- Molecuilder-devel

[SCM] MoleCuilder branch Refactoring_QtMoleculeList_as_QModel created. v1.4.9-40-g2050b29
by git＠ins.uni-bonn.de 29 Jan '15

29 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Refactoring_QtMoleculeList_as_QModel has been created at 2050b29519e754ad0beb183c35ca29f6a1821f0d (commit) - Log ----------------------------------------------------------------- commit 2050b29519e754ad0beb183c35ca29f6a1821f0d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:44:56 2015 +0100 Commented-out all debugging messages in QtMoleculeList rewrite. commit 2696b18ee037df67c33588e50eedff4bd5d454dd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 23 00:05:47 2015 +0100 Visibility checkstate is working for molecule and group item. - signals are emitted and states are correctly changed, tested on amylose molecule in a box filled with ~3000 water molecules. commit d2dbb5d0e44b22b8ce90269637cb0083893cd951 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 21:01:55 2015 +0100 Moved rowsSelected() over to QtMoleculeListView. commit 53c1ffef25e1f1a2be3255d54d76e7406c289ab9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 15:04:26 2015 +0100 Modified QtMoleculeList to use QtMoleculeItemFactory. - setOccurrence() gives index of row back if it should be romoved. - i.e. moving a row and removing the row entirely does not mix. Updating it and then removing it is ill-spent time. - split off removing a group item from setting its occurrence. - emitDirtyState() only uses the first column item despite for the dirty items set. Otherwise we have multiple moves of the same row. - this is safer than removing the entry in MoleculeBiMap right away as thread in GUI and Action thread do not access in an orderly fashion. - using vector of molecule pointers and set operations to fulfil validity of updates. commit 6d1e0a20c242ab6c7b0ace4bf93ff53336b9cc26 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 14:33:42 2015 +0100 Added a slew of specific QtMoleculeItem for each of the COLUMNs. - all are produced solely by the factory and are very specific. commit bed759c3580c014ab9c1b68a1a4aac91cd7ea811 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 13:26:55 2015 +0100 Added basic QtMoleculeItem and ...Factory. commit f62e60b49352956721b98a4106d50c6f681b3f7d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 13:22:39 2015 +0100 Moved QtMoleculeList files into own subfolder. - added QtMoleculeListView. - we are going to need a lot of classes for this to work properly. commit 1c339020006b5484f510d76a06f91189152fffd5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 23:33:09 2015 +0100 Header row is correct again in QtMoleculeList. - had to overwrite headerData(). commit 8ccf3bf66a4ce9f95ab6fdbedd40c087b343c68d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 23:32:34 2015 +0100 First change to convert QtMoleculeList into QStandardItemModel. - this will keep the QtMoleculeList up-to-date automatically. commit 6770fae428b376912daabc349a23817dfb4f32e9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 20:43:05 2014 +0100 Extracted add/removeItem in QtMoleculeList, no more complete refilling on update. - this is unfinished as we can't find the item to a molecule that is about to be removed. We have to switch to Qt's Model/View ... argh. commit 0a5beb2d06fe674eb3c4ac2eacac4d873e32ee7f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 17:08:59 2015 +0100 MEMFIX: removeAtomsinMolecule() worked directly with molecule::iterator which accesses invalid memory. - now, we copy all atom pointers prior to removal and work only on this copy commit 24edfefcd1e3d9e98ec524cea974f518103d90f6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 14:34:20 2015 +0100 Added AboutToBeRemoved channel to molecule. - this allows UI elements to remove all items related a molecule's presence before any destructor has started doing something. Note that subjectKilled() does not work here, as "higher" (in inheritance hierarchy) have already been called and changed the instance. We need to know right when the instance is still intact. commit d050880efce3b9d1088af54300c3f85b8668e1ff Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jan 17 17:45:07 2015 +0100 FIX: Atom is notified when its father dies and resets father to itself then. - this caused a segfault with FormatParser::save() when a copied molecule's atoms is stored. commit 910a5d3c24251e841b550140856bdc84d981ff30 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 12:38:34 2015 +0100 atom::father is now accessible through getter and setter only. - this allows to manage signing on and off to and from father to be notified when it's destroyed. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch SphericalPointDistribution created. v1.4.9-63-gb1da407
