtomInserted/Removed of QtObservedMolecule sends ptr as unique key.
      tempcommit: Removed atomDelayed stuff in QtObservedInstanceBoard's header.
      Removed last...removed in QtObservedInstanceBoard.
      SignedOn_t in QtObservedInstanceBoard is again just a set.
      FIX: GLWorldScene's moleculesAtomRemoved was checking QtObservedAtomMap.
      GLWorldScene RemovedMolecules now uses QtObservedMolecule* as key.
      FIX: emit changed signal before moleculeEmptied.
      FIX: QtObservedAtom's AtomMoleculeIndex was not informed of molecule index changes.
      GLWorldScene also takes note of empty molecule.
      Enhanced documentation for Qt constructs.
      FIX: Renamed FitParticleCharges -> FitPartialCharges.
      Added regression test for fill-regular-grid that with minimum distance.
      FIX: Filling actions did not use minimum distance for tesselated surface.
      Brought GuiChecks up to speed again.
      DISTFIX: Added AdjacencyMatcher and TriangleMatcher noinst targets.
      TESTFIX: Needed to check whether long-range capability is compiled in.
      Set version to 1.5.2.
      Half of the bonds are showing up again.
      FIX: GLMoleculeObject_atom did reset position not bonds on bondsChanged.
      FIX: QtObserved... did not destroyObservedValues() so far.
      GUITESTS: Decreased waiting times in QtGUI's test mode.
      All QtObserved..::update..() now use the atom or molecule ref instead of index getter.
      Added getObserved..() functions to QtObservedInstanceBoard that take Observable.
      Moved QtElementList into own subfolder.
      QtObservedAtom and ..Molecule now have internal selfref.
      Added QtObservedAtomObserver to ElementList subfolder.
      QtElementList uses QtObservedAtomObserver and is no longer Observer itself.
      FIX: molecule did not notify about FormulaChanged at the right moments.
      FIX: molecule::SetNameFromFilename did not notify about MoleculeNameChanged.
      Added QtObservedMoleculeObserver that relays signals on all QtObservedMolecule's.
      Removed emitDirtyState callback from QtMoleculeItem.
      Removed QtMoleculeList::informDirtyState(), callback is not needed anymore.
      Removed all mutexes and updateDirtyStates() in QtMoleculeList, replaced by simpler slots.
      QtMoleculeItemFactory is pure static.
      FIX: QtMoleculeList::moveItem() does not need to search for groupitem.
      QtMoleculeItems do not store ObservedMolecule::ptr any longer.
      Added missing updateState() to QtMoleculeList.
      FIX: QtMoleculeList's FormulaVisibilityCountMap was not inserted into on new group item.
      Introduced unique and permanent ObservedValue_Index_t.
      Added convenience function to return current id for given index.
      QtObserved...Observed now get index on ...Removed() signal.
      MoleculeList discerns between internal and external name change.
      Changed slots of GLWorldScene and GLWorldView.
      FIX: Removed some unnecessary observer code from GLWorldView.
      Removed GLMoleculeObject_molecule::getPresentAtoms() and changed atomRemoved slot of GLMoleculeObject_molecule.
      Removed unneeded specialization ObservedValue_UpdateAtoms.
      FIX: QtObservedMolecule::initObservedValues was still static.
      QtObservedAtom uses new index internally.
      QtObservedMolecule also uses new index internally.
      FIX: Removed GLMoleculeObject_molecule's molref.
      Added QtObservedBond, managed by QtObservedInstanceBoard.
      Modified all GLMoleculeObjects and GLWorldScene to the new QtObservedBond.
      Removed partial specialization of ObservedValue_wCallback for index.
      getObserved...() checks whether id is still present.
      QtObservedBond now simply gets both QtObservedAtoms on construction.
      FIX: QtObservedAtom: getAtomMolecule() -> getMoleculeIndex().
      Only GLWorldScene creates stuff, GLMoleculeObject_.. are just visual reps.
      QtObservedBond also offers direct access to stored QtObservedAtoms as const refs.
      QtObservedAtom only offers direct access to associated const QtObservedMolecule ref.
      GLWorldScene now properly reassigns parents of GLMoleculeObjects.
      FIX: GLMoleculeObject_molecule only updates tesselation hull when necessary.
      FIX: made disconnect() check for NULL pointers.
      QtObservedAtom uses fixed index which it returns.
      QtObservedBond uses fixed index which it returns.
      QtObservedMolecule uses fixed index which it returns.
      FIX: QtMoleculeList should not use getIdtoIndex unnecessarily.
      GLWorldScene's parent maps now store the parent as ObservedValue_Index_t.
      GLWorldScene can now reparent atoms and bonds whose molecule is instantiated later.
      FIX: MoleculeList crashed when selected molecule changed its place.
      FIX: Empty row in QtMoleculeList was not deleted.
      FIX: ObservedValue_Index_t is now the memory address of the Observer instance.
      Added checks abd verbosity to reparenting in GLWorldScene.
      QtObserved... signals indexChanged does not transmit ids anymore.
      QtObservedBond returns ::ptr instead of ptr from left and right atom.
      FIX: GLMoleculeObject_atom did not use QtObservedAtom for selected.
      GLWorldScene needs to store observed values to ensure duration of their lifetime.
      GLWorldScene removes stored observed values only after both parent is NULL and atomRemoved() came in.
      GLWorldScene now holds onto atoms and bonds until ..Removed() signal and parent(s) is reset.
      Protecting access to atom and bond functions in GLWorldScene with mutexes.
      Split ObservedValueIndexLookup such that it is protected under atom or bond mutex.
      Made GLWorldScene::resetParent() safe for multiple threads.
      FIX: molecule returned BondCount twice as large.
      FIX: GLWorldScene::removeBond() needs to check whether molecule changed already.
      FIX: PdbParser scanned through all present atoms once per ATOM line.
      QtObservedInstanceBoard::get..ToIndex() now serve -1 as illegal id when index not found
      FIX: QtMoleculeList has flag to tell when nameChanged came from outside.
      FIX: QtMoleculeListView::rowsSelected() checks for illegal id from get..ToIndex().
      FIX: GLWorldScene used iterator also in NDEBUG, connect still outside mutex.
      Set version to 1.5.3.

