- Molecuilder-devel

[SCM] branch Remove_CodeMountain deleted. v1.5.1-183-gdb5b62b
by git＠ins.uni-bonn.de 19 Apr '16

19 Apr '16

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 --

1 0

[SCM] branch Remove_CodeMountain created. v1.5.1-183-gdb5b62b
by git＠ins.uni-bonn.de 12 Apr '16

12 Apr '16

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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Tue Apr 12 16:35:58 2016 +0200 tempcommit: Merge with 086f051e commit 825c7ed3596e1d94cc5b4f27102455e4647a6b97 Author: Frederik Heber <heber(a)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(a)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(a)ins.uni-bonn.de> Date: Tue Apr 12 16:16:14 2016 +0200 tempcommit: Merge with 782db0ab commit eea78c0d7166e3637206212ba13e3f9a6dd47574 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Apr 12 16:14:04 2016 +0200 tempcommit: Merge with 086f051e commit 17ba709f275827ed7424859e673696da75b6a8e1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Apr 12 16:13:25 2016 +0200 tempcommit: Merge with 5aa9bdc9 commit c82b71e3278112dd2233ce092d1652a395bd03d4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Apr 12 16:01:47 2016 +0200 tempcommit: Merge with 086f051ef commit 822e7249d092c590282f19171e5416e65781b44b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Apr 12 15:56:01 2016 +0200 tempcommit: Merge with d76f20fc commit 0e0f07fb96d436b48feb009e0e0f7876a4381ef3 Author: Frederik Heber <heber(a)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(a)ins.uni-bonn.de> Date: Tue Apr 12 15:19:02 2016 +0200 tempcommit: Merge with 5520c7ce commit c20b16de10cd11cac879cb42abb2b1bd73691bb8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Apr 12 14:54:58 2016 +0200 tempcommit: Merge with 086f051 commit b7f2a1ffd7a93fe656b6b6c874c788bac4904d22 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Apr 12 14:38:28 2016 +0200 tempcommit: Merge with 5aa9bdc99 commit 086f051efc730d759ac49dfe9222ce188f6d7f8b Author: Frederik Heber <heber(a)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(a)ins.uni-bonn.de> Date: Tue Apr 12 13:45:06 2016 +0200 tempcommit: Merge with 5aa9bdc commit d76f20fc5f2efb513f20aff1e080aff697b04ad2 Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Thu Apr 7 18:10:42 2016 +0200 tempcommit: Merge with 40595019 commit 64da96da774da113e4f19083f58694f06376faba Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Apr 7 18:10:30 2016 +0200 tempcommit: Merge with bc661027 commit eed94790c1fa61e71584ef16a562ffae6f9f1340 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Apr 7 18:10:12 2016 +0200 tempcommit: Merge with 40595019 commit ecfa6770a680537135a89bcd3ba760fba2bb5fd9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Apr 7 18:09:25 2016 +0200 tempcommit: Merge with bc661027 commit 3917d2223c179b9e7e42a0f0528c806f5dfe9763 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Apr 7 18:08:38 2016 +0200 tempcommit: Merge with 40595019 commit 2eab9d414c6fa8b6b5dbe020bf1500836880e1ce Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Apr 7 18:08:15 2016 +0200 tempcommit: Merge with e45f9d60 commit c83d065633a9f5e621ef896c2a7af5c8bd906997 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Apr 7 18:07:58 2016 +0200 tempcommit: Merge with bc661027 commit 40595019c19b21f387a2f0d83e6aeed1f5a722a8 Author: Frederik Heber <heber(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Tue Mar 29 16:54:47 2016 +0200 tempcommit: Merge with e45f9d60 commit 23e92625c10c58235154c2c8e6e51cd5e59120a2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Mar 29 16:53:56 2016 +0200 tempcommit: Merge with e45f9d604 ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch NoPartialSpecialization_ObservedValue_wCallback created. v1.5.1-145-g6edc017
by git＠ins.uni-bonn.de 24 Mar '16