by git＠ins.uni-bonn.de 29 Jan '15

29 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, SphericalPointDistribution has been created at b1da40790a94dda83c5afbc4a9e1fd91285b21b8 (commit) - Log ----------------------------------------------------------------- commit b1da40790a94dda83c5afbc4a9e1fd91285b21b8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 01:25:11 2015 +0100 Enhanced add-bonds and remove-bonds to multiply selected pairs of atoms. - renamed add/remove-bond -> add/remove-bond(s) to emphasize this. - added regression test on three selected atoms. - modified userguide entry for both actions. commit 6758ce600114c8bfdf12e41bc2b39a0d021466f5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 01:24:41 2015 +0100 Added regression test fpr saturate-atoms. commit d9b819d927b3f1cc62c418ebd4aca69a976d6727 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 01:23:53 2015 +0100 tempcommit: Fixes to SaturateAction. commit 0bdc6f874c9c0aea3ba0d076b185865624cd478f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 29 01:19:19 2015 +0100 Added saturate-atoms to userguide. commit 569f490abdc4a60746f286c6ccb061729eeacc34 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 22:58:34 2015 +0100 tempcommit: Trimmed down SphericalPointDistribution to what I need at the moment. commit 793c74fe4fa3879cb7f93aad97048ec86310ab2e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 27 22:28:27 2015 +0100 Added SaturateAction that uses SphericalPointDistribution. commit 6b19aef6c7f98466ca9c6eeceb0604044b3f2cdf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jun 4 13:23:31 2014 +0200 Added more unit test functions up to N=8 to SphericalPointDistributionUnitTest. - marked unit test as XFAIL. commit 6f68f0881c206ec6f8b977e689babbae38754909 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri May 30 15:31:15 2014 +0200 Moved all code from header of SphericalPointDistribution into cpp module. commit 14baa9e9958c57e564ca77a3793083610b986892 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 20:15:26 2014 +0200 Added unit tests for SphericalPointDistribution. commit 76ddb844841b32a86427bed99a53004b71bd8381 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu May 29 13:29:03 2014 +0200 Added matchSphericalPointDistributions() to SphericalPointDistribution. - so far we do nothing. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Refactoring_QtMoleculeList_as_QModel deleted. v1.4.9-39-g2bb2b47
by git＠ins.uni-bonn.de 29 Jan '15

29 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Refactoring_QtMoleculeList_as_QModel has been deleted was 2bb2b47cb4b0f7f9c6d4bd039a749533cbcf526e ----------------------------------------------------------------------- 2bb2b47cb4b0f7f9c6d4bd039a749533cbcf526e Commented-out all debugging messages in QtMoleculeList rewrite. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch SeveralGUIFixes deleted. v1.4.9-65-ge83aca7
by git＠ins.uni-bonn.de 29 Jan '15

29 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, SeveralGUIFixes has been deleted was e83aca7ab965d17d3fe72ff5ab7e657327061bda ----------------------------------------------------------------------- e83aca7ab965d17d3fe72ff5ab7e657327061bda tempcommit: Looking for bug to wrongly scaled bond length after width change. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch SeveralGUIFixes created. v1.4.9-65-ge83aca7
by git＠ins.uni-bonn.de 26 Jan '15

26 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, SeveralGUIFixes has been created at e83aca7ab965d17d3fe72ff5ab7e657327061bda (commit) - Log ----------------------------------------------------------------- commit e83aca7ab965d17d3fe72ff5ab7e657327061bda Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 12:07:22 2015 +0100 tempcommit: Looking for bug to wrongly scaled bond length after width change. - this seems to be a bug in Qt3D ... we should check this on Ubuntu 14.04 commit e5a4de9d12b3462673384b90ec21994a00901104 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 22:19:53 2015 +0100 FIX: QDebugStream is now protected against multiple writes to log window. - writes bracketed with bool. - we had multiple, seemingly random segfaults in QDebugStream when inserting new text. commit 66316d0cad6f435e2f0143d8e573ffd37bc989ed Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 18:37:49 2015 +0100 FIX: MPQCCommandFragmentController failed to add jobs due to false return value type. - bool is now an unsigned int. - kudos to Ralph Thesen und Sambasiva Rao Chinnamsetty for stumbling over the bug. commit 66821020c7999d6f6e2762a441294d20d960afaf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 16:51:25 2015 +0100 FIX: FragmentationAutomationAction checks