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


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From git at ins.uni-bonn.de  Thu Apr 28 20:27:54 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 28 Apr 2016 20:27:54 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM]  branch stable updated. v1.5.3
Message-ID: <20160428182756.113815FD70@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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- Log -----------------------------------------------------------------
-----------------------------------------------------------------------

Summary of changes:
 configure.ac                                       |   10 +-
 doc/userguide/userguide.xml                        |   13 +-
 src/Actions/AtomAction/AddAction.cpp               |   73 +-
 src/Actions/FillAction/FillRegularGridAction.cpp   |    4 +-
 src/Actions/FillAction/FillSurfaceAction.cpp       |    3 +-
 src/Actions/FillAction/FillVolumeAction.cpp        |    4 +-
 src/Actions/FillAction/SuspendInMoleculeAction.cpp |    1 -
 .../AnalyseFragmentationResultsAction.cpp          |   57 +-
 src/Actions/GlobalListOfActions.hpp                |    2 +-
 src/Actions/GraphAction/UpdateMoleculesAction.cpp  |   17 +-
 src/Actions/Makefile.am                            |    6 +-
 src/Actions/MoleculeAction/BondFileAction.def      |    2 -
 src/Actions/MoleculeAction/ChangeNameAction.def    |    2 -
 .../LinearInterpolationofTrajectoriesAction.def    |    2 -
 src/Actions/MoleculeAction/LoadAction.cpp          |   20 +-
 src/Actions/MoleculeAction/RemoveAction.cpp        |    2 +-
 .../RotateAroundSelfByAngleAction.def              |    1 -
 .../RotateToPrincipalAxisSystemAction.def          |    2 -
 src/Actions/MoleculeAction/SaveAdjacencyAction.def |    2 -
 src/Actions/MoleculeAction/SaveBondsAction.def     |    2 -
 .../MoleculeAction/SaveTemperatureAction.def       |    2 -
 .../PotentialAction/FitCompoundPotentialAction.cpp |    1 +
 .../PotentialAction/FitCompoundPotentialAction.def |   13 +-
 ...argesAction.cpp => FitPartialChargesAction.cpp} |   16 +-
 ...argesAction.def => FitPartialChargesAction.def} |    8 +-
 ...argesAction.hpp => FitPartialChargesAction.hpp} |    4 +-
 src/Actions/PotentialAction/FitPotentialAction.cpp |    1 +
 src/Actions/PotentialAction/FitPotentialAction.def |   13 +-
 src/Actions/UndoRedoHelpers.cpp                    |   15 +-
 src/Actions/WorldAction/InputAction.cpp            |   12 +-
 src/Actions/WorldAction/RepeatBoxAction.cpp        |    4 -
 src/Analysis/analysis_bonds.cpp                    |   15 +-
 src/Analysis/analysis_bonds.hpp                    |    9 +-
 src/Analysis/analysis_correlation.cpp              |   27 +-
 .../AnalysisCorrelationToPointUnitTest.cpp         |    1 -
 .../AnalysisCorrelationToPointUnitTest.hpp         |    1 -
 .../AnalysisCorrelationToSurfaceUnitTest.cpp       |    1 -
 .../AnalysisCorrelationToSurfaceUnitTest.hpp       |    1 -
 .../unittests/AnalysisPairCorrelationUnitTest.cpp  |    1 -
 .../unittests/AnalysisPairCorrelationUnitTest.hpp  |    1 -
 src/Analysis/unittests/CountBondsUnitTest.cpp      |    9 +-
 src/Analysis/unittests/CountBondsUnitTest.hpp      |    3 +-
 src/Atom/AtomObserver.cpp                          |   51 +-
 src/Atom/AtomObserver.hpp                          |   26 +-
 src/Atom/AtomicInfo.cpp                            |   13 +
 src/Atom/AtomicInfo.hpp                            |    1 +
 src/Atom/atom.cpp                                  |   59 +-
 src/Atom/atom.hpp                                  |   25 +-