24 Mar '16

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, NoPartialSpecialization_ObservedValue_wCallback has been created at 6edc017981e57df23f15b819c4092694ba7617a8 (commit) - Log ----------------------------------------------------------------- commit 6edc017981e57df23f15b819c4092694ba7617a8 Author: Frederik Heber <heber(a)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 308e76a8dc4f3a4646260f791bb8aa2bbe7ea553 Author: Frederik Heber <heber(a)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 e45f9d604da9f01dd096d0245966e128a47bdea8 Author: Frederik Heber <heber(a)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 8c41b46c5d77804c6c27ac0178f48edfebd75385 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 24 14:13:31 2016 +0100 FIX: Removed GLMoleculeObject_molecule's molref. commit 1efb10c3bde0338622331a99dc4a832e1da6f6f7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 23 10:56:51 2016 +0100 QtObservedMolecule also uses new index internally. commit 99f83adf828e55135a6b94e900c0b8d3b722582a Author: Frederik Heber <heber(a)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 215f91ec10671daed809d3c448e7c7336f148789 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 23 10:58:26 2016 +0100 FIX: QtObservedMolecule::initObservedValues was still static. commit 0e89e7546661f91dbbd6c2155158aba832848a47 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 23 11:06:23 2016 +0100 Removed unneeded specialization ObservedValue_UpdateAtoms. commit 1c865975af56e0f660c047eaa80f36cdbd1417cf Author: Frederik Heber <heber(a)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 d6b2f48175aab4be80acb30b0a596b23c50c979b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Mar 22 00:32:47 2016 +0100 Removed GLMoleculeObject_molecule::getPresentAtoms(). commit 42b7bc539ded6099277bc19d4d5f0dd29386a98a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Mar 22 00:12:07 2016 +0100 FIX: Removed some unnecessary observer code from GLWorldView. commit 559c169d9bab287bc1d64551dc69a69a6a890e26 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Mar 21 23:36:39 2016 +0100 Changed slots of GLWorldScene and GLWorldView. commit 80d5f8c7f79f1976214e864dcd5991aef0e9107f Author: Frederik Heber <heber(a)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 065754567547d81ffafcd44d36a6cdb9bf24d238 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Mar 21 22:13:43 2016 +0100 QtObserved...Observed now get index on ...Removed() signal. commit d4bb75e3379171a82130ee35472f06649ce61cb4 Author: Frederik Heber <heber(a)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 bc66102736ae00e45fcce642667ee01f45f12ea9 Author: Frederik Heber <heber(a)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 edb3d4d7404d39070664eb268fff7f714400974c Author: Frederik Heber <heber(a)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 9a408faa37d8e1013d9c99e293839ed2655fcea2 Author: Frederik Heber <heber(a)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 6347c7609f85fbb2510f87b124843d0a876fdfa6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Mar 21 20:43:25 2016 +0100 FIX: QtMoleculeList::moveItem() does not need to search for groupitem. commit 4f5cfe2ec2334ee2a4747dff407f15fb6b8e2c10 Author: Frederik Heber <heber(a)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 5520c7cea27ea5dcd6bd63a41133132823e0ed72 Author: Frederik Heber <heber(a)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. commit 24eb6b9e8f3b4ff8f95f2e26c0a57c2296d904de Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Mar 18 10:46:52 2016 +0100 Removed QtMoleculeList::informDirtyState(), callback is not needed anymore. - this was the target of emitDirtyState() from QtMoleculeItem. - the event system will now run independently between the items and their list. commit 7993fe252cb5b1325c70e077e87cf14aefe1b912 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Mar 18 10:39:37 2016 +0100 Removed emitDirtyState callback from QtMoleculeItem. - this does not seem to be needed any longer, probably since introduction of QtObservedMolecule. commit 9242598314ccb08531f6506da54bb5a30b948820 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 17 11:26:19 2016 +0100 Added QtObservedMoleculeObserver that relays signals on all QtObservedMolecule's. commit 1c9eb831f805f2e14267bc2d65deaa3b33e61d68 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Mar 21 20:48:52 2016 +0100 FIX: molecule::SetNameFromFilename did not notify about MoleculeNameChanged. commit d316ad175d80f2441d92437f76c6c09371a17998 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Mar 21 20:45:59 2016 +0100 FIX: molecule did not notify about FormulaChanged at the right moments. - we need to notify just when we've really changed the formula and not in some other function that is called before. commit bfd520cb09f18eefc8811390bd36115b92325263 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 17 10:52:26 2016 +0100 QtElementList uses QtObservedAtomObserver and is no longer Observer itself. commit 6a7353e36c3512675d0e16c1907644a20941cc39 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 16 11:00:40 2016 +0100 Added QtObservedAtomObserver to ElementList subfolder. commit bfd5d5f31700046d9d9fbae826f67fa4cefc283f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 16 11:20:09 2016 +0100 QtObservedAtom and ..Molecule now have internal selfref. - this can be used to convert a ptr to the instance into a shared_ptr that can be sent around easily and safely. - QtObservedInstanceBoard is factory of QtObserved... and assigns them their self reference right after instantiation. commit 1e1893b5d6284fd9ea1d43b7e76cd5088bb46e48 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 16 11:00:24 2016 +0100 Moved QtElementList into own subfolder. commit 7f1c00600c607f53c051131adf78bbf8bb34c4d7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 16 10:12:28 2016 +0100 Added getObserved..() functions to QtObservedInstanceBoard that take Observable. - this is for the transition to ObservedValueContainers using Observable refs as keys. commit f35f7edd5263c493f767a7510ab79feebd7cb651 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Mar 14 10:51:32 2016 +0100 All QtObserved..::update..() now use the atom or molecule ref instead of index getter. - the update() is called instantly by the Observable. Hence, the ref is still fully valid and always more recent than the index that needs updating. Also, it is way faster, as no lookup in the World is required and function may even get inlined. commit d845bd63611561992e0e940661aaf16d3210566b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:22:16 2015 +0100 GUITESTS: Decreased waiting times in QtGUI's test mode. commit c44763216bce0786fbe760047847c64ee5774937 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Feb 26 22:26:55 2016 +0100 FIX: QtObserved... did not destroyObservedValues() so far. commit 14de9a4486de47e18a486b04ecd54cd7f8f428cb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 3 21:46:55 2016 +0100 FIX: GLMoleculeObject_atom did reset position not bonds on bondsChanged. commit 35ab6270d6095c79bce01c0cc0f21789355d58ca Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Mar 1 18:00:08 2016 +0100 Half of the bonds are showing up again. - but the other half is missing because then one of the QtObservedAtoms is not present yet? commit b6af884ef8deb1d0bee3add52fccfa49405e922d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Feb 26 10:57:36 2016 +0100 Set version to 1.5.2. - MoleCuilder library is now 15:2:0. - Codename "Baade" (The Baade 1952 was the first German jet passenger jet airliner). commit 835b534f9c100ac279ff0fbe104d05901bbc813f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 2 17:01:34 2016 +0100 TESTFIX: Needed to check whether long-range capability is compiled in. - we check for "contains long-range information" and only then check whether the resulting forces are correct. commit 2edf77120707be27630da194a92b100fa915ab7d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Mar 2 16:57:35 2016 +0100 DISTFIX: Added AdjacencyMatcher and TriangleMatcher noinst targets. - distcheck failed on install-check on them. - adjacencymatcher and trianglematcher don't ust AUTOTEST_PATH but topdir. commit af340c21b5447cefb53f0abf8de5efbe586d4b7b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 27 12:49:57 2016 +0100 Brought GuiChecks up to speed again. - regression tests AnalyseFragmentationResults, Tremolo BondFile, and FitPotential had changed. commit df0c802c02abf1177a70b2bafe46af86cee53ad4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 16 14:49:23 2016 +0100 FIX: Filling actions did not use minimum distance for tesselated surface. - added IsCloseEnoughSurface_FillPredicate which requires a minimum distance to the tesselated surface (but does not care about the sign) and combines it with an additonal IsInsideSurface_FillPredicate. - this is now used in regular-grid, surface, and volume fill actions when a non-zero minimum distance is given. - TESTFIX: Test is now working. commit b9d387d86af35ffb36dbc15f04ebe37e10d50d98 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 16 15:47:20 2016 +0100 Added regression test for fill-regular-grid that with minimum distance. - test is marked as XFAIL for now due to missing minimum distance consideration. commit 50d49dca91aa5db281d312ca5ee0fbad52557a21 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 11:59:21 2016 +0100 FIX: Renamed FitParticleCharges -> FitPartialCharges. - fitting partial charges is much clearer and the proper word for the action, also the class that does all the work is called PartialNucleiChargeFitter. - all files, all classes. - also renamed fit-particle-charges -> fit-partial-charges, also all files, within all tests and the command itself. commit 0824dd198ecf3d9295689829ad5f5377ecad4aae Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 14 13:33:22 2016 +0100 Enhanced documentation for Qt constructs. commit 4a187da588168135074399b9ba5c32060010ab65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 16 09:32:23 2016 +0100 GLWorldScene also takes note of empty molecule. - this is for the case when a molecule is signalled empty before it signals ready for removal. This may happen cause the empty and the removal signal come from different sources, empty from GLMoleculeObject_molecule and removal from the board. commit 1187c54972b86c05d22e6c40e217c82f0d98ed65 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 14 19:49:24 2016 +0100 FIX: QtObservedAtom's AtomMoleculeIndex was not informed of molecule index changes. - hence, we return the QtObservedMolecule of the molecule to which the atom is associated. And this reference is updated whenever the associated molecule changes. - getAtomMoleculeIndex() -> getAtomMolecule(). - signal renamed moleculeIndexChanged -> moleculeChanged. commit 640cbdb89dc10dbb4cf5d04d394d31e596e89c46 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 14 13:29:24 2016 +0100 FIX: emit changed signal before moleculeEmptied. commit e29427a0d9159d203db020168941388686e2332b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 16:43:33 2016 +0100 GLWorldScene RemovedMolecules now uses QtObservedMolecule* as key. - moleculeId_t is not unique, a new molecule of the same id might have already been instantiated. The shared_ptrs live till the end, hence the memory address can be safely used as unique key to the respective molecule instance. - signatures of signal removeMolecule() and slots moleculeRemoved() and moleculeEmptied() changed from id to this ptr. commit 805fdc2cd99d90fe43f515b48ca05c3a3a41ad5c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 16:30:05 2016 +0100 FIX: GLWorldScene's moleculesAtomRemoved was checking QtObservedAtomMap. - however, the atom may already be a different one. Also, we do not even need it as we obtain the molecule from QtObservedMolecule directly. - also, molecule may no longer be present in MoleculesInSceneMap but still in RemovedMolecules and no molecule with same id already instantiated ... commit 5c9604040c713fbb9e27910f306ad00d9fa4b903 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 15:50:41 2016 +0100 SignedOn_t in QtObservedInstanceBoard is again just a set. - we do not need multiple entries for molecule anymore. commit 8b59ddd233f0c59db6375c4778cb46d1b338b803 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 15:48:14 2016 +0100 Removed last...removed in QtObservedInstanceBoard. - this does not do anything useful anymore, we may just pass the id we obtained from ObservedValuesContainer as Qt signal. commit 92af1b793de96102c8be702763589db17d977682 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 15:47:51 2016 +0100 tempcommit: Removed atomDelayed stuff in QtObservedInstanceBoard's header. commit 96e145752e3ea9373cf157ac1cef8e9f90fcd147 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 27 22:29:01 2016 +0100 AtomInserted/Removed of QtObservedMolecule sends ptr as unique key. - this is used to associate the atom with the right molecule. This is needed in case when the molecule is deleted and a new one with the same id is created. If signals are delayed, we need to know which atomInserted/Removed signal to associated with which GLMoleculeObject_molecule. commit bcf9cda81fdd86254068b3785852032702603546 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 27 22:24:07 2016 +0100 GLWorldScene places GLMoleculeObject_molecule into extra list before removal. - GLMoleculeObject_molecule sends signal when no atoms are left. - GLMoleculeObject_molecule is destroyed when signal is obtained and we have placed it in removal list before. commit 23221f089340ed3767f2e9a84cf97029b3012e2b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 14:53:48 2016 +0100 Removed RefCounted... again. commit 59f1bcc899a181c8225110eb43adbf27eb563d57 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 09:36:58 2016 +0100 All ..Inserted/..Removed signals now go through GLWorldScene. - this should enforce synchronicity of the signals. If we mix direct and queued connections, then this cannot be ensured. - the idea is that GLWorldScene gets all Inserted/Removed signals for atoms and molecules from the QtObservedInstanceBoard. It connects to each QtObservedMolecule and thus can call the GLMoleculeObject_molecule's atomInserted, atomRemoved functions in sequence. - removed RemovalMolecules, no longer needed. - we now enforce with mutexes that instantation of molecule and MissedStateMap do not interfere, i.e. it is always perfectly clear whether to push a signal into the Map or whether to call the function of the present GLMolObj_mol. - FIX: MoleculesInScene_mutex has not been used properly, now is. - DOCU: Updated construct qt-gu documentation with the new concept. commit 03e69e2faa3ae6d3c118759dd157a9b956ddfa77 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:48:51 2016 +0100 FIX: GLMoleculeObject_.. does not care whether selection state did not change. - maybe we just got the event too late and actually two changes occured in between. commit 8281ccea226e5aed0efe851c821e72456e18aa1a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 13:00:38 2016 +0100 FIX: Making sure that atomInserted is received from same source in GLWorldScene and GLMoleculeObject_molecule. - otherwise we cannot guarantee that the events are processed in order. commit 1c096148307b79af138ecbd1dba0c35ec4c1f96f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 26 17:16:19 2016 +0100 FIX: indexChanged from QtObserved... transmit both old and new id. commit 62a0eef42ed46a0537c81d7f76901e4ce65870a9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 11:28:10 2016 +0100 QtObserved... now count the subjectKilled() from the containes values. - we no longer loop this through the ObservedValuesContainer. - also initObservedValues() is not longer a static function but now used inside the QtObserved..'s cstor. commit 1b07b163ff2a979bea3ff3471229c224b188c9f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 18:34:22 2016 +0100 QtObservedInstanceBoard now sends QtObserved..::ptr around in signals. - this should get rid of the problem that we need to keep the QtObservedAtom until it was requested at least once. And we don't know for how long. Now, we simply place the shared_ptr into the signal (to which it seems to be copied) and hence a representation of the atoms remains valid. - cstor of GLMoleculeObject_.. take Observed.. as ref. commit e7ed1225571e2d20981b7286641dbef4de5f758f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 18:11:16 2016 +0100 Combined checks into checkRemoval() in ObservedValuesContainer. commit 387a84787571a9fe001752d730c47ee72648aa70 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:26:38 2016 +0100 FIX: Added mutex to ObservedValuesContainer to ensure atomic access. commit 5aec20876fc61913a0a9d0db96a5769b7fff9150 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:24:10 2016 +0100 QtElementList must not use atom but only QtObservedAtom. commit 4cac6c7fe7e045f8f1e784e13c28d4d3956f9b58 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:22:56 2016 +0100 CHECK: Don't admonish empty missed states in GLWorldScene? - skipped in subsequent loop anyway. commit 7ded1c2e6b5dc07f58723eaa1665215ba1d857b4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:22:13 2016 +0100 GLMoleculeObject_atom and .._molecule don't get QtObserved... right away. - needs to be checked for empty instance first. commit 3fe31809465087526b25224aaeb6783b78d555b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:20:13 2016 +0100 CHECK: tempcommit: Removed Cacheable of TesselationHull for GLMoleculeObject_molecule. - this may cause hiccups with the observed instances with the O/O system and makes no sense anyway as it gets updated all the time? commit aa41a3a0c4aa0434fa825ce5e429d9b4d7108bbd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:19:00 2016 +0100 QtMoleculeList must not use QtObservedMolecules in lists but only request them on need. commit 6bce885acd98d96636737b70f18bfe8b5bd3c0af Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:17:39 2016 +0100 ObservedValuesContainer now asserts that observedinstance has been requested at least once before deletion. - this should prevent that the observed instance is instantiated and deleted before the signal has gotten through to the GUI. - get() returns NULL when not present. commit 3933429afa47ad6263c5bf2c22e8580eda18fe37 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 19:42:38 2015 +0100 FIX: ObservesValuesContainer uses internal struct for two iterators for observedvalues. - we need these two additional iterators (apart from the deque) in order to step through the created instances one-by-one as they are expected in this manner by the QtGUI which, though lacking behind, is trying to process all the seen events. commit 0af22d62caf516e8c8477d17013633d973652fad Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 15:28:53 2015 +0100 FIX: ObservedValuesContainer uses deque for internal observed values. - it may happen that an atom is created before the _visual representation_ got destroyed (and hence it's QtObserved... would be destroyed). In that case the QtObservedInstanceBoard fails with an assertion. - Now, we use a deque. At the front end, we have all the observedvalues that have not yet been deleted, on the back end we have the observedvalues to the currently active instance. - removed unused getRefCount(). commit b4358580663f9c1c016fb856bc7bb23862101215 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:20:43 2015 +0100 Removed QtSelectionChangedAgent. - it is no longer used. We either listen to molecule/atom's selection changes directly or to all of them via the respective relay, i.e. MoleculeObserver. commit 0f368b73ae46e213e4c9d728e86e305aa897fa50 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:14:32 2015 +0100 Removed QtSelectionAgent usage in QtMoleculeListView. - instead we subscribe to MoleculeObserver directly. commit 5cd3a33dde0272c791c7c835e2462b3665503c8f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 18:12:08 2015 +0100 Removed QtSelectionUsage in GLWorldView and related. - instead GLMoleculeObject_.. directly use observedvalue to