FragmentControllers' exitflags. - this way we can tell when the connection to the server fails and we need to interrupt the Action and return failure. commit d915f7956e372b428d5f1e29dac552785a15c3a9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 16:50:27 2015 +0100 FIX: ActionSequence now checks whether an Action in the sequence fails. - otherwise if we are to repeat the sequence for 200 steps and one of the Actions fails on the first step, we still go through all of the remaining steps. commit c5b67886320da2341ee9debe98857c3dcd310784 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 14:31:53 2015 +0100 Added BondGraph::checkBondDegree, FragmentationAction only resets degrees when incorrect. - this fixes the bug where the molecular dynamics actions would flip the double bonds in an aromatic ring during the simulation steps because the bond degrees are reset even though the bond graph is present and should be re-used. commit 7614bbdf5ab794816579d338583dbffc805fc41d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 14:30:48 2015 +0100 Added correct-bonddegree to MolDyn and StructOpt Actions. - this is not really necessary as FragmentationAction will correct bond degrees but it is nonetheless cleaner this way. commit b5642b098bdc8ce4d30e084a5d2196d90d1d5eb5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:57:10 2015 +0100 FIX: MakroAction had ref to ActionSequence, hence removing actions would do so permanently. - this fixes the segfault when calling a MakroAction such as MolecularDynamics and unchecking output-every-step, causing the OutputAction to be removed from the sequence, and when re-performing Action with again unchecked option, the action cannot be removed any longer. - now each MakroAction has its own copy of the sequence, it is copied on clone and may be freely manipulated. commit 3dca11658d0c26ca4ec03795f113bfed5a5e2530 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:37:44 2015 +0100 Undoing atom/molecule removal will also recreate bonds. commit f82008d985e0e63d38c3d296f1aa9c6add203c4c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:34:57 2015 +0100 Renamed Bond::Contains to Bond::ContainsNr() and added ::ContainsId(). - I just stumbled over this, trying to recreate bonds from removed atoms and Contains looks for the Nr not the Id ... commit e7cf5be9f4cc5f16f898a6c7e5b427d97835c088 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 23 20:43:55 2015 +0100 FIX: Action..::outputAsPython now accesses parameters via getUnvalidated(). - added Value::getUnvalidated() and Parameter::getUnvalidated() for access at store-session. - this fixes a bug when OutputAsAction had been used whose filename would no longer be valid as the file now exists. This would cause an assertion and the whole OutputAsAction would fail. commit dc0642fc1a4eb53147c23a507d5ddfa9d0ef06a7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:44:56 2015 +0100 tempcommit: Commented-out all debugging messages in QtMoleculeList rewrite. Merge with ... commit 9d622f6f69e19a9b2cb08476a77f6dc0cdc14c86 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 12:15:08 2015 +0100 tempcommit: Fixes to QtMoleculeList. Merge with ... - using vector of molecule pointers and set operations to fulfil validity of updates. commit 08915c9d88c94f542b0b8ffa782b7b109cb8302c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 23 19:25:38 2015 +0100 tempcommit: MoleculeRemoved channels just makes mol inserted into toBeRemoved. Merge with ... - this is safer than removing the entry in MoleculeBiMap right away as thread in GUI and Action thread do not access in an orderly fashion. commit ee617a5ea465afe71546de922fe6a67f130150f7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 23 00:05:47 2015 +0100 Visibility checkstate is working for molecule and group item. - signals are emitted and states are correctly changed, tested on amylose molecule in a box filled with ~3000 water molecules. commit 0da9b3193f1851d475315d6686aff09b53ab09bc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 19 19:18:52 2015 +0100 DROPME: qDebug on selectionChanged() in view. commit 5a9c977ffe22ccf75bfe553b851830db9036052a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 19 19:16:54 2015 +0100 tempcommit: Fixing updateItemStates() such that different updates don't interfere with one another. - i.e. moving a row and removing the row entirely does not mix. Updating it and then removing it is ill-spent time. - split off removing a group item from setting its occurrence. - emitDirtyState() only uses the first column item despite for the dirty items set. Otherwise we have multiple moves of the same row. commit 6fac57fc6f8d6a0a1d77838b1a6d4e7be8ddbf73 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 