 src/Atom/atom_observable.hpp                       |    2 +
 src/Atom/unittests/AtomObserverUnitTest.cpp        |   47 +-
 src/Atom/unittests/AtomObserverUnitTest.hpp        |    5 +-
 src/Bond/AdjacencyMatcher/Makefile.am              |    4 +
 src/EntityObserver.hpp                             |   72 +
 src/EntityObserver_impl.hpp                        |   63 +
 src/Filling/Makefile.am                            |    2 +
 ...pp => IsCloseEnoughToSurface_FillPredicate.cpp} |   23 +-
 .../IsCloseEnoughToSurface_FillPredicate.hpp       |   28 +
 .../Predicates/IsInsideSurface_FillPredicate.cpp   |    3 +-
 src/Filling/Preparators/BaseFillerPreparator.cpp   |   13 +-
 src/Filling/Preparators/BaseFillerPreparator.hpp   |    3 +-
 src/Fragmentation/Exporters/ExportGraph.cpp        |   10 +-
 src/Fragmentation/Exporters/ExportGraph.hpp        |    5 +-
 .../Exporters/ExportGraph_ToFiles.cpp              |    5 -
 .../Exporters/ExportGraph_ToFiles.hpp              |    2 +-
 src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp |    1 -
 src/Fragmentation/Fragmentation.cpp                |    2 +-
 .../FunctionApproximation.cpp                      |   14 +-
 .../FunctionApproximation.hpp                      |   16 +-
 src/Graph/ConnectedSubgraph.cpp                    |    3 -
 src/Graph/DepthFirstSearchAnalysis.cpp             |    3 -
 src/LinkedCell/LinkedCell.cpp                      |    4 +-
 src/LinkedCell/LinkedCell_View.cpp                 |   10 +-
 src/LinkedCell/types.hpp                           |    2 +-
 src/LinkedCell/unittests/LinkedCellUnitTest.cpp    |    2 +-
 .../unittests/LinkedCell_ViewUnitTest.cpp          |    4 +-
 src/LinkedCell/unittests/Makefile.am               |    1 -
 src/Makefile.am                                    |    6 +-
 src/MoleculeListClass.hpp                          |   62 -
 .../AtomObserverStub.cpp => MoleculeObserver.cpp}  |   35 +-
 src/MoleculeObserver.hpp                           |   41 +
 src/Parser/MpqcParser.cpp                          |    3 -
 src/Parser/PcpParser.cpp                           |    3 -
 src/Parser/PdbParser.cpp                           |   30 +-
 src/Parser/Psi3Parser.cpp                          |    3 -
 src/Parser/TremoloParser.cpp                       |    3 -
 src/Parser/XmlParser.cpp                           |    3 -
 src/Parser/XyzParser.cpp                           |    3 -
 src/Potentials/PotentialTrainer.cpp                |    3 +-
 src/Potentials/PotentialTrainer.hpp                |    1 +
 src/Tesselation/TriangleMatcher/Makefile.am        |    4 +
 src/Tesselation/boundary.cpp                       |   24 -
 src/Tesselation/boundary.hpp                       |    2 -
 src/UIElements/Makefile.am                         |   24 +-
 .../Qt4/InstanceBoard/ObservedValue_types.hpp      |   37 +
 .../Qt4/InstanceBoard/ObservedValue_wCallback.hpp  |   77 +
 .../Qt4/InstanceBoard/ObservedValuesContainer.hpp  |  169 +
 .../InstanceBoard/ObservedValuesContainer_impl.hpp |  208 +
 .../Qt4/InstanceBoard/QtObservedAtom.cpp           |  457 ++
 .../Qt4/InstanceBoard/QtObservedAtom.hpp           |  304 +
 .../Qt4/InstanceBoard/QtObservedBond.cpp           |  388 ++
 .../Qt4/InstanceBoard/QtObservedBond.hpp           |  328 +
 .../Qt4/InstanceBoard/QtObservedInstanceBoard.cpp  |  421 ++
 .../Qt4/InstanceBoard/QtObservedInstanceBoard.hpp  |  177 +
 .../Qt4/InstanceBoard/QtObservedMolecule.cpp       |  548 ++
 .../Qt4/InstanceBoard/QtObservedMolecule.hpp       |  327 +