get notified when they have been (un)selected. commit 9e91009d544fc61e030a8be326f6ecf498ee577a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 12:43:34 2015 +0100 Added ObservedValue for selection status of atoms and molecules to QtObserved... commit 6d49259bafd61830ac9106d84b6cec884637ff2a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 17:06:18 2015 +0100 FIX: QtObservedInstanceBoard needs to allow delayed atomInserted from World. - we may get the notification from molecule before we get the insertion from the World. Hence, we store any ids obtained from molecule insertion if the set of the new atom's observed values have not been generated yet. commit 42d7dc3402f1a14a69a2363de27cfdc8b4008d7e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:22:39 2015 +0100 QtInfoBox disconnects signals. commit 4e6ffe2dae92054b52a94a8f11d2d364f8117035 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:15:58 2015 +0100 FIX: ObservedValue need to be removed with a bit of delay. - ObservedValue has higher priority than e.g. QtObservedAtom. Hence, will also receive subjectKilled() before QtObservedAtom does. But right after all of these are received(), ObservedValueContainer will remove the instance which drops the shared ptr's count to zero (because Observer/Observables do not store shared_ptr but only ptrs!) and its dstor is called. Therefore, QtObservedAtom cannot access the ObservedValue any longer and this is against how the design was meant to be (ObservedValue lives at least as long as respective side in Qt needs access to its information). commit 04c3a3bef347017439e9f064f0b080ae18219eab Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 15:15:23 2016 +0100 QtObservedAtom, ..Molecule, and ObservedValue_wCallback have flag to indicate invalid callback. - due to Qt's signal/slot destruction, which follows no proper order, we need to invalidate callback when their owners are destroyed. Each has a note-function() that flips the boolean to show the callbacks invalidity. - TODO: So far this is not nice, especially w.r.t to ObservedValue_wCallback because of templatization. We cannot place them in a loop and this makes this very error-prone once more Values are added ... commit b2c2e4f3957f35f792eec4674734751c82230bcb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:07:39 2015 +0100 FIX: Qt's parent properly set from QtMainWindow's point of view. commit cf9287e3938da7fd4de24bd9343447e4933b3199 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 15:07:55 2015 +0100 Equipped QtInfoBox with mutex and split clearTabs(). - this avoids a memory corruption with signal/slots as the first atomRemoved() signal also removes the molecule and hence the QtObservedMolecule ptr who is the recipient of the subsequent moleculeRemoved() signal. commit 3b9aa1d67a8d8ea7123888eda5cdd0f9d1ac1060 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:54:29 2015 +0100 FIX: All ObservedValue getters now return const references. - this should avoid some unnecessary copying. commit 367489fe69bf3b53792dde0165df1c41347c98b6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:06:30 2015 +0100 QtInfoBox now obtains information completely from QtObservedInstanceBoard and ObservedValues. commit 5a9e34e889a8bb41b432e388eef49d7d852b91b0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 20 21:02:22 2016 +0100 Extended QtObservedMolecule by Center, NonHydrogenCount, and BondCount. commit fe493f0b6a5c03db3a98e1675bb7eb8dab1a974a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 20 21:04:06 2016 +0100 Extended QtObservedAtom by Name and Molecule. commit deb5eeddb3629c9e2305e74eefb6a494be1ecceb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:15:14 2015 +0100 Removed molecule's AboutToBeRemoved channel. commit ca1535f36cf69069e69bd2f95dfffcb3dca61a70 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 23:21:30 2015 +0100 All QtMoleculeItem now heed QtObservedMolecule and QtMoleculeList takes InstanceBoard. - QtMoleculeItems no longer use Observer/Observable but get updates via signal/slot from QtObservedMolecule. - QtMoleculeList listens to its molecule signals. commit 1b6415a5788dfb3c4db5f526ae11cb7c65e04a4c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 22:55:51 2015 +0100 Added AtomCount and FormulaChanged to QtObservedMolecule. commit ab628cf93050382a100c064a0e77ac121d09789a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 19:38:02 2015 +0100 FIX: ObservedValue_wCallback needs to call callback() only on last channel's signOff(). commit 68418ebdce3a77f78915901a8e48bd7cf1632f6c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 15:41:13 2015 +0100 ObservedValuesContainer now stores QtObserved.. instances directly. - we need this as QtObservedAtom and ..Molecule must signOn() to World's instance right away. If later requests to ObservedValuesContainer::get() cause new signOn()s, then these might fail. - we now work with QtObserved..::ptr directly everywhere. commit 90821d3e29139e45d3df56d7c7f116d631c88f26 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 15:07:59 2016 +0100 Moved countSubjectKilled related code from QtObservedInstanceBoard into ObservedValuesContainer. - this avoids some more duplicated code. commit 494478e91be04149753f2f153a7dfad4d8911944 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 13:52:29 2015 +0100 Extracted all ObservedValue functionality out of GLMoleculeObject_molecule. - see previous commit for explanations. commit 65c3231ff9731698df9e1c840c3c6b5d4c56b2cf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 11:46:45 2015 +0100 Extracted all ObservedValue functionality out of GLMoleculeObject_atom. - i.e. GLMoleculeObject_atom is reduced to simple displaying, updated via Qt signals. These signals are connected to a QtObservedAtom which in turn now contains all the ObservedValue functionality. - this is preparatory for having a single (Observed)Atom as representer of its associated World's atom in the QtGui part of the code. commit 41e2870206d294aab5deb395396ac66cc7e3c0ab Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 10:52:10 2015 +0100 Extracted functions handling refcounting of ObservedValues into ObservedValuesContainer. - this avoids a lot of code duplication. commit 98c35cae2ab1845620fc345902fa7bd0a1ab5d53 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:57:10 2015 +0100 Added rudimentary getter and returner for ObservedAtom/..Molecule() to InstanceBoard. commit 0070aa122a6cee1ec7c2dcbadb8a53a98d6eac6d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:24:10 2015 +0100 Added QtObservedAtom and ..Molecule() instances. commit 2f7988dfca2f351ead05e5302eafd42b83b2f353 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:23:09 2015 +0100 Moved and renamed QtInstanceInformationBoard -> QtObservedInstanceBoard. - this is preparatory for adding ObservedAtom and ObservedMolecule classes that combine all observed information on either type. commit 0f7ffe77d9333b4c1f491534cd62859d247be023 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 10:09:33 2016 +0100 Changed connections between GLWorldScene, GLWorldView and GLMoleculeObject_molecule. commit 8d5fbf175be3a0dab17997f67f03c1284b6174fb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 12:09:33 2016 +0100 GLMoleculeObject_atom, _bond, _molecule all use QtInstanceInformationBoard passed via GLWorldScene. commit 47f0e469e70ba79ff1b52d056bf13f5b859efce4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:13:14 2015 +0200 FIX: QtMoleculeItem not signing off after subjectKilled(). commit 15c8a9b3bc531ef54d3a92deddc382002414247c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 17:42:17 2015 +0200 Added QtInstanceInformationBoard that handles ObservedValues through the QtGui interface. - this is meant as a instantiator of all ObservedValue's needed by QtGui for representing information from the World. The ObservedValue's are instantiated separately w.r.t. to the instance for the visual representation. This is light-weight and can be performed in the same thread, while the visual representation's instantiation can be done elsewhere and there we just need to access the ready ObservedValue's that exist as long as they are needed by the QtGui. commit 026bef57c11cf9d09d87056dab378f0b357f2a4c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 12:01:10 2016 +0100 Changed GLMoleculeObject_...:countSubjectKilled() to taking id parameter. - this is a precursor for when the ObservedValues reside with QtInstanceInformationBoard. - enhanced ObservedValue_wCallback to take a bound getIndex function(). - additionally, we route internally to ObservedValue::get() and this gets us out of the painful situation where we need to supply an index getter to the ObservedValue that monitors the index (and hence must be present already to bind to its get function). commit 099f67dcc87a9df01ccc2248c45c7116c48065cb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 15:28:19 2015 +0200 GLMoleculeObject_bond's ObservedValues is now all static. - again, the same change as with .._molecule and .._atom. commit 16bd376fd9b011d5e40fc688f849c8418b4ad1f9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:55:30 2015 +0200 GLMoleculeObject_atom's ObservedValues is now all static. - this is equivalent to the changes to GLMoleculeObject_molecule. commit 8688ef11c8d02f39202bf756a4085f44860a00df Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:40:14 2015 +0200 GLMoleculeObject_molecule's ObservedValues is now all static. - this is preparatory for extracting their instantation to an external class InstanceInformationBoard that keeps track of the lives of instances in the World that are needed inside QtGui (e.g. for visual representation). commit 7a205a4846f42ef74b0d22155039fb2430f0b719 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:18:30 2015 +0200 FIX: GLMoleculeObject_molecule::updateAtoms() used DisplayAtoms directly. - we need an old and a new set, i.e. the difference needs to be discernable between updates. However, so far we updated the old set directly, too. commit 2831b30765e296e23df0592428b94ccda962210e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:17:43 2015 +0200 FIX: QtInfoBox only updatePage() when ref still present (no subjectKilled() yet). commit 7c7c4adf3a00ea2410433016fef5f193bab8b957 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 13:51:16 2015 +0200 FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule wrapped into vector. - the idea is that a GLMoleculeObject may only remove itself _after_ each and every contained Observer has gotten the subjectKilled() signal from the Observables. Only then will destroying the Object and its members thereby not cause any signOff() which try to access Observables or their channels which are no longer present. This can be imagined as a graph where we have to start destroying object at the very bottom. - This is the avoid the following conflict: A superior object gets note of a molecule to be removed. It sends the visual representation a signal to remove itself, which causes it to use signOff(). On a parallel track (in another thread) we have the observed object calling subjectKilled() to inform any Observer about its immediate destruction. These two tracks collide. Now, we let first pass all subjectKilled() and when the last Observable has gotten its signal, we begin destroying the visual rep. - rerouted signal/slots accordingly. commit e254484494f1093b5f83e79385d6f87cc3ea6588 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:59:22 2015 +0200 FIX: GLMoleculeObject_molecule::subjectKilled() should not call deactivateObserver(). - we just take note that we are signedOff. commit 7cf0eb032ca83b8e15e932a9dd7f082786feb596 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:58:31 2015 +0200 FIX: GLWorldScene has additional moleculePrepared... slots and signals. - i.e. we first insert into MoleculesInMap via direct connection and then signal is emitted (queued) to construct the actual GLMoleculeObject_molecule. commit 4ab5dc2d675790fb54b5022635e15dcf8d3b234d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:56:48 2015 +0200 FIX: GLMoleculeObject_molecule still contained hack to get upper bound on molecule's bounding box. - we don't longer need the hack as we have the molecule cleverly updating the box and an ObservedValue. commit b375e75acf766a9f5578729254211000e199fa9a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 15 11:08:37 2015 +0200 QtFavoriteActions uses ObservedValue for checking last queued action's name. commit db842b5a355e9a83147ac367d4d8dc4c59c84161 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 22:41:30 2015 +0100 FIX: molecule's BoundingBoxSweepingAxis used unordered set of atomids. - this needs to be an ordered set to prevent O(N) access on updating values. commit 951aa6b5136585c823675ec3a59de8c81dde36ef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 20:50:22 2015 +0100 Removed molecule's resetFormula() and doCountBonds() and doCountNoNonHydrogen(). - we don't do these as Cacheables anymore. commit 29f7c188ea15c5c8fca7515e7de0b3e3dba29423 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 20:49:43 2015 +0100 Molecule now has maps with old values for bond counts and element number per atom. - this allows to update the total bond count and the formula in an O(N log N) fashion. commit c0f2fc40afbd5e6b6af4eef0a9cd8ea285a6ec5f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 10:27:51 2015 +0100 atom now uses associate... and disassociatedAtomWithMolecule(). - this is used to gather all functions that need to be called when a new atom joins a molecule such as signing on to certain channels or updating certain internal values of the molecule. commit eb65529c0c104468ebb5dd1b5f2de9f79ed5933a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:19:10 2015 +0100 Deleted MoleculeListClass. - finally ... some veeeery old legacy stuff is gone. commit 2affd161725660cecea8012a86f29f70ce24015a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:02:58 2015 +0100 Removed molecules_deprecated from World and unnecessary includes of MoleculeListClass and all insert/erase. - this goes along the lines of removing "remove me when we don't need MoleculeCistClass anymore". commit df5b8cdff0a450470b90841942f9cb13a5178c97 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:16:33 2015 +0100 Replaced MoleculeListClass in ExportGraph by vector of molecules. - AddHydrogenCorrection did never really worked and is dropped (was commented out in .._ToFiles anyway). commit 2bfc5b108b5b586dc7738bcfddb9149a69e37af0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:06:45 2015 +0100 Replaced MoleculeListClass in analysis_bonds by vector of molecules. - TESTFIX: also adapted CountBondsUnitTest. commit ada8dfef364eee1a6c3f429cb379f943b505b5d5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:06:27 2015 +0100 Removed FindEmbeddingHole which lacked implementation so far. commit d4ba3fafe2170e6e52d61b230122d20b71113b61 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 15:23:09 2015 +0100 Extracted common code out of Molecule/AtomObserver into EntityObserver. - also all channels are generated as a static vector via boost::assign. - removed AtomObserverStub, does not work anymore with extracted EntityObserver. commit 5d8f4f5fc5c4b1c6be8cfb8f938b76cfd81bf228 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 16:10:47 2015 +0100 Added MoleculeObserver as pendant to AtomObserver for molecules. commit 4a328ffbbc4084c5418a999a594c586287c63bf1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 16:09:49 2015 +0100 FIX: AtomObserver was not up-to-date with respect to atom's channels. commit 7f1865dc7e5a73a96f5e2c5a9661cb6ee25690f7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:28:10 2015 +0100 Added template functions to (un)set vector of instances in a row. commit b71881221de8cd8ae1667781df5037eb270b146e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:18:42 2015 +0100 Added select() and unselect() functions to atom and molecule, also SelectionChanged channel. - this allows for more specific selection changs to be signalled. - this extends the current World's SelectionChanged channel that informs about selection changes by a more fine-grained/instance-specific change signalling. commit a0fa14a3e9ff30898a2e49b8bf38eb75471bf23b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 27 22:08:26 2015 +0100 FIX: Fixed wrong paths for adjacency and trianglematcher in regression and GuiChecks tests. commit 687ef1d1fe6172d488a7bae7ccdc73d6216d8992 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:36:21 2015 +0100 FIX: molecuilder.py is now loaded after GUI is done initializing. - otherwise consequences of loaded session (atoms, ...) are not displayed. - originally, this was done on purpose as it is quicker to just load stuff into the world and then tell the GUI to show what's there. However, now, due to constraints with different threads, this is no longer possible. commit cbd4099da1d7c6d1c7365e77187667a67c86b111 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 20 21:02:03 2016 +0100 Added Cacheable MoleculeCenter to molecule which is cleverly updated. commit d93d2c1fddecb0223bade802972bb4bb9747f3a0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 8 16:47:17 2016 +0100 FIX: Long-range forces were not added onto atom's forces. - this was with highest level forces obtained from fragmentation for the short-range interactions but not for the long-range interactions. - TESTS: added additional tests to Fragmentation AnalyseFragmentationResults to compare long-range forces written to tremolo file in the same way as is already done with short-range. - TESTFIX: Needed to re-calculate all Fragment result files, did for short-range and both long-range versions. Energies slightly changed and thus also derived values. commit 45b45dd0d98b38f4881b800ac2ff9ab159d576e1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 8 11:26:55 2016 +0100 FIX: PdbParser would calculate trajectors over all atoms, not just given set. - this is only to determine maximum number of trajectory steps but nonetheless unnecessary. commit 7daf73cc475692eebaceda7e13ff1d21adc69d5d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 8 16:07:21 2016 +0100 LinkedCell's LinkedList is now a vector and no longer a set. - this was causing conflicts in tests as the order of the atoms/TesselPoints in the LinkedList returned by getAllNeighbors() would depend on the order in memory and not on the geometrical ordering or on the ids. - TESTFIX: needed to replace use of insert() in (unit)tests by push_back. But all in all only Molecules Removal regression test's pdb file is affected. commit 87cadb7754911b9e3eae7d6f1889641edb3b3953 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 8 23:58:43 2016 +0100 TESTS: Trimmed down TREMOLO dbond regression test. commit d7206401c4f0b3e9118d4797f54e939795871655 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 8 19:03:59 2016 +0100 TESTS: Trimmed down PopMoleculesSelection regression test. - this should speed up testing with debug enabled. commit b40690bfddf335b2e572dfb6c23adfe8588d60ed Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 8 18:44:31 2016 +0100 Fit..PotentialAction now allow setting maximum number of optimization iteration. - also reduced default value to 100 instead of 1000 for speeding up tests. commit b8f2eaf14d7c6a6b31dcd5b85abd1ba743a81e94 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 8 18:00:06 2016 +0100 FIX: PotentialTrainer did not use user-specified threshold so far. - TESTFIX: Decreased l2 tolerance in FitPotential regression tests to further speed up tests. This is especially true for the enable-debug variant, where 3 of 5 tests take more than 15 minutes. commit 08111add4e3854b9642bec0ae60b58fb491ec273 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Feb 8 11:03:27 2016 +0100 FIX: Added copy cstor for AtomicInfo. - otherwise AtomicInfo is constructed twice and gives output message twice. - MoleculeRemoveAction uses AtomicInfo cstor indirectly to avoid copy. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch Delay_MoleculeRemoved created. v1.5.1-97-g2ab346b
by git＠ins.uni-bonn.de 20 Feb '16