19 19:16:13 2015 +0100 tempcommit: FIxing accesses to already deleted molecules due to their row becoming unselected before destruction. commit 08f25e3aed02e5896599ac806543bcbcd6769c8b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 23:56:51 2015 +0100 tempcommit: Added selecting braces to select() calls in QtMoleculeListView. Required? Useful? commit ae0310fb681c73af0d74798d4dd9bf91fc5f4e7f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 23:55:30 2015 +0100 DROPME: In case you need to see when selectionChanged() is triggered in QtMoleculeListView. - uncomment me! commit 0371cb1fc2a6163b8df394f5db19a615e8922eaa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 23:54:30 2015 +0100 tempcommit: QtMoleculeList removes group items after setOccurrence(). - setOccurrence() gives index of row back if it should be romoved. commit b63a112570a1c4f216f02010c05a882c467882e3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 21:07:11 2015 +0100 tempcommit: Removed emitDataChanged() and updateSteps() is just void. commit d77afe108713a7a8d5b245b5fd77bf10eda67de6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 21:01:55 2015 +0100 Moved rowsSelected() over to QtMoleculeListView. commit 7a53bcd163402f54a72241cbe2bfd3e54c389c84 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 20:00:01 2015 +0100 tempcommit: Fix to factory for visitem selectable. Merge with ... commit dbcbcc2de2fdfdbc0eb120616ac11017d973cd01 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 18:56:25 2015 +0100 tempcommit: Fixes to list. Merge with ... commit c91d016d3a652cb44adb74e54c6c4722925cab6e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 18:55:45 2015 +0100 tempcommit: Fixes to specific items. Merge with ... commit b3b5fe4d571cbd6546f3df2b7130b435bf574121 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 17:08:42 2015 +0100 tempcommit: Fixes to list. Merge with ... commit 674ab4de68b797f20f8a397aacec35896d421c39 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 17:08:27 2015 +0100 tempcommit: Fixes to items. Merge with ... commit 3f2f38368024d5a70d6b54c4b6a98ff6a5917fef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 15:04:26 2015 +0100 Modified QtMoleculeList to use QtMoleculeItemFactory. commit e2c12d9350e39dd6772f70233c1cf65fecc4b078 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 14:33:42 2015 +0100 Added a slew of specific QtMoleculeItem for each of the COLUMNs. - all are produced solely by the factory and are very specific. commit aac20a7748ce394b1787cbb85c01c694317adf35 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 13:26:55 2015 +0100 Added basic QtMoleculeItem and ...Factory. commit 11fca39b215de52d5b248e0ab1b949afa6bdba16 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 13:22:39 2015 +0100 Moved QtMoleculeList files into own subfolder. - added QtMoleculeListView. - we are going to need a lot of classes for this to work properly. commit c122211ef5fbd30855d6bbca7f4182fe7c0b04d8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 23:33:09 2015 +0100 Header row is correct again in QtMoleculeList. - had to overwrite headerData(). commit 3d9f245199267605d22fec011bd1e71a555a8fed Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 23:32:34 2015 +0100 First change to convert QtMoleculeList into QStandardItemModel. - this will keep the QtMoleculeList up-to-date automatically. commit 11aa68b4eb0deeac242bb25cc1651efab67025c2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 21:05:41 2014 +0100 tempcommit: New update scheme for QtMoleculeList requires changing flag to prevent VisibilityChanged() trigger. commit 95f44cfa70e7c8ce7126ed5b5a4098812a3bd357 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 20:43:05 2014 +0100 tempcommit: Extracted add/removeItem in QtMoleculeList, no more complete refilling on update. - this is unfinished as we can't find the item to a molecule that is about to be removed. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Refactoring_QtMoleculeList_as_QModel created. v1.4.9-39-g2bb2b47
by git＠ins.uni-bonn.de 26 Jan '15