 src/UIElements/Qt4/QtMainWindow.cpp                |   28 +-
 src/UIElements/Qt4/QtMainWindow.hpp                |    7 +-
 src/UIElements/Qt4/QtUIFactory.cpp                 |    5 +-
 src/UIElements/TextUI/TextWindow.cpp               |   48 +-
 src/UIElements/TextUI/TextWindow.hpp               |    6 +
 .../Views/Qt4/{ => ElementList}/QtElementList.cpp  |  103 +-
 .../Views/Qt4/{ => ElementList}/QtElementList.hpp  |   32 +-
 .../Qt4/ElementList/QtObservedAtomObserver.cpp     |   76 +
 .../Qt4/ElementList/QtObservedAtomObserver.hpp     |   60 +
 .../Views/Qt4/MoleculeList/QtMoleculeItem.cpp      |  131 +-
 .../Views/Qt4/MoleculeList/QtMoleculeItem.hpp      |   88 +-
 .../Qt4/MoleculeList/QtMoleculeItemFactory.cpp     |   51 +-
 .../Qt4/MoleculeList/QtMoleculeItemFactory.hpp     |   27 +-
 .../Views/Qt4/MoleculeList/QtMoleculeList.cpp      |  617 +-
 .../Views/Qt4/MoleculeList/QtMoleculeList.hpp      |  119 +-
 .../Views/Qt4/MoleculeList/QtMoleculeListView.cpp  |  122 +-
 .../Views/Qt4/MoleculeList/QtMoleculeListView.hpp  |   24 +-
 .../MoleculeList/QtObservedMoleculeObserver.cpp    |  101 +
 .../MoleculeList/QtObservedMoleculeObserver.hpp    |   66 +
 .../SpecificItems/QtMoleculeItem_atomcount.hpp     |   49 +-
 .../SpecificItems/QtMoleculeItem_formula.hpp       |   50 +-
 .../SpecificItems/QtMoleculeItem_name.hpp          |   56 +-
 .../SpecificItems/QtMoleculeItem_occurrence.hpp    |   19 +-
 .../SpecificItems/QtMoleculeItem_visibility.hpp    |   28 +-
 .../Views/Qt4/Plotting/QSeisPlotPage.cpp           |   10 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp       |  265 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp       |   80 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp       |  265 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp       |   84 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp   |  714 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp   |  127 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp     |  958 ++-
 src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp     |  136 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp      |  154 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp      |   24 +-
 src/UIElements/Views/Qt4/QtInfoBox.cpp             |  157 +-
 src/UIElements/Views/Qt4/QtInfoBox.hpp             |   53 +-
 .../Views/Qt4/QtSelectionChangedAgent.cpp          |  158 -
 .../Views/Qt4/QtSelectionChangedAgent.hpp          |   58 -
 src/UIElements/Views/Qt4/QtToolBar.hpp             |   11 +
 .../Views/Qt4/QtToolBar_QtFavoriteActions.cpp      |   31 +-
 src/World.cpp                                      |  106 +-
 src/World.hpp                                      |   58 +-
 src/builder_init.cpp                               |   12 +-
 src/cleanUp.cpp                                    |    3 +
 src/documentation/constructs/qt-gui.dox            |  151 +-
 src/molecule.cpp                                   |  197 +-
 src/molecule.hpp                                   |   91 +-
 src/moleculelist.cpp                               |  659 --
 ...egular-grid-with-minimum-distance-to-surface.at |   32 +
 tests/GuiChecks/Filling/testsuite-filling.at       |    1 +
 ...suite-fragmentation-analyse-fragment-results.at |   34 +-
 tests/GuiChecks/Makefile.am                        |  349 +-
 .../testsuite-molecules-tremolo-dbond-file.at      |    6 +-
 .../testsuite-potential-fit-partial-charges.at}    |   16 +-
 .../testsuite-potential-fit-potential.at           |   14 +-
 tests/GuiChecks/Potential/testsuite-potential.at   |    2 +-