20 Feb '16

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 created at 2ab346bcd181e1e10519dfaf059aa12f4f18f525 (commit) - Log ----------------------------------------------------------------- commit 2ab346bcd181e1e10519dfaf059aa12f4f18f525 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 16 09:32:23 2016 +0100 GLWorldScene also takes note of empty molecule. - this is for the case when a molecule is signalled empty before it signals ready for removal. This may happen cause the empty and the removal signal come from different sources, empty from GLMoleculeObject_molecule and removal from the board. commit d4bb8e15de0d028d802c313f15f03ab815fe52eb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 14 19:49:24 2016 +0100 FIX: QtObservedAtom's AtomMoleculeIndex was not informed of molecule index changes. - hence, we return the QtObservedMolecule of the molecule to which the atom is associated. And this reference is updated whenever the associated molecule changes. - getAtomMoleculeIndex() -> getAtomMolecule(). - signal renamed moleculeIndexChanged -> moleculeChanged. commit 8fac83241dd570c90c2bb0764d03605a59774f34 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 14 13:33:22 2016 +0100 tempcommit: Enhanced docu commit 20a1e9520ec99c1c5797e908233b65eb611adf6b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:21:16 2015 +0200 DROPME: Removed logging into QtLogBox for debugging. commit a9813320bbb63feb3ecdb108ca6130acd57b4fe7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 14 13:30:26 2016 +0100 tempcommit: Merge with 46973b3c commit cac1c1056f4866c23d6d954fda1314581bc49778 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Feb 14 13:29:24 2016 +0100 FIX: emit changed signal before moleculeEmptied. commit 46973b3c6009b987df2d1a2f18e88bc51e2b7d11 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 16:43:33 2016 +0100 GLWorldScene RemovedMolecules now uses QtObservedMolecule* as key. - moleculeId_t is not unique, a new molecule of the same id might have already been instantiated. The shared_ptrs live till the end, hence the memory address can be safely used as unique key to the respective molecule instance. - signatures of signal removeMolecule() and slots moleculeRemoved() and moleculeEmptied() changed from id to this ptr. commit c528fd1d4072d78990470faa4b0628122e9dfa36 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 16:30:05 2016 +0100 FIX: GLWorldScene's moleculesAtomRemoved was checking QtObservedAtomMap. - however, the atom may already be a different one. Also, we do not even need it as we obtain the molecule from QtObservedMolecule directly. - also, molecule may no longer be present in MoleculesInSceneMap but still in RemovedMolecules and no molecule with same id already instantiated ... commit 3f00190ead3a1e2b5aa3eb0db5f48c0f64055e39 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 15:50:41 2016 +0100 SignedOn_t in QtObservedInstanceBoard is again just a set. - we do not need multiple entries for molecule anymore. commit d595d10d97ff28d917460646b119cff66c665b20 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 15:48:14 2016 +0100 Removed last...removed in QtObservedInstanceBoard. - this does not do anything useful anymore, we may just pass the id we obtained from ObservedValuesContainer as Qt signal. commit a0e8a35992485bc183af33fdace406503ea4b49c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 13 15:47:51 2016 +0100 tempcommit: Removed atomDelayed stuff in QtObservedInstanceBoard's header. commit 34e47cb6848c3cda1b210a0e7f317c2a924d8bc3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:22:16 2015 +0100 TEMP: Decreased waiting times in QtGUI's test mode. commit 178c147450531d80569a189fe4c34af69de4e4a5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 27 22:29:01 2016 +0100 AtomInserted/Removed of QtObservedMolecule sends ptr as unique key. - this is used to associate the atom with the right molecule. This is needed in case when the molecule is deleted and a new one with the same id is created. If signals are delayed, we need to know which atomInserted/Removed signal to associated with which GLMoleculeObject_molecule. commit 2220ee136e81b70f32f8f2aa3fb5dcc0356c8fff Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 27 22:24:07 2016 +0100 GLWorldScene places GLMoleculeObject_molecule into extra list before removal. - GLMoleculeObject_molecule sends signal when no atoms are left. - GLMoleculeObject_molecule is destroyed when signal is obtained and we have placed it in removal list before. commit c7622c49ce87c648ab2e12d8b4cc15ac6e2b1283 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 14:53:48 2016 +0100 Removed RefCounted... again. commit b9c95d65f97a99999c0747693845e4399ce64509 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 09:36:58 2016 +0100 All ..Inserted/..Removed signals now go through GLWorldScene. - this should enforce synchronicity of the signals. If we mix direct and queued connections, then this cannot be ensured. - the idea is that GLWorldScene gets all Inserted/Removed signals for atoms and molecules from the QtObservedInstanceBoard. It connects to each QtObservedMolecule and thus can call the GLMoleculeObject_molecule's atomInserted, atomRemoved functions in sequence. - removed RemovalMolecules, no longer needed. - we now enforce with mutexes that instantation of molecule and MissedStateMap do not interfere, i.e. it is always perfectly clear whether to push a signal into the Map or whether to call the function of the present GLMolObj_mol. - FIX: MoleculesInScene_mutex has not been used properly, now is. - DOCU: Updated construct qt-gu documentation with the new concept. commit db0b591344484f5d9444cdfb8463beb1f54adb6e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:48:51 2016 +0100 FIX: GLMoleculeObject_.. does not care whether selection state did not change. - maybe we just got the event too late and actually two changes occured in between. commit 239282d0a3f78dfb3708317c784b5d231ecd4fbf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 13:00:38 2016 +0100 FIX: Making sure that atomInserted is received from same source in GLWorldScene and GLMoleculeObject_molecule. - otherwise we cannot guarantee that the events are processed in order. commit 391db539061b5ea01288e04e0be7c2af7c038d28 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 26 17:16:19 2016 +0100 FIX: indexChanged from QtObserved... transmit both old and new id. commit aaff9d0b03031d940f0393147343bae28357e429 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 11:28:10 2016 +0100 QtObserved... now count the subjectKilled() from the containes values. - we no longer loop this through the ObservedValuesContainer. - also initObservedValues() is not longer a static function but now used inside the QtObserved..'s cstor. commit 9effd271fd2b270a2b85bada2ab23aa04c779b6e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 18:34:22 2016 +0100 QtObservedInstanceBoard now sends QtObserved..::ptr around in signals. - this should get rid of the problem that we need to keep the QtObservedAtom until it was requested at least once. And we don't know for how long. Now, we simply place the shared_ptr into the signal (to which it seems to be copied) and hence a representation of the atoms remains valid. - cstor of GLMoleculeObject_.. take Observed.. as ref. commit c0eb7d3e362158cb0c0b7fa9aad6c8fe73f97fe1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 18:11:16 2016 +0100 Combined checks into checkRemoval() in ObservedValuesContainer. commit 6af47207350e353430f1f7797d21b49ff4334644 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:26:38 2016 +0100 FIX: Added mutex to ObservedValuesContainer to ensure atomic access. commit 0763d47c85d68f48b090823b77f9880a69cdd8a0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:24:10 2016 +0100 QtElementList must not use atom but only QtObservedAtom. commit f28676387f23eef7e5309120f4d23161308b9f0f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:22:56 2016 +0100 CHECK: Don't admonish empty missed states in GLWorldScene? - skipped in subsequent loop anyway. commit eac949c47715473df2e2eab0d7ed6010ce0209d7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:22:13 2016 +0100 GLMoleculeObject_atom and .._molecule don't get QtObserved... right away. - needs to be checked for empty instance first. commit 49304ec9c3204630839da64e6ab794283945030c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:20:13 2016 +0100 CHECK: tempcommit: Removed Cacheable of TesselationHull for GLMoleculeObject_molecule. - this may cause hiccups with the observed instances with the O/O system and makes no sense anyway as it gets updated all the time? commit af8b2740086778f0b354ff713720f2fc4656756b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:19:00 2016 +0100 QtMoleculeList must not use QtObservedMolecules in lists but only request them on need. commit bf9bae4a21412ed9f848c008daf4da68a17341ed Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:17:39 2016 +0100 ObservedValuesContainer now asserts that observedinstance has been requested at least once before deletion. - this should prevent that the observed instance is instantiated and deleted before the signal has gotten through to the GUI. - get() returns NULL when not present. commit f9ea954a9527c505fe36e310ee6f51bbade0055b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 19:42:38 2015 +0100 FIX: ObservesValuesContainer uses internal struct for two iterators for observedvalues. - we need these two additional iterators (apart from the deque) in order to step through the created instances one-by-one as they are expected in this manner by the QtGUI which, though lacking behind, is trying to process all the seen events. commit 0ce43805b209245ae6fcbc802c627f0d009497be Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 15:28:53 2015 +0100 FIX: ObservedValuesContainer uses deque for internal observed values. - it may happen that an atom is created before the _visual representation_ got destroyed (and hence it's QtObserved... would be destroyed). In that case the QtObservedInstanceBoard fails with an assertion. - Now, we use a deque. At the front end, we have all the observedvalues that have not yet been deleted, on the back end we have the observedvalues to the currently active instance. - removed unused getRefCount(). commit 5da4fd30e48f36d4ecd9bac041f73a2e6ac8887b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:20:43 2015 +0100 Removed QtSelectionChangedAgent. - it is no longer used. We either listen to molecule/atom's selection changes directly or to all of them via the respective relay, i.e. MoleculeObserver. commit 9a1db189144ea0b278de8d9c0ad29d385949ebbb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:14:32 2015 +0100 Removed QtSelectionAgent usage in QtMoleculeListView. - instead we subscribe to MoleculeObserver directly. commit 415db69ecabe7f555661f1e7579b0b8d075c3a64 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 18:12:08 2015 +0100 Removed QtSelectionUsage in GLWorldView and related. - instead GLMoleculeObject_.. directly use observedvalue to get notified when they have been (un)selected. commit e4b42e22f8a68f638ef2a9df3aa12c10386cbb9b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 12:43:34 2015 +0100 Added ObservedValue for selection status of atoms and molecules to QtObserved... commit e6c198b4be118612cea65aa257f28621f5b16701 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 17:06:18 2015 +0100 FIX: QtObservedInstanceBoard needs to allow delayed atomInserted from World. - we may get the notification from molecule before we get the insertion from the World. Hence, we store any ids obtained from molecule insertion if the set of the new atom's observed values have not been generated yet. commit 04e569ce2099047b583a12650c5ebcde3a49961b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:22:39 2015 +0100 QtInfoBox disconnects signals. commit e7bb881ed9f58e2c22dd0869961b5bd9a55016b5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:15:58 2015 +0100 FIX: ObservedValue need to be removed with a bit of delay. - ObservedValue has higher priority than e.g. QtObservedAtom. Hence, will also receive subjectKilled() before QtObservedAtom does. But right after all of these are received(), ObservedValueContainer will remove the instance which drops the shared ptr's count to zero (because Observer/Observables do not store shared_ptr but only ptrs!) and its dstor is called. Therefore, QtObservedAtom cannot access the ObservedValue any longer and this is against how the design was meant to be (ObservedValue lives at least as long as respective side in Qt needs access to its information). commit 4ba1b53e8d95205782eda4a858e07c33adfac38a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 15:15:23 2016 +0100 QtObservedAtom, ..Molecule, and ObservedValue_wCallback have flag to indicate invalid callback. - due to Qt's signal/slot destruction, which follows no proper order, we need to invalidate callback when their owners are destroyed. Each has a note-function() that flips the boolean to show the callbacks invalidity. - TODO: So far this is not nice, especially w.r.t to ObservedValue_wCallback because of templatization. We cannot place them in a loop and this makes this very error-prone once more Values are added ... commit 6f11c4fe477cec9427f318924dd3d0369c4d6612 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:07:39 2015 +0100 FIX: Qt's parent properly set from QtMainWindow's point of view. commit a0cf64018031e9496781d57fbef8cdaec91e6cba Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 15:07:55 2015 +0100 Equipped QtInfoBox with mutex and split clearTabs(). - this avoids a memory corruption with signal/slots as the first atomRemoved() signal also removes the molecule and hence the QtObservedMolecule ptr who is the recipient of the subsequent moleculeRemoved() signal. commit c65382fc37f5b6f7c05ab057f888984bc5e4b599 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:54:29 2015 +0100 FIX: All ObservedValue getters now return const references. - this should avoid some unnecessary copying. commit 91832398adba0d5709e15d89cda4f6e24bea5851 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:06:30 2015 +0100 QtInfoBox now obtains information completely from QtObservedInstanceBoard and ObservedValues. commit e85a5ad57177978407f0a20c917d463485ea19bd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 20 21:02:22 2016 +0100 Extended QtObservedMolecule by Center, NonHydrogenCount, and BondCount. commit f2bb5d23965a2ee076a0defa547b06efbb7cf0d3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 20 21:04:06 2016 +0100 Extended QtObservedAtom by Name and Molecule. commit 3cc1074b484f32fa2adb1c83e1af02ccdb23daf2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:15:14 2015 +0100 Removed molecule's AboutToBeRemoved channel. commit a8b0d1002ec1a33d463ce79203c7659ea1342d5f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 23:21:30 2015 +0100 All QtMoleculeItem now heed QtObservedMolecule and QtMoleculeList takes InstanceBoard. - QtMoleculeItems no longer use Observer/Observable but get updates via signal/slot from QtObservedMolecule. - QtMoleculeList listens to its molecule signals. commit c5224fe04c74e9e8ba4b0d4de21c886a9a92f6e6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 22:55:51 2015 +0100 Added AtomCount and FormulaChanged to QtObservedMolecule. commit 132ffdd62ee515e3d415cd8a3638a22137276828 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 19:38:02 2015 +0100 FIX: ObservedValue_wCallback