26 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Refactoring_QtMoleculeList_as_QModel has been created at 2bb2b47cb4b0f7f9c6d4bd039a749533cbcf526e (commit) - Log ----------------------------------------------------------------- commit 2bb2b47cb4b0f7f9c6d4bd039a749533cbcf526e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 25 13:44:56 2015 +0100 Commented-out all debugging messages in QtMoleculeList rewrite. commit 03cf90c84932a65aa722e39fa564b51181c7cbb1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 23 00:05:47 2015 +0100 Visibility checkstate is working for molecule and group item. - signals are emitted and states are correctly changed, tested on amylose molecule in a box filled with ~3000 water molecules. commit c59f1a35a51372ee57590c81a99c6f6d9ff622ea Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 21:01:55 2015 +0100 Moved rowsSelected() over to QtMoleculeListView. commit 68d4f24f2968697b350551826294fe044088bdc7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 15:04:26 2015 +0100 Modified QtMoleculeList to use QtMoleculeItemFactory. - setOccurrence() gives index of row back if it should be romoved. - i.e. moving a row and removing the row entirely does not mix. Updating it and then removing it is ill-spent time. - split off removing a group item from setting its occurrence. - emitDirtyState() only uses the first column item despite for the dirty items set. Otherwise we have multiple moves of the same row. - this is safer than removing the entry in MoleculeBiMap right away as thread in GUI and Action thread do not access in an orderly fashion. - using vector of molecule pointers and set operations to fulfil validity of updates. commit b7d482662e59198ecddf867c88a3be65c0a1635e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 14:33:42 2015 +0100 Added a slew of specific QtMoleculeItem for each of the COLUMNs. - all are produced solely by the factory and are very specific. commit 01d7e63798545f7949b8286553219ad7c9851d49 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 13:26:55 2015 +0100 Added basic QtMoleculeItem and ...Factory. commit 38f27e4ea2d51e19164f46c0753f22f9ebb1af20 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 13:22:39 2015 +0100 Moved QtMoleculeList files into own subfolder. - added QtMoleculeListView. - we are going to need a lot of classes for this to work properly. commit d1b423c692cd2bc0d4c15dd4c8ad930621c8902d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 23:33:09 2015 +0100 Header row is correct again in QtMoleculeList. - had to overwrite headerData(). commit f88d67d2be0f4df9388bdbde47d7869bc974c3ac Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 23:32:34 2015 +0100 First change to convert QtMoleculeList into QStandardItemModel. - this will keep the QtMoleculeList up-to-date automatically. commit 833a99815b6afcce0bdc82a545dbfcac84d93310 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 20:43:05 2014 +0100 Extracted add/removeItem in QtMoleculeList, no more complete refilling on update. - this is unfinished as we can't find the item to a molecule that is about to be removed. We have to switch to Qt's Model/View ... argh. commit 0b647c9e59733b7e1d4b8ef0d009708482611b95 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 17:08:59 2015 +0100 MEMFIX: removeAtomsinMolecule() worked directly with molecule::iterator which accesses invalid memory. - now, we copy all atom pointers prior to removal and work only on this copy commit 05d8f2ae2489b99804f31755a570c04b1efe9891 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 14:34:20 2015 +0100 Added AboutToBeRemoved channel to molecule. - this allows UI elements to remove all items related a molecule's presence before any destructor has started doing something. Note that subjectKilled() does not work here, as "higher" (in inheritance hierarchy) have already been called and changed the instance. We need to know right when the instance is still intact. commit d31ee25de8775d8057b2d8a73e5c8dae03b53efc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jan 17 17:45:07 2015 +0100 FIX: Atom is notified when its father dies and resets father to itself then. - this caused a segfault with FormatParser::save() when a copied molecule's atoms is stored. commit cf5b40740d5d7a75cc4d37649723d13c88ecb510 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jan 17 16:54:36 2015 +0100 FIX: On defined LOG_OBSERVER we also enableLogging() in main(). - I always forget how to get the log to be actually printed to the screen. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Refactoring_QtMoleculeList_as_QModel deleted. v1.4.9-52-g6d7da81
by git＠ins.uni-bonn.de 26 Jan '15

26 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Refactoring_QtMoleculeList_as_QModel has been deleted was 6d7da8177f55bd8747b9974ab3fc035ca2bffade ----------------------------------------------------------------------- 6d7da8177f55bd8747b9974ab3fc035ca2bffade DROPME: qDebug on selectionChanged() in view. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Refactoring_QtMoleculeList_as_QModel created. v1.4.9-52-g6d7da81
by git＠ins.uni-bonn.de 20 Jan '15