 tests/GuiChecks/adjacencymatcher.in                |    4 +-
 tests/GuiChecks/trianglematcher.in                 |    4 +-
 tests/Python/AllActions/options.dat                |    1 +
 .../RegularGrid/post/amylose_filled_water.pdb      |  812 +++
 .../RegularGrid/pre/amylose_straightened_more.pdb} |  470 +-
 .../regression/Filling/RegularGrid/pre}/water.pdb  |    8 +-
 ...egular-grid-with-minimum-distance-to-surface.at |   31 +
 tests/regression/Filling/testsuite-filling.at      |    1 +
 .../LongRange/OBC/BondFragment_Eigenhistogram.dat  |   12 +-
 .../LongRange/OBC/BondFragment_Eigenvalues.dat     |   10 +-
 .../post/LongRange/OBC/BondFragment_Energy.dat     |   10 +-
 .../post/LongRange/OBC/BondFragment_Forces.dat     |   12 +-
 .../LongRange/OBC/BondFragment_IndexedEnergy.dat   |   42 +-
 .../LongRange/OBC/BondFragment_LongRangeEnergy.dat |   12 +-
 .../LongRange/OBC/BondFragment_LongRangeForces.dat |    7 +
 .../post/LongRange/OBC/BondFragment_Times.dat      |   12 +-
 .../post/LongRange/OBC/BondFragment_VMGEnergy.dat  |   13 +-
 .../post/LongRange/OBC/BondFragment_VMGForces.dat  |    7 +
 .../post/{ => LongRange/OBC}/alkane-3.data         |   16 +-
 .../LongRange/PBC/BondFragment_Eigenhistogram.dat  |   12 +-
 .../LongRange/PBC/BondFragment_Eigenvalues.dat     |   10 +-
 .../post/LongRange/PBC/BondFragment_Energy.dat     |   10 +-
 .../post/LongRange/PBC/BondFragment_Forces.dat     |   12 +-
 .../LongRange/PBC/BondFragment_IndexedEnergy.dat   |   42 +-
 .../LongRange/PBC/BondFragment_LongRangeEnergy.dat |   12 +-
 .../LongRange/PBC/BondFragment_LongRangeForces.dat |    7 +
 .../post/LongRange/PBC/BondFragment_Times.dat      |   12 +-
 .../post/LongRange/PBC/BondFragment_VMGEnergy.dat  |   13 +-
 .../post/LongRange/PBC/BondFragment_VMGForces.dat  |    7 +
 .../post/{ => LongRange/PBC}/alkane-3.data         |   14 +-
 .../ShortRange/BondFragment_Eigenhistogram.dat     |   12 +-
 .../post/ShortRange/BondFragment_Eigenvalues.dat   |   10 +-
 .../post/ShortRange/BondFragment_Energy.dat        |   12 +-
 .../post/ShortRange/BondFragment_Forces.dat        |   10 +-
 .../post/ShortRange/BondFragment_IndexedEnergy.dat |   42 +-
 .../post/ShortRange/BondFragment_Times.dat         |   12 +-
 .../pre/BondFragmentLongRangeResults_OBC.dat       |  296 +-
 .../pre/BondFragmentLongRangeResults_PBC.dat       |  296 +-
 .../pre/BondFragmentShortRangeResults.dat          |   93 +-
 ...suite-fragmentation-analyse-fragment-results.at |   30 +-
 tests/regression/Makefile.am                       |    3 +-
 .../Molecules/BondFile/pre/silica.dbond.0000       |   17 +-
 .../Molecules/BondFile/pre/silica.pov1.0000.pdb    | 7164 +-------------------
 .../testsuite-molecules-tremolo-dbond-file.at      |    6 +-
 .../Molecules/Remove/post/id0_2_missing.pdb        |   14 +-
 .../regression/Molecules/Remove/post/water_box.pdb |   14 +-
 .../pre/homology_grid.dat                          |    0
 .../pre/water.pdb                                  |    0
 .../testsuite-potential-fit-partial-charges.at}    |   12 +-
 .../testsuite-potential-fit-potential.at           |   22 +-
 tests/regression/Potential/testsuite-potential.at  |    2 +-
 .../Molecules/PopMoleculeSelection/post/box.xyz    |  841 +--
 .../Molecules/PopMoleculeSelection/post/empty.xyz  |    2 +-
 .../PopMoleculeSelection/post/id2_4_missing.xyz    | 1025 ---
 .../PopMoleculeSelection/post/water_id2_4.xyz      |    8 +-
 .../Molecules/PopMoleculeSelection/pre/box.xyz     |  841 +--
 218 files changed, 8578 insertions(+), 15368 deletions(-)