needs to call callback() only on last channel's signOff(). commit 47a352f3cec8a123ee22d88ecee2d1d041a4a828 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 15:41:13 2015 +0100 ObservedValuesContainer now stores QtObserved.. instances directly. - we need this as QtObservedAtom and ..Molecule must signOn() to World's instance right away. If later requests to ObservedValuesContainer::get() cause new signOn()s, then these might fail. - we now work with QtObserved..::ptr directly everywhere. commit d60447008a45476644c41a76ca5613715cd8f8d1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 15:07:59 2016 +0100 Moved countSubjectKilled related code from QtObservedInstanceBoard into ObservedValuesContainer. - this avoids some more duplicated code. commit ea7aa119dca805ba2726e17315bfed05895acfdc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 13:52:29 2015 +0100 Extracted all ObservedValue functionality out of GLMoleculeObject_molecule. - see previous commit for explanations. commit 4f4f230d4c5db356e10b4d799e2c8b413773a772 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 11:46:45 2015 +0100 Extracted all ObservedValue functionality out of GLMoleculeObject_atom. - i.e. GLMoleculeObject_atom is reduced to simple displaying, updated via Qt signals. These signals are connected to a QtObservedAtom which in turn now contains all the ObservedValue functionality. - this is preparatory for having a single (Observed)Atom as representer of its associated World's atom in the QtGui part of the code. commit 59470e71db3b190bd2a12c44b61c4de5c616916c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 10:52:10 2015 +0100 Extracted functions handling refcounting of ObservedValues into ObservedValuesContainer. - this avoids a lot of code duplication. commit a4276876e2a9d6c9687febd0327f4688a63e1da2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:57:10 2015 +0100 Added rudimentary getter and returner for ObservedAtom/..Molecule() to InstanceBoard. commit f6f122b85ec7c94026afa0f4b08367484aae48d7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:24:10 2015 +0100 Added QtObservedAtom and ..Molecule() instances. commit 21d0652520527d71c5cea3ba8e2681f4f08b9bce Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:23:09 2015 +0100 Moved and renamed QtInstanceInformationBoard -> QtObservedInstanceBoard. - this is preparatory for adding ObservedAtom and ObservedMolecule classes that combine all observed information on either type. commit ee5160a077a48901ce7f835e992ed264db812227 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 10:09:33 2016 +0100 Changed connections between GLWorldScene, GLWorldView and GLMoleculeObject_molecule. commit a65e0b67ed0a6b6fd6b35cb956b20c0d4f9ad33d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 12:09:33 2016 +0100 GLMoleculeObject_atom, _bond, _molecule all use QtInstanceInformationBoard passed via GLWorldScene. commit c85bb1e66c4f9743fdf0a2b8870aa26fc38e431a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:13:14 2015 +0200 FIX: QtMoleculeItem not signing off after subjectKilled(). commit 9140be0febff13d22ce6bcb71d21138fddcd35bf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 17:42:17 2015 +0200 Added QtInstanceInformationBoard that handles ObservedValues through the QtGui interface. - this is meant as a instantiator of all ObservedValue's needed by QtGui for representing information from the World. The ObservedValue's are instantiated separately w.r.t. to the instance for the visual representation. This is light-weight and can be performed in the same thread, while the visual representation's instantiation can be done elsewhere and there we just need to access the ready ObservedValue's that exist as long as they are needed by the QtGui. commit f57e61aaf0b459993a691b4a9cff578b6345c375 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jan 25 12:01:10 2016 +0100 Changed GLMoleculeObject_...:countSubjectKilled() to taking id parameter. - this is a precursor for when the ObservedValues reside with QtInstanceInformationBoard. - enhanced ObservedValue_wCallback to take a bound getIndex function(). - additionally, we route internally to ObservedValue::get() and this gets us out of the painful situation where we need to supply an index getter to the ObservedValue that monitors the index (and hence must be present already to bind to its get function). commit 6b45920ff0a52121d125e701e7fb4d85ed58fd98 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 15:28:19 2015 +0200 GLMoleculeObject_bond's ObservedValues is now all static. - again, the same change as with .._molecule and .._atom. commit 6eaa82e7a26f048c6512b94dea2eb302298822c7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:55:30 2015 +0200 GLMoleculeObject_atom's ObservedValues is now all static. - this is equivalent to the changes to GLMoleculeObject_molecule. commit 321c7dea664c07848c54013a3e15d9ecf01fe4fb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:40:14 2015 +0200 GLMoleculeObject_molecule's ObservedValues is now all static. - this is preparatory for extracting their instantation to an external class InstanceInformationBoard that keeps track of the lives of instances in the World that are needed inside QtGui (e.g. for visual representation). commit 05ba5b55fb52838ab990c6dd31b204452e6bcb0a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:18:30 2015 +0200 FIX: GLMoleculeObject_molecule::updateAtoms() used DisplayAtoms directly. - we need an old and a new set, i.e. the difference needs to be discernable between updates. However, so far we updated the old set directly, too. commit cc3c8e1e36354a11e275092cff6288dad75ad8a9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:17:43 2015 +0200 FIX: QtInfoBox only updatePage() when ref still present (no subjectKilled() yet). commit 10bbe9b776c5a20167fd7cc820200b66ef1588c3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 13:51:16 2015 +0200 FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule wrapped into vector. - the idea is that a GLMoleculeObject may only remove itself _after_ each and every contained Observer has gotten the subjectKilled() signal from the Observables. Only then will destroying the Object and its members thereby not cause any signOff() which try to access Observables or their channels which are no longer present. This can be imagined as a graph where we have to start destroying object at the very bottom. - This is the avoid the following conflict: A superior object gets note of a molecule to be removed. It sends the visual representation a signal to remove itself, which causes it to use signOff(). On a parallel track (in another thread) we have the observed object calling subjectKilled() to inform any Observer about its immediate destruction. These two tracks collide. Now, we let first pass all subjectKilled() and when the last Observable has gotten its signal, we begin destroying the visual rep. - rerouted signal/slots accordingly. commit 8658fc191ae135c34f2d21313b756c55ffb61e6f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:59:22 2015 +0200 FIX: GLMoleculeObject_molecule::subjectKilled() should not call deactivateObserver(). - we just take note that we are signedOff. commit f3bd2cebfbc61b098881c201fa969063c01f349b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:58:31 2015 +0200 FIX: GLWorldScene has additional moleculePrepared... slots and signals. - i.e. we first insert into MoleculesInMap via direct connection and then signal is emitted (queued) to construct the actual GLMoleculeObject_molecule. commit 429e503bff3e82beb64c71600ed21b706bd81c22 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:56:48 2015 +0200 FIX: GLMoleculeObject_molecule still contained hack to get upper bound on molecule's bounding box. - we don't longer need the hack as we have the molecule cleverly updating the box and an ObservedValue. commit df79560385cd2d9459b42a93e582168727c21890 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 15 11:08:37 2015 +0200 QtFavoriteActions uses ObservedValue for checking last queued action's name. commit e009eea1371a8dd4558fbc793246af4e1e9d0f24 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:19:10 2015 +0100 Deleted MoleculeListClass. - finally ... some veeeery old legacy stuff is gone. commit 2ed9a4294dd146843081650daa89354695eec349 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:02:58 2015 +0100 Removed molecules_deprecated from World and unnecessary includes of MoleculeListClass and all insert/erase. - this goes along the lines of removing "remove me when we don't need MoleculeCistClass anymore". commit 4d216e26ad3517403f70279e309b2ee4c6842ee2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:16:33 2015 +0100 Replaced MoleculeListClass in ExportGraph by vector of molecules. - AddHydrogenCorrection did never really worked and is dropped (was commented out in .._ToFiles anyway). commit 33a5aabd092cc7765f707789b6ba4a3490028790 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:06:45 2015 +0100 Replaced MoleculeListClass in analysis_bonds by vector of molecules. - TESTFIX: also adapted CountBondsUnitTest. commit b57db5a78544db163b3c6275983ec9b213a26827 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:06:27 2015 +0100 Removed FindEmbeddingHole which lacked implementation so far. commit d83b52100dfec33f4ddd2815582827bace607492 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 22:41:30 2015 +0100 FIX: molecule's BoundingBoxSweepingAxis used unordered set of atomids. - this needs to be an ordered set to prevent O(N) access on updating values. commit c432d18f42e325a2f169a2653fd49bdfc32bc24a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 20:50:22 2015 +0100 Removed molecule's resetFormula() and doCountBonds() and doCountNoNonHydrogen(). - we don't do these as Cacheables anymore. commit 8969b61553800ba52878de3b91c89c6f23fa1090 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 20:49:43 2015 +0100 Molecule now has maps with old values for bond counts and element number per atom. - this allows to update the total bond count and the formula in an O(N log N) fashion. commit 6cb80f99db5a2450db0eb06fc18d7e8c8a147d00 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 10:27:51 2015 +0100 atom now uses associate... and disassociatedAtomWithMolecule(). - this is used to gather all functions that need to be called when a new atom joins a molecule such as signing on to certain channels or updating certain internal values of the molecule. commit 478f022aa5d48250ed57122715799e60483eb0be Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 15:23:09 2015 +0100 Extracted common code out of Molecule/AtomObserver into EntityObserver. - also all channels are generated as a static vector via boost::assign. - removed AtomObserverStub, does not work anymore with extracted EntityObserver. commit 65ca0d1d41b6372eed995b8e5a54c2b5e0f6b615 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 16:10:47 2015 +0100 Added MoleculeObserver as pendant to AtomObserver for molecules. commit d039bd4461ac831022e029952a45b02e44ad5b28 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 16:09:49 2015 +0100 FIX: AtomObserver was not up-to-date with respect to atom's channels. commit bef4ed290985bf049b3536347e3c5e79836e5364 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:28:10 2015 +0100 Added template functions to (un)set vector of instances in a row. commit b4c2efb00fce28e93f0bcb27e2a40f04ecab3449 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:18:42 2015 +0100 Added select() and unselect() functions to atom and molecule, also SelectionChanged channel. - this allows for more specific selection changs to be signalled. - this extends the current World's SelectionChanged channel that informs about selection changes by a more fine-grained/instance-specific change signalling. commit 5f2a4375a503f5f31dfa656ba5565c3ca8b2d919 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 27 22:08:26 2015 +0100 FIX: Fixed wrong paths for adjacency and trianglematcher in regression and GuiChecks tests. commit 9a3d6d6f5cecf9270f4ee3c29a4c29745e026d52 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:36:21 2015 +0100 FIX: molecuilder.py is now loaded after GUI is done initializing. - otherwise consequences of loaded session (atoms, ...) are not displayed. - originally, this was done on purpose as it is quicker to just load stuff into the world and then tell the GUI to show what's there. However, now, due to constraints with different threads, this is no longer possible. commit 5bae86fe04b56eef1124d392a765338281d24e2b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 20 21:02:03 2016 +0100 Added Cacheable MoleculeCenter to molecule which is cleverly updated. commit 918a6c769ce4a33562acd67bec9f9a666ad82db8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 20 21:03:52 2016 +0100 Added extra signal MoleculeChanged to AtomObservable. commit 8ad68b373314b5f34d43573103b2586c095bf875 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 13:09:43 2015 +0100 AddAction and UndoRedoHelpers' AddAtomsFromAtomicInfo use recreate..(). commit 5cf34106ca5c1b4a21a25e3e9adb431e3c4d9404 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 13:08:04 2015 +0100 Added recreateAtom() and recreateMolecule() to World. - in order to overcome problems with Qt signals being delayed so much that in between sending and receiving the id of a newly instantiated atom has changed, we need to set the right id (after undo/redo commands) right away. For this, these two new functions are well-suited. commit 840d02f1fb7052798b00efee6a12f7321a6c9c33 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:21:37 2015 +0200 FIX: not using const ref in binding updateBoundingBox() for molecule. commit 7eec6456e9c2eb4a4374698da0f448bfa54864bc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:42:13 2015 +0200 FIX: World needs to first destroy the molecule, then release its ids. - this is similar to the change for the atom. commit 4965d9f2a24a4bb68714efa5b3489fe9b1452f2f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 21:48:20 2015 +0200 FIX: World::destroy..() did not emit SelectionChanged signal. commit 50c45feb1ed40d339274e6c14569d5ece8740d03 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 14 11:18:05 2015 +0200 FIX: Fitting domain to window on QtMainWindow's init. commit e2c2b1d3b49c0c109d15999a9c101eaf6f3bfe17 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 14 10:57:37 2015 +0100 World's ObservedContainer no longer observe. - This requires CodePatterns 1.3.1 from now on. - I had misunderstood what Till had planed with these ObservedContainers for a long time: I though they would cause an OBSERVE signal for every iterator step but this is not the case. Rather they accumulate all OBSERVE signals to have them fire AFTER the loop is done. This is achieved through the depth count of the observer protectors. - Sadly, this runs against what we do with the lastchangedatom. We need the information right away as we the Observer/Observable stuff does not transport any information and always updating all is way too costly. - Hence, in CodePatterns we have implemented an UnobservedIterator which is used in ObservedContainer and does not cause any OBSERVE signals. - The source of the problem was createAtom() in a loop over selectedAtoms and these atoms not getting created (w.r.t QtInstanceBoard) before the molecule's got note of it (cause they are at depth 1). ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] annotated tag v1.5.1 created. v1.5.1
by git＠ins.uni-bonn.de 07 Feb '16