20 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Refactoring_QtMoleculeList_as_QModel has been created at 6d7da8177f55bd8747b9974ab3fc035ca2bffade (commit) - Log ----------------------------------------------------------------- commit 6d7da8177f55bd8747b9974ab3fc035ca2bffade Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 19 19:18:52 2015 +0100 DROPME: qDebug on selectionChanged() in view. commit a4a7981b8868086d6c252d0e54775cd2cd3ad3f5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 19 19:16:54 2015 +0100 tempcommit: Fixing updateItemStates() such that different updates don't interfere with one another. - i.e. moving a row and removing the row entirely does not mix. Updating it and then removing it is ill-spent time. - split off removing a group item from setting its occurrence. - emitDirtyState() only uses the first column item despite for the dirty items set. Otherwise we have multiple moves of the same row. commit ec326ba50b072979492745c2e2172c51c4eb3dd2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 19 19:16:13 2015 +0100 tempcommit: FIxing accesses to already deleted molecules due to their row becoming unselected before destruction. commit fbbcf29cccd73cf39860fc1cff15afd62be64525 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 23:56:51 2015 +0100 tempcommit: Added selecting braces to select() calls in QtMoleculeListView. Required? Useful? commit cd71ac37b4704fb39be660a90192fb43880edbfc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 23:56:13 2015 +0100 tempcommit: Forgot include Log.hpp. Merge with bf653ed3 commit 0bb38dd0a7cabf95eac8f7371c4846f0dde1e9cd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 23:55:30 2015 +0100 DROPME: In case you need to see when selectionChanged() is triggered in QtMoleculeListView. - uncomment me! commit d59430f920128744587098a60ad3f17a0cccb3e6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 23:54:30 2015 +0100 tempcommit: QtMoleculeList removes group items after setOccurrence(). - setOccurrence() gives index of row back if it should be romoved. commit 33bccc3a8773c80a3e86b49a55b57ee4663e6e1c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 21:07:11 2015 +0100 tempcommit: Removed emitDataChanged() and updateSteps() is just void. commit 905aab313523bd703588667ab2b1a6a20a502c95 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 21:01:55 2015 +0100 Moved rowsSelected() over to QtMoleculeListView. commit 6c83cb8435d1cc9f5d75883a4adac67883e78fa3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 20:00:01 2015 +0100 tempcommit: Fix to factory for visitem selectable. Merge with ... commit 43c2c5f2c0061f6c074db1c5e28733820a379a8b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 18:56:25 2015 +0100 tempcommit: Fixes to list. Merge with ... commit a4d3505d1eb7b980eb50509cbfe97b67ef43cbda Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 18:55:45 2015 +0100 tempcommit: Fixes to specific items. Merge with ... commit 085f5ee30a82c7c59d0f9a733ec01b5d79c11319 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 18:04:15 2015 +0100 tempcommit: Fixes to AtomicInfo. Merge with 7201245d commit 9687c375de7e71742901e6936529bb0eed8ddc67 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 17:08:59 2015 +0100 MEMFIX: removeAtomsinMolecule() worked directly with molecule::iterator which accesses invalid memory. - now, we copy all atom pointers prior to removal and work only on this copy commit bf653ed3d885937035bbd46c4b57849329859fd1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 17:08:42 2015 +0100 tempcommit: Fixes to list. Merge with ... commit a1c0514155482769be23698d779dbb61f380353b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 17:08:27 2015 +0100 tempcommit: Fixes to items. Merge with ... commit 2751be088eab0d7de5c3c588d4af20f9374745ef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 15:04:26 2015 +0100 Modified QtMoleculeList to use QtMoleculeItemFactory. commit 6a35c5639cf5f023922f72c1284c8b9139012780 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 14:33:42 2015 +0100 Added a slew of specific QtMoleculeItem for each of the COLUMNs. - all are produced solely by the factory and are very specific. commit 4421864ac11477a8d49ccf3e75bbd4f0b17a0f81 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 14:34:20 2015 +0100 Added AboutToBeRemoved channel to molecule. - this allows UI elements to remove all items related a molecule's presence before any destructor has started doing something. Note that subjectKilled() does not work here, as "higher" (in inheritance hierarchy) have already been called and changed the instance. We need to know right when the instance is still intact. commit 9cea08be99892d2650848acd5ed6ea9ce5ffe2c4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 13:26:55 2015 +0100 Added basic QtMoleculeItem and ...Factory. commit 71ec6bdac615f8d5171097bcc528ec3c75db40da Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 18 13:22:39 2015 +0100 Moved QtMoleculeList files into own subfolder. - added QtMoleculeListView. - we