 rename src/Actions/PotentialAction/{FitParticleChargesAction.cpp => FitPartialChargesAction.cpp} (93%)
 rename src/Actions/PotentialAction/{FitParticleChargesAction.def => FitPartialChargesAction.def} (91%)
 rename src/Actions/PotentialAction/{FitParticleChargesAction.hpp => FitPartialChargesAction.hpp} (81%)
 create mode 100644 src/EntityObserver.hpp
 create mode 100644 src/EntityObserver_impl.hpp
 copy src/Filling/Predicates/{IsInsideSurface_FillPredicate.cpp => IsCloseEnoughToSurface_FillPredicate.cpp} (66%)
 create mode 100644 src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.hpp
 delete mode 100644 src/MoleculeListClass.hpp
 rename src/{LinkedCell/unittests/stubs/AtomObserverStub.cpp => MoleculeObserver.cpp} (59%)
 create mode 100644 src/MoleculeObserver.hpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/ObservedValue_types.hpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/ObservedValue_wCallback.hpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedBond.cpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedBond.hpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp
 create mode 100644 src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp
 rename src/UIElements/Views/Qt4/{ => ElementList}/QtElementList.cpp (67%)
 rename src/UIElements/Views/Qt4/{ => ElementList}/QtElementList.hpp (52%)
 create mode 100644 src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp
 create mode 100644 src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.hpp
 create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp
 create mode 100644 src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.hpp
 delete mode 100644 src/UIElements/Views/Qt4/QtSelectionChangedAgent.cpp
 delete mode 100644 src/UIElements/Views/Qt4/QtSelectionChangedAgent.hpp
 delete mode 100755 src/moleculelist.cpp
 create mode 100644 tests/GuiChecks/Filling/RegularGrid/testsuite-fill-regular-grid-with-minimum-distance-to-surface.at
 rename tests/GuiChecks/Potential/{FitParticleCharges/testsuite-potential-fit-particle-charges.at => FitPartialCharges/testsuite-potential-fit-partial-charges.at} (69%)
 create mode 100644 tests/regression/Filling/RegularGrid/post/amylose_filled_water.pdb
 copy tests/{Tesselations/Convex/amylose/pre/amylose.pdb => regression/Filling/RegularGrid/pre/amylose_straightened_more.pdb} (60%)
 copy {data/molecules => tests/regression/Filling/RegularGrid/pre}/water.pdb (54%)
 create mode 100644 tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid-with-minimum-distance-to-surface.at
 create mode 100644 tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_LongRangeForces.dat
 create mode 100644 tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_VMGForces.dat
 copy tests/regression/Fragmentation/AnalyseFragmentationResults/post/{ => LongRange/OBC}/alkane-3.data (61%)
 create mode 100644 tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_LongRangeForces.dat
 create mode 100644 tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_VMGForces.dat
 copy tests/regression/Fragmentation/AnalyseFragmentationResults/post/{ => LongRange/PBC}/alkane-3.data (66%)
 rename tests/regression/Potential/{FitParticleCharges => FitPartialCharges}/pre/homology_grid.dat (100%)
 rename tests/regression/Potential/{FitParticleCharges => FitPartialCharges}/pre/water.pdb (100%)
 rename tests/regression/Potential/{FitParticleCharges/testsuite-potential-fit-particle-charges.at => FitPartialCharges/testsuite-potential-fit-partial-charges.at} (83%)
 delete mode 100644 tests/regression/Selection/Molecules/PopMoleculeSelection/post/id2_4_missing.xyz