07 Feb '16

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "". The annotated tag, v1.5.1 has been created at 8628c5ce0731da346d2e96b8261e2218d4b3667b (tag) tagging 69a4206f578e3716755e03e48a082cebd3b0db64 (commit) replaces v1.5.0 tagged by Frederik Heber on Sat Feb 6 23:39:44 2016 +0100 - Log ----------------------------------------------------------------- Incorporated libcodepatterns rename and other fixes for debian packaging. More efficient bounding box in molecule, effectively O(log N). Enhanced hbond distances with more values and consolidated from optimization calculations. VMG forces now are also working for the long-range part. Interdistance now combines couples of fragments till a given order. Smearing of electronic charge distributions greatly improves electronic long-range component. This version contains the following branches: 69a4206 Candidate_v1.5.1 (setting version and updating debian information) 62d092e Enhancing_Interdistance (combining two fragments up to given order and additional smearing of electronic charge component) 7537d19 Fix_VMGForces (long-range forces are now stored and written to file) b61bd5e Fix_debianpackaging (various fixes for creating debian package) dace6c7 Fix_molecuilderguitest_with_valgrind (fix to guitest and valgrind) 2f429ef Better_HBondDistances (more values and also taken from VSpeShape optimization calculations) e39e7a31Molecule_Enhanced_BoundingBox (more efficient way of maintaining a good bounding box of each molecule) ceaab1d AtomAlwaysHasMolecule (atom always associated with a (possibly new) molecule to make it always visible in GUI) 08d9df7 Rename_libcodepatterns (renaming codepatterns -> libcodepatterns) Frederik Heber (47): Package CodePatterns is now called libcodepatterns. FIX: Rename codepatterns -> libcodepatterns. FIX: tests/GuiChecks/atlocal lacked valgrind variable. FIX: Shared libraries's Makefile.am rules are now consistent. FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob. FIX: When there's just a single fragment, don't remove the fullsolution. Added new SetValues FragmentForces. Added extraction of long-range forces from VMGData's array f. Split off sampled_potential im VMGDataMap_t into separate fusion container. FIX: Help on SetBoundaryConditionsAction did not have capitalized condition name. FIX: SaturateAction would use double instead of single hydrogen bond length. Assertion in SaturateBond now states element. MpqcParser additionally allows to save optimization jobs. Added Hbonddistance and -angle for sodium (Na). FIX: Element's HBondDistance and HBondAngle were not initialized as -1. Entered HBondDistance results from VSpeShape into elements_db. Elements are now parsed as string (and tried for being int). Changed debian files to heber(a)molecuilder.com and changed boost dep. Added all required libboost.. to Build-depends. Fixed levmar m4 to use pkgconfig and locate. AddAtom now adds a molecule (atom always associated with a molecule). FIX: World needs to first destroy the atom, then release its ids. FIX: Removed double coding in molecule::erase(). Again changes to obtain correct longrange forces, also forces are optional. MPQCData now also uses FragmentForces (instead of typedef forcevector). Added gathering of full and longrange forces into extra file. Added debugging changes to InterfaceVMGJob on force summation. FIX: Need to divide by global number of particles, when summing later, in ExportSolution. Removing setting net force to zero and setting hasForce to true. Exracted several functions out of Interfragmenter::operator(). Interfragmenter now combines two fragments up to (in sum) till MaxOrder. Added Interfragmenter::findLargestCutoff() to find largest Rcut not causing additional inter-fragments. Adding warning when inter-distance is given less then minimum required rcut. Added ChargeSmearer that is only compiled for CONDVMG. Modified WindowGrid_converter::addWindowOntoGrid(): first reset, then write values. Added new option DoSmearElectronicCharges to FragmentationAutomationAction. Rewrote ChargeSmearer to use visitor pattern. FIX: BondGraph::Createdjacency compare atoms on position in memory. Implemented more efficient per-molecule bounding box information. Merge branch 'AtomAlwaysHasMolecule' into Candidate_v1.5.1 Merge branch 'Molecule_Enhanced_BoundingBox' into Candidate_v1.5.1 Merge branch 'Better_HBondDistances' into Candidate_v1.5.1 Merge branch 'Fix_molecuilderguitest_with_valgrind' into Candidate_v1.5.1 Merge branch 'Fix_debianpackage' into Candidate_v1.5.1 Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.1 DEBIANFIX: requiring libcodepatterns instead of ..-dev variant. Set version to 1.5.1. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch stable updated. v1.5.1
by git＠ins.uni-bonn.de 07 Feb '16