are going to need a lot of classes for this to work properly. commit 7201245d2992523e563f42369a783fa754dc6727 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jan 17 17:45:07 2015 +0100 FIX: Atom is notified when its father dies and resets father to itself then. - this caused a segfault with FormatParser::save() when a copied molecule's atoms is stored. commit 3ad2450bb0028bf058ae85b0623abc071c9de168 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jan 17 16:54:36 2015 +0100 FIX: On defined LOG_OBSERVER we also enableLogging() in main(). - I always forget how to get the log to be actually printed to the screen. commit e47928afcf78a50557fed4bb2fad1352977d9c00 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 23:33:09 2015 +0100 Header row is correct again in QtMoleculeList. - had to overwrite headerData(). commit c7e492208819e918720140a33925327e06eb3106 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 23:32:34 2015 +0100 First change to convert QtMoleculeList into QStandardItemModel. - this will keep the QtMoleculeList up-to-date automatically. commit cc2a7c82060caac7beeffe067410d94ce90e9126 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 21:05:41 2014 +0100 tempcommit: New update scheme for QtMoleculeList requires changing flag to prevent VisibilityChanged() trigger. commit e33f9222f71ae4e54c5e3fa9fed0dbcf6e6d049e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 20:43:05 2014 +0100 tempcommit: Extracted add/removeItem in QtMoleculeList, no more complete refilling on update. - this is unfinished as we can't find the item to a molecule that is about to be removed. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules created. v1.4.9-25-g4f2895f
by git＠ins.uni-bonn.de 15 Jan '15

15 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been created at 4f2895fe90439ea317f5f52995da2eaa9bd4aac7 (commit) - Log ----------------------------------------------------------------- commit 4f2895fe90439ea317f5f52995da2eaa9bd4aac7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 9 12:24:22 2015 +0100 FIX: World::SetTime() erased molecules twice. - once in SetTime() and then again in DFS.Update...(). commit 066442d357f0a016de2922eff675320398a5ba17 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:37:33 2014 +0100 Added TranslateMolecule action. - added translate-molecule to userguide. - added translate-miolecule regression tests. - TranslateAtoms now has extra option position. commit a84e8d0ab1d22d7db69a2ac4a869d411549a066b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:45:44 2014 +0100 Added Push/PopMolecules selection action. - added push-molecule to userguide. - added regression tests to Push/PopMoleculeSelection. commit 3213f29e16ba9cf8c7dc57a7343907df2ec3988a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:37:06 2014 +0100 Added Push/PopAtom selection actions. - added push-atom to userguide. - added regression tests to Push/PopAtomsSelection. commit cad38353d3b80b389bc34215a1350cc486705ef7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 20:32:31 2014 +0100 Added push/pop[Atoms|Molecules]Selection to World. - this is mostly convenience for MakroActions to use selections and still keep the selection from the user. commit 2440cedf30e76a68e8eff1d2567f19c1b9e114ca Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 14 21:31:24 2015 +0100 FIX: Changed SuspendInMoleculeAction to catch segfault when rho=1 was given. - however, the action is still not tested to work. - TESTFIX: suspend-in-water gets parameter density via "density" not via "suspend-in-water", set desired density to faulting 1 for the moment. - TESTFIX: added water molecule to test.conf, to have at least two molecules. commit 601ef8103d4e9e074f5fdcf17ea01dec9372e95f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 20:10:19 2014 +0100 FIX: ActionQueue is no longer cleared when Action fails. - we only remove the present and all following Actions. - also cleaned up threaded/non-threaded parts of ActionQueue: CurrentAction, tempQueue is solely used in threaded part. commit 33c97e84dae27f29caf454929853623b09c497bb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 19:15:47 2014 +0100 FIX: Failing Actions do not clear ActionQueue/History anymore. commit 52cd7bb206bec24c016935f40237d8c5102ab6aa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 21:38:29 2014 +0100 FIX: Bonds from new molecules are instantiated, too. - when filling in molecules, initially empty molecules are created and atoms added lateron. Added atoms would not add their already present atoms but only new ones via an Observer update. Now when an atom is inserted, all bonds if any are added. commit c01fec6a0c349cdec638b991086b581c75b3eccc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 