hooks/post-receive
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From git at ins.uni-bonn.de  Thu Apr 28 20:30:35 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 28 Apr 2016 20:30:35 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Delay_MoleculeRemoved deleted.
	v1.5.1-97-g2ab346b
Message-ID: <20160428183035.5255F5FD70@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 branch, Delay_MoleculeRemoved has been deleted
       was  2ab346bcd181e1e10519dfaf059aa12f4f18f525

- Log -----------------------------------------------------------------
2ab346bcd181e1e10519dfaf059aa12f4f18f525 GLWorldScene also takes note of empty molecule.
-----------------------------------------------------------------------


hooks/post-receive
-- 



From git at ins.uni-bonn.de  Thu Apr 28 20:30:54 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 28 Apr 2016 20:30:54 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Fix_QtGUI_crashes_continued
	deleted. v1.5.0-250-g0921907
Message-ID: <20160428183054.E0B4B5FD70@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
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The branch, Fix_QtGUI_crashes_continued has been deleted
       was  0921907155034f939032245c16467eaab6889d87

- Log -----------------------------------------------------------------
0921907155034f939032245c16467eaab6889d87 FIX: GLWorldScene now silently drops atomRemoved on missing molecules.
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hooks/post-receive
-- 



From git at ins.uni-bonn.de  Thu Apr 28 20:33:53 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 28 Apr 2016 20:33:53 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch
	Fix_QtGui_Testmode_not_showing_atoms deleted. v1.5.0-165-ga35ec4c
Message-ID: <20160428183353.1AFCC5FD70@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
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The branch, Fix_QtGui_Testmode_not_showing_atoms has been deleted
       was  a35ec4c8e5faf96b7ba725efe7b25ad23853df09

- Log -----------------------------------------------------------------
a35ec4c8e5faf96b7ba725efe7b25ad23853df09 MODIFYME: World's ObservedContainer no longer observe.
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hooks/post-receive
-- 



From git at ins.uni-bonn.de  Thu Apr 28 20:35:56 2016
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 28 Apr 2016 20:35:56 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.12 deleted. v1.4.12
Message-ID: <20160428183556.C7E325FD70@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 deleted
       was  0ea4ddbf6833adf1a4a2ada1981935715775879f

- Log -----------------------------------------------------------------
0ea4ddbf6833adf1a4a2ada1981935715775879f Set version to v1.4.12.
-----------------------------------------------------------------------


hooks/post-receive
--