07 Feb '16

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, stable has been updated via 69a4206f578e3716755e03e48a082cebd3b0db64 (commit) via 9ae11c8ffa4dc0d34f93a07bcb120ad35c686947 (commit) via 3690e473417f286de3e772d934f7ae47120b763c (commit) via d1831e68610ffad961ff27e9f13c54a4ae810a1d (commit) via e38750985965a330bae6c625523a373491b95349 (commit) via d26fb7625dde5c4fa08b01ff2fa421d45b545931 (commit) via 6a922b176cac1093a59e5316e5fc5f8b18a99813 (commit) via 9a8a6bb95a3a7a6f0fa93fc6a5b64041d47de9c7 (commit) via e39e7a39013eb9930f8d044d1a2c5297df13da96 (commit) via e3e52ab3453d1812f2502d0534b424543c3505e8 (commit) via 62d092e08dbdb67e4f00547587c38322bf8bb828 (commit) via 17e4fde191dda907bf7bd206803886c13e02d440 (commit) via 445ce6d3846182eaf130a6a73ea863d0a443e6f0 (commit) via cceb8cfe148cf346613694b5f15bde9f95e63393 (commit) via 92232f71902106c7de16c1208aa802471f88fbb1 (commit) via cee9e8b8d814bc0aaefacaf9bdc81d5ca2f2876b (commit) via b1c5f46c2e8356c3a5cb7319f77fe3e21793f787 (commit) via 0d90534c2cfcca7121d5161e6f235225bdb4c0df (commit) via 7537d191a569f0b72f4ef6db9b9ae70d575a463f (commit) via 00d815ca595052983db7c34a5f62e31c775c680e (commit) via 6e73f5af95ffb4eb1a979d776df10f17828e74f9 (commit) via ff347fc31ed5cd23e7ad30c79dd005ca9145acb2 (commit) via 20bb3b83b5704876159d8aeede5c88f78cb27559 (commit) via 94db134a7b8bcdb17a2134fe1c6ca1aed4aded49 (commit) via a06378771ff430b3ce4652d680ae761a08426668 (commit) via 59e799680d2829d1437a7c22cb6820332ca100a5 (commit) via ceaab1dbd47046505deba359f3a96512689de872 (commit) via b61bd5e8f51d73a916f0e0a2fcd4dcadcf84dfd8 (commit) via 6227207a85bc7078c5be7985f12def5bac3f8287 (commit) via 3c6b4067162cb45d4e7ac87de102c3c8683d0a5b (commit) via 2f429ef69adf29a1bf0267338e9cecd1fb5b238c (commit) via 3b1c369fabf5039957cb70e0059346c668d0eebf (commit) via c85c2e7c1a8f696987bf232998d8eef09d386b99 (commit) via 4f8079f804337514271581f8a67c750b656f2fbb (commit) via e3c4c532b457c1d83d8ac94e74300e037b757ace (commit) via 6c30ab3e28b74461e5739b1fae84da32b57c8642 (commit) via d79ca1b812618b68d1781fb9ef48651c790f66f0 (commit) via 2a7dbe1527726bfd2bc8d6793a86c59deefc3fdf (commit) via 83a425eb7c3e26118a81096a43c79ffe877b2113 (commit) via ce98747dfef7546f47996405283750bc34c9ad5d (commit) via d200ae2e4a4f8002d6ef527fd7bfa418be477b9c (commit) via 057c8a49f208862ececbcb5c1adeaf0566d89313 (commit) via 9593d16ae241f82c256733f785601e2e0cfb9b29 (commit) via c20839bcb1af30decfbda10a56579a6b43c683be (commit) via dace6c77620134a6d8c643e895a7d94794d97f13 (commit) via 08d9df7e636ea0df65e73df162455c8f47deb448 (commit) via ba353982fb33936c0b6e4c92a14dba221dc08c56 (commit) from bff5e273091c20e062b35677796d4f022e572385 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 69a4206f578e3716755e03e48a082cebd3b0db64 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 21 13:48:19 2016 +0100 Set version to 1.5.1. - MoleCuilder library is now 15:1:0. - Codename "Volleyball" (the 5-1 formation in volleyball has only a single setter with five possible attackers). commit 9ae11c8ffa4dc0d34f93a07bcb120ad35c686947 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 6 23:38:33 2016 +0100 DEBIANFIX: requiring libcodepatterns instead of ..-dev variant. commit 3690e473417f286de3e772d934f7ae47120b763c Merge: d1831e6 62d092e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 2 18:50:29 2016 +0100 Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.1 commit d1831e68610ffad961ff27e9f13c54a4ae810a1d Merge: e387509 b61bd5e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Feb 2 18:50:22 2016 +0100 Merge branch 'Fix_debianpackage' into Candidate_v1.5.1 commit e38750985965a330bae6c625523a373491b95349 Merge: d26fb76 dace6c7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 31 13:47:23 2016 +0100 Merge branch 'Fix_molecuilderguitest_with_valgrind' into Candidate_v1.5.1 commit d26fb7625dde5c4fa08b01ff2fa421d45b545931 Merge: 6a922b1 2f429ef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 31 13:47:12 2016 +0100 Merge branch 'Better_HBondDistances' into Candidate_v1.5.1 commit 6a922b176cac1093a59e5316e5fc5f8b18a99813 Merge: 9a8a6bb e39e7a3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 31 13:47:04 2016 +0100 Merge branch 'Molecule_Enhanced_BoundingBox' into Candidate_v1.5.1 commit 9a8a6bb95a3a7a6f0fa93fc6a5b64041d47de9c7 Merge: 08d9df7 ceaab1d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jan 31 13:46:56 2016 +0100 Merge branch 'AtomAlwaysHasMolecule' into Candidate_v1.5.1 commit e39e7a39013eb9930f8d044d1a2c5297df13da96 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 31 14:38:50 2015 +0200 Implemented more efficient per-molecule bounding box information. - molecule now has internal bimaps to know the extent of itself in a cheap way, right map needs to be multiset_of to allow for non-unique values. - moved BoundingBoxInfo from GLMolObject to molecule. - is itself a Cacheable and is requested from GLMoleculeObject_molecule on new channel BoundingBoxChanged. - Cacheable listens to AtomInserted, AtomRemoved, and AtomMoved. - in molecule::changeAtomId() we also change BoundingBoxSweepingAxis entry. commit e3e52ab3453d1812f2502d0534b424543c3505e8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jan 30 18:46:50 2016 +0100 FIX: BondGraph::Createdjacency compare atoms on position in memory. - this caused every and again failures in tests as an atom with an earlier id might end up at a "later" memory position resulting in flipped positions in e.g. PDB CONECT entries (regression tests molecules remove failed). ----------------------------------------------------------------------- Summary of changes: LinearAlgebra-debug.pc.in | 2 +- MoleCuilder.pc.in | 1 + configure.ac | 56 +++-- debian/changelog | 16 +- debian/control | 18 +- debian/copyright | 2 +- m4/ax_codepatterns.m4 | 14 +- m4/qwt.m4 | 6 + makeDebianPackage.sh | 3 +- src/Actions/AtomAction/AddAction.cpp | 113 ++++++--- src/Actions/AtomAction/AddAction.def | 4 +- src/Actions/AtomAction/SaturateAction.cpp | 2 +- .../AnalyseFragmentationResultsAction.cpp | 40 +++- .../FragmentationAction/FragmentationAction.cpp | 15 +- .../FragmentationAutomationAction.cpp | 8 +- .../FragmentationAutomationAction.def | 11 +- .../WorldAction/SetBoundaryConditionsAction.def | 2 +- src/Atom/atom.cpp | 5 +- src/Element/element.cpp | 4 +- src/Element/elements_db.cpp | 50 ++-- src/Element/unittests/ElementUnitTest.cpp | 4 +- .../Automation/ResultContainer_impl.hpp | 2 +- .../Automation/VMGFragmentController.cpp | 9 +- .../Automation/VMGFragmentController.hpp | 4 +- src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp | 2 +- src/Fragmentation/Exporters/SaturatedBond.cpp | 6 +- src/Fragmentation/Interfragmenter.cpp | 258 ++++++++++++++------- src/Fragmentation/Interfragmenter.hpp | 72 +++++- src/Fragmentation/Makefile.am | 7 - .../Containers/FragmentationLongRangeResults.cpp | 50 +++- .../Containers/FragmentationLongRangeResults.hpp | 19 +- .../Containers/FragmentationShortRangeResults.cpp | 2 +- .../Summation/Containers/MPQCData.hpp | 13 +- .../Summation/Containers/MPQCDataFused.hpp | 4 +- src/Fragmentation/Summation/Containers/VMGData.cpp | 4 +- src/Fragmentation/Summation/Containers/VMGData.hpp | 13 +- .../Summation/Containers/VMGDataFused.hpp | 10 +- .../Summation/Containers/VMGDataMap.hpp | 42 +++- .../Summation/Containers/VMGData_printKeyNames.hpp | 5 +- .../Summation/Converter/DataConverter.hpp | 39 +++- src/Fragmentation/Summation/Makefile.am | 7 - .../Summation/SetValues/FragmentForces.cpp} | 82 ++++--- .../Summation/SetValues/FragmentForces.hpp | 71 ++++++ src/Fragmentation/Summation/SetValues/Makefile.am | 2 + src/Graph/BondGraph.hpp | 12 +- src/Jobs/ChargeSmearer.cpp | 166 +++++++++++++ src/Jobs/ChargeSmearer.hpp | 141 +++++++++++ src/Jobs/InterfaceVMGJob.cpp | 59 +++-- src/Jobs/InterfaceVMGJob.hpp | 6 + src/Jobs/MPQCCommandJob.cpp | 4 +- src/Jobs/Makefile.am | 9 +- src/Jobs/VMGJob.cpp | 8 +- src/Jobs/VMGJob.hpp | 8 +- src/Jobs/WindowGrid_converter.cpp | 61 +++-- src/Jobs/WindowGrid_converter.hpp | 3 +- src/Makefile.am | 2 +- src/Parameters/Specifics/Value_element.cpp | 14 +- src/Parameters/Specifics/Value_elements.cpp | 16 +- src/Parser/MpqcParser.cpp | 13 ++ src/Parser/MpqcParser_Parameters.cpp | 24 ++ src/Parser/MpqcParser_Parameters.hpp | 14 ++ src/Parser/unittests/ParserMpqcUnitTest.cpp | 4 + src/UIElements/CommandLineUI/CommandLineParser.cpp | 4 +- .../Query/ElementCommandLineQuery.cpp | 15 +- .../Query/ElementsCommandLineQuery.cpp | 43 +++- src/UIElements/Makefile.am | 42 +++- src/UIElements/Views/Qt4/Plotting/Makefile.am | 30 ++- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 12 +- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp | 27 +-- src/World.cpp | 2 +- src/controller_MPQCCommandJob.cpp | 2 +- src/molecule.cpp | 113 +++++++-- src/molecule.hpp | 75 ++++++ tests/GuiChecks/atlocal.in | 1 + tests/Python/AllActions/options.dat | 1 + tests/regression/Atoms/Add/post/test.in | 1 + tests/regression/Atoms/Add/post/test.pdb | 2 +- tests/regression/Atoms/Remove/post/test.in | 1 + .../Atoms/Saturate/post/saturated_carbon.xyz | 10 +- .../Atoms/Saturate/post/saturated_nitrogen.xyz | 8 +- tests/regression/Parser/Mpqc/post/doublewater.in | 1 + tests/regression/Parser/Mpqc/post/empty.in | 1 + tests/regression/Parser/Mpqc/post/test.in | 1 + tests/regression/Parser/Mpqc/post/testCLHF.in | 1 + tests/regression/Parser/Mpqc/post/testCLKS.in | 1 + tests/regression/Parser/Mpqc/post/testMBPT2.in | 1 + tests/regression/Parser/Mpqc/post/testMBPT2_R12.in | 1 + tests/regression/Parser/Mpqc/pre/testCLHF.in | 1 + tests/regression/Parser/Mpqc/pre/testCLHF_n.in | 1 + .../Parser/Mpqc/pre/testCLHF_n_ascend_ids.in | 1 + .../Parser/Mpqc/pre/testCLHF_n_mixed_ids.in | 1 + tests/regression/Parser/Mpqc/pre/testCLKS.in | 1 + tests/regression/Parser/Mpqc/pre/testMBPT2.in | 1 + tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in | 1 + tests/regression/Parser/Mpqc/pre/water.in | 1 + .../Parser/SetParameters/Mpqc/post/testCLHF.in | 1 + .../Parser/SetParameters/Mpqc/pre/testCLHF.in | 1 + 97 files changed, 1638 insertions(+), 431 deletions(-) copy src/{Jobs/MPQCJob.cpp => Fragmentation/Summation/SetValues/FragmentForces.cpp} (50%) create mode 100644 src/Fragmentation/Summation/SetValues/FragmentForces.hpp create mode 100644 src/Jobs/ChargeSmearer.cpp create mode 100644 src/Jobs/ChargeSmearer.hpp hooks/post-receive --

1 0

[SCM] branch Fix_QtGUI_crashes_continued created. v1.5.0-250-g0921907
by git＠ins.uni-bonn.de 08 Jan '16

08 Jan '16

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, Fix_QtGUI_crashes_continued has been created at 0921907155034f939032245c16467eaab6889d87 (commit) - Log ----------------------------------------------------------------- commit 0921907155034f939032245c16467eaab6889d87 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 17:05:43 2016 +0100 FIX: GLWorldScene now silently drops atomRemoved on missing molecules. - atomRemoved can never be the first state in the MoleculeMissedStateMap. Hence, we simply drop it. This may happen because moleculeRemoved comes from a different source, namely QtObservedInstanceMap, while the atomRemoved come from the QtObservedMolecule which tends to live longer than said signal. commit ec321804292a97d34bb26587e3fe2b8b1a43e678 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 16:41:41 2016 +0100 tempcommit: no need to check shared_ptr on moleculeInserted, must be valid. commit 2cdcb23f962770ee9cf471544c0581ec4c05a0b8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 15:22:15 2016 +0100 tempcommit: Merge with ee50e14d commit d0b888a94fb428bbcc757e67be14f47893a9fd4a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 15:16:45 2016 +0100 tempcommit: Merge with ac2103d commit 09a6c97709e0408e3e5b3fcc3845937a782b96d5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 14:53:48 2016 +0100 tempcommit: Removed RefCounted..., see e57e681 and d078781 commit ac2103d29beb835e86df5fa9cd9e9d8ef7ac8174 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 14:39:09 2016 +0100 tempcommit: Removed lastmoleculeatomremoved. - this is possible since we only need atomid on atomRemoved and no longer the molecule. commit db61f2172a50d2287def408b81b96a198ebcc4f1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 14:32:28 2016 +0100 tempcommit: Merge with a9ea4c3 commit 9261a183d06b55cb6e1e021c14a69fa520466461 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 14:32:14 2016 +0100 Revert "FIX: QtObservedInstanceBoard needs to allow delayed atomInserted from World." This reverts commit cc163a44c3213da4172f9eac182a2c4b77bb5226. Conflicts: src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp commit a9ea4c30536ba2ff49144db73e6dc0876a0475e3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 8 11:53:41 2016 +0100 All ..Inserted/..Removed signals now go through GLWorldScene. - this should enforce synchronicity of the signals. If we mix direct and queued connections, then this cannot be ensured. - the idea is that GLWorldScene gets all Inserted/Removed signals for atoms and molecules from the QtObservedInstanceBoard. It connects to each QtObservedMolecule and thus can call the GLMoleculeObject_molecule's atomInserted, atomRemoved functions in sequence. - removed RemovalMolecules, no longer needed. - we now enforce with mutexes that instantation of molecule and MissedStateMap do not interfere, i.e. it is always perfectly clear whether to push a signal into the Map or whether to call the function of the present GLMolObj_mol. - FIX: MoleculesInScene_mutex has not been used properly, now is. - DOCU: Updated construct qt-gu documentation with the new concept. commit 8a24dbd9cd64e15defe5cc225390da901df3e7bb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 18:38:35 2016 +0100 Revert "tempcommit: Using DirectConnection for atom/mol&Inserted/Removed in GLWorldScene." This reverts commit aefccd58536b7616bb4e51dd22617a08fb9d891a. commit ddc5e15177eeb38b6816d7443d99dac43176c368 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:55:38 2016 +0100 tempcommit: Merge with efd477f9 commit b21b5f47b6e96b21ee1e8025470f71a1ff4450c4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:52:14 2016 +0100 tempcommit: Making sure that new molecule is not already contained in MoleculesInSceneMap. Merge with ddf19b58 commit a19108d20bd3fc4a565fec5afbac157482a27831 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:51:24 2016 +0100 tempcommit: Moved mutex locking to begin of GLWorldScene's atomInserted. Merge with 338e3a86 commit aefccd58536b7616bb4e51dd22617a08fb9d891a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:50:54 2016 +0100 tempcommit: Using DirectConnection for atom/mol&Inserted/Removed in GLWorldScene. commit cec8e8a3e0446ef39961b9de5e6ea2f42129c310 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:50:07 2016 +0100 DROPME?: Added mutex to GLMoleculeObject_molecule. - this is to ascertain atomic access to atomInserted/..Removed. commit 74c6c813d6b4d2c251dd5c7f74565a85cb8594a8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:48:51 2016 +0100 FIX: GLMoleculeObject_.. does not care whether selection state did not change. - maybe we just got the event too late and actually two changes occured in between. commit efd477f9d8864134247cc14138c659f0776f6671 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 17:47:51 2016 +0100 tempcommit: FIX: indexChanged from QtObserved... transmit both old and new id. Move before 51d0c6 (~1) commit 51d0c644310219d6d5ab884b74596ee6c2139bb3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 13:00:38 2016 +0100 FIX: Making sure that atomInserted is received from same source in GLWorldScene and GLMoleculeObject_molecule. - otherwise we cannot guarantee that the events are processed in order. commit bbb87b0cf45b9a7a6fb0604d92e3ad9cbcaeb399 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 12:49:11 2016 +0100 tempcommit: Merge with ddf19b58 commit 8a9950837f49dee03c8b757d5f974496a247e6db Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 12:34:29 2016 +0100 tempcommit: Cstors of GLMoleculeObject_... now take ref of QtObserved.. - this should avoid a copy. commit fe7089e1ff5861b194ca4c826ab98c39cbd43719 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 11:54:03 2016 +0100 tempcommit: Merge with 2d8c1fd commit 5a566cf1a755228d132e41c20fe04594a6cc29e6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 11:52:41 2016 +0100 tempcommit: Also removed DirectConnection from atomInserted/..Removed in GLWorldScene. commit e9f6499ca33d9ef38769c22f41af92684baeea67 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 11:39:05 2016 +0100 Revert "tempcommit: GLWorldScene parses all signals as DirectConnection." This reverts commit f80eaaea3563b692eaa3e489f4b7061080a67972. commit 2d8c1fde07672454df251161b276fe5f132cff12 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 11:28:10 2016 +0100 QtObserved... now count the subjectKilled() from the containes values. - we no longer loop this through the ObservedValuesContainer. - also initObservedValues() is not longer a static function but now used inside the QtObserved..'s cstor. commit 8843889c1ef190f0a24d3be6ad4380626240a0d4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 10:58:49 2016 +0100 tempcommit: GLWorldScene::moleculeInserted used while loop for unknown reasons. - was this meant to parse one state change after the other? Makes no sense if multiple changes are checked for cancellation and effectively only a single change is treated. commit 7ba8e68ccd5a7bfd8e0c25ed3a021a48ee29a6e5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 10:58:44 2016 +0100 tempcommit: Merge with ddf19b58 commit f80eaaea3563b692eaa3e489f4b7061080a67972 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 10:56:32 2016 +0100 tempcommit: GLWorldScene parses all signals as DirectConnection. - this should rid us of the problem that moleculeInserted is parsed far too late. Some time later me way want to split the function into two parts: one taking the direct connection and preparing the grounds and the latter function instantiating the visual representation, ... commit d6eb80f3130f333ade51f2daf89295d87ee9b6d5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 10:51:58 2016 +0100 FIX: GLWorldScene did not remove all state changes but only last. - we multiple state changes cancelled each other we still only removed the first. This causes more atomRemoved.. than atomInsertedStates. commit bc46986001df9dd2e61d7c4b92fbdcee2c9c0f50 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jan 7 10:50:53 2016 +0100 tempcommit: Forgot to change QtMoleculeList::moleculeInserted slot to QtObservedMolecule::ptr. - this should go with the respective change to QtObservedInstanceBoard. commit ddf19b58d1ac3930b454aa85911320a28cb74550 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 18:34:22 2016 +0100 tempcommit: QtObservedInstanceBoard now sends QtObserved..::ptr around in signals. - this should get rid of the problem that we need to keep the QtObservedAtom until it was requested at least once. And we don't know for how long. Now, we simply place the shared_ptr into the signal (to which it seems to be copied) and hence a representation of the atoms remains valid. commit 3d2e92b0639205634206ea59e81d437de844fffc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 18:33:24 2016 +0100 tempcommit: ObservedValuesContainer::get() returns NULL when not present. commit 284abf83904e93341a889f76dc81e93d76218682 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 18:12:57 2016 +0100 tempcommit: Removed RequestedObjects from ObservedValuesContainer again. - this is no longer needed since we place the QtObserved... into the emitted signal of the QtObservedInstanceBoard. commit a5689ef9efcc1f990761b481837e03460e140369 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 18:11:16 2016 +0100 tempcommit: Combined checks into checkRemoval() in ObservedValuesContainer. commit 454b7a19cf7559fb3da1718904e728cbceba08f1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jan 6 09:36:58 2016 +0100 tempcommit: DOCU: Updated Qt docu. Not complete yet, lacks QtObservedInstanceBoard. commit 95f4a381105b7093a1ac773071f329b66b022f97 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:26:38 2016 +0100 FIX: Added mutex to ObservedValuesContainer to ensure atomic access. commit 5b5d9eb7fb95441ebc7ac69e3ef894dd4bf08282 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:24:44 2016 +0100 tempcommit: QtInfoBox checks whether QtObserved... is not empty instance. commit 9e3be15c587be3531b8a119782b3a1fc410f1057 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:24:10 2016 +0100 tempcommit: QtElementList must not use atom but only QtObservedAtom. commit be638d204a999992573c887e23179a07a1c7630d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:22:56 2016 +0100 CHECK: Don't admonish empty missed states in GLWorldScene? - skipped in subsequent loop anyway. commit 70bf97f94e711c9cf3ababf78189ac26b86394fd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:22:13 2016 +0100 tempcommit: GLMoleculeObject_atom and .._molecule don't get QtObserved... right away. - needs to be checked for empty instance first. commit 3cd9923ab5c1a376ab5d1511e7dffba778f345ac Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:20:13 2016 +0100 CHECK: tempcommit: Removed Cacheable of TesselationHull for GLMoleculeObject_molecule. - this may cause hiccups with the observed instances with the O/O system and makes no sense anyway as it gets updated all the time? commit 5392e2ba062445ba88fb6bed8402ec93ebb52995 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:19:00 2016 +0100 tempcommit: QtMoleculeList must not use QtObservedMolecules in lists but only request them on need. commit dd31d1aa6043ad86163cd7ea9e9952e01c443cc4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 23:17:39 2016 +0100 ObservedValuesContainer now asserts that observedinstance has been requested at least once before deletion. - this should prevent that the observed instance is instantiated and deleted before the signal has gotten through to the GUI. commit 3e46781a8560df24014d0440462f7777ceb2f12f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 16:04:25 2016 +0100 tempcommit: Merge with e57e6813 commit dcc0a282ed0c8e11eb1dc0fb2ce24ce72a95fb0a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jan 5 16:03:41 2016 +0100 tempcommit: Merge with e228f3ba commit e57e6813337f7b23f99230d3a8763799b039d3e8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 19:42:38 2015 +0100 FIX: ObservesValuesContainer uses internal struct for two iterators for observedvalues. - we need these two additional iterators (apart from the deque) in order to step through the created instances one-by-one as they are expected in this manner by the QtGUI which, though lacking behind, is trying to process all the seen events. commit d0787813dd4c36dbc270d9f829d4cc322177168b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 15:28:53 2015 +0100 FIX: ObservedValuesContainer uses deque for internal observed values. - it may happen that an atom is created before the _visual representation_ got destroyed (and hence it's QtObserved... would be destroyed). In that case the QtObservedInstanceBoard fails with an assertion. - Now, we use a deque. At the front end, we have all the observedvalues that have not yet been deleted, on the back end we have the observedvalues to the currently active instance. - removed unused getRefCount(). commit 90e83e6ae3a1184c1604d0f9b57513eccad8fe13 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 13:38:20 2015 +0100 tempcommit: QItemSelection could not be used in signal/slot. Merge with ??? commit b784d8eac83f9216d29184e613c047d2efa0a1d4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 12:14:14 2015 +0100 tempcommit: Merge with ee50e14 commit c9a65da8e53c958bffa0e0dd0301f42580392b3c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:29:50 2015 +0100 tempcommit: Merge with bbb2e1436e commit 47fce732b348206cdd279110b80a200a7d271e7c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:19:37 2015 +0100 tempcommit: SortIndex was introduced someplace else in .._ToFiles. Merge with 425b45f commit f02d8aa8ff32ea14579c73582474fcde3c4f14b7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:19:10 2015 +0100 Deleted MoleculeListClass. - finally ... some veeeery old legacy stuff is gone. commit 06dbd0e6951d9520b418f6a079fdf76d60acc68b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:17:36 2015 +0100 Removed molecules_deprecated from World. commit 425b45f24dca7ce6c8b50b24d4f145f46e2359c1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:16:33 2015 +0100 Replaced MoleculeListClass in ExportGraph by vector of molecules. - AddHydrogenCorrection did never really worked and is dropped (was commented out in .._ToFiles anyway). commit bbb2e1436ea2ce70dc939e56012ce98d8cc9eb32 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:06:45 2015 +0100 Replaced MoleculeListClass in analysis_bonds by vector of molecules. - TESTFIX: also adapted CountBondsUnitTest. commit 625b0bd95fbf61f686957ee83c4892ca4cc2b10a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:06:27 2015 +0100 Removed FindEmbeddingHole which lacked implementation so far. commit efb2ab366300483a625cbd87e9747993161be3a1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 11:02:58 2015 +0100 Removed unnecessary includes of MoleculeListClass and all insert/erase. - this goes along the lines of removing "remove me when we don't need MoleculeCistClass anymore". commit e7747c1446d44bfddbd892647a8c5398fad85ae5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 22:41:30 2015 +0100 FIX: molecule's BoundingBoxSweepingAxis used unordered set of atomids. - this needs to be an ordered set to prevent O(N) access on updating values. commit 32f4221997842b58e97cbb884e3073fda9f1b4ec Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 20:50:22 2015 +0100 Removed molecule's resetFormula() and doCountBonds() and doCountNoNonHydrogen(). - we don't do these as Cacheables anymore. commit ee50e14d4bad15fd8f511e5dc83c51e88ba77ae3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 20:49:43 2015 +0100 Molecule now has maps with old values for bond counts and element number per atom. - this allows to update the total bond count and the formula in an O(N log N) fashion. commit 533acaeb3eaf112a055991697406d5eaec3c0701 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 30 10:27:51 2015 +0100 atom now uses associate... and disassociatedAtomWithMolecule(). - this is used to gather all functions that need to be called when a new atom joins a molecule such as signing on to certain channels or updating certain internal values of the molecule. commit 0e7426222c65c3cb0d9d2fb70f2bd2b89d51f8ab Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 19:54:38 2015 +0100 tempcommit: Merge with 46836ac8 commit 8de4f974c4e1dd56c55f7b30a489931ece3ff288 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 16:10:47 2015 +0100 tempcommit: Merge with 3944f4ad9 commit f6d54548592c9ac4b83a48ec5ccecc80412ddd13 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 15:42:57 2015 +0100 tempcommit: Removed AtomObserverStub. Does not work anymore with extracted EntityObserver? commit e5be5106b616