19:41:27 2014 +0100 Undo/Redobuttons are grayed out when respective Action not possible. commit 867473fc81f5f56ef4a2749de5a2256f208084b8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 18:29:46 2014 +0100 Added new RemoveAction for molecules. - also add regression test. - added remove-molecule to userguide. commit 596cfa877bf5ca9866344e3bf0623e4704009c17 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 09:28:58 2014 +0100 Extended UndoRedoHelpers by AddingMultipleMoleculesfromAtomicInfo. commit d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 09:28:30 2014 +0100 Extended selection action for Molecule ids to multiple ids. commit b6d92e374e7b56b8a8b8399faf64a7363294d1b4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Dec 6 00:06:53 2014 +0100 GLWorldView's view may be changed via keyboard (especially zoom). - Zoom and keys distance change scaled by eye-center distance. commit f115ccd1f9b646866bddc9583360ebb5e27593b9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 3 23:15:42 2014 +0100 For GLMoleculeObject_atom element and position are only reset..() on hook'ed in draw(). - similarly as with GLMoleculeObject_molecule, we check in draw() when need to reset..() and do it before the actual drawing. This speeds up a lot. commit a7aebd81a7ffd4f46af11dbf5e777b8833c831cf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 3 20:20:31 2014 +0100 World removes empty molecules. - on destroyAtom() of molecule's last atom, destroyMolecule() is called. - FIX: destroyMolecule(molecule *) did use OBSERVE unncessarily. This caused seg'fault. - extracted removeAtomsinMolecule from molecule class. This is necessary since World will automatically remove empty molecules. commit 7b93f9dad1f3a6bad5e0303472273227cebbcc50 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Nov 18 20:52:44 2014 +0100 Added MeshFreeType to GLMoleculeObject. commit 3eb91c4b2479f25056f44fbdb7275387992fccea Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Nov 16 17:31:35 2014 +0100 Molecule's Visibility can be changed "group-wise". - FIX: Removed this funny clear() on update() signal. Also using notifications now, which appear less often. commit 9a7ef90a4cc774b21092647cb1d743b0a756dbb6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 23:35:35 2014 +0100 Molecules can be (un)selected by clicking on the tesselation hull. commit 2b596f94d8d4eaae7f603d8c5e7e9546cc3cfe3f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 23:26:05 2014 +0100 Hovering over molecules is working including update of QtInfoBox. - SelectionBox is drawn again when molecule is fully shown. commit 7b59843c6e0fcf96629146aac977053a6deaab43 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 20:01:33 2014 +0100 GLMoleculeObject_molecule listens to AtomMoved signal to update hull only when necessary. commit c32d21acd3e47b463b8a5f9dc56fe34113509f73 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 19:14:17 2014 +0100 Molecule relays atom's PositionChanged as AtomMoved signal. - this allows to update tesselation hull only when something changed. commit 34e7fdbe244fe3d4cc7ffaf1162683ab8c7eff45 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Nov 6 00:22:55 2014 +0100 GLMoleculeObject_molecule display tesselated surface in m_visible case. - set TesselationHull radius to 2., independent of mol's bounding sphere. - added bool to indicate when subjectKilled() had been called. commit 739ee9365702db570a88ff6eecfa0f87be1ec93b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 5 23:00:40 2014 +0100 GLMoleculeObject have m_visible, settable in QtMoleculeList. - is connected via QtMainWindow an GLWorldView, GLWorldScene. - i.e. molecule's atoms and bond display can now be switched on and off. commit 8c001aeb40538cff3bf30540d0cc0b8359472d75 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 5 20:19:42 2014 +0100 GLMoleculeObject_atoms and .._bonds are now children of .._molecule. - GLMoleculeObject::initialize() is now virtual. - .._molecule is now draw()ing its children, i.e. initialize() of .._molecule calls in turn those of .._atom and .._bond. Similarly with draw. - molecule has a lastchangedatom member variable now. - FIX: molecule::getBoundingSphere() did not check for no atoms. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules deleted. v1.4.9-27-g65550d8
by git＠ins.uni-bonn.de 15 Jan '15

15 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been deleted was 65550d858d4c18ea86fba70e93129adfcf2b20a0 ----------------------------------------------------------------------- 65550d858d4c18ea86fba70e93129adfcf2b20a0 FIX: World::SetTime() erased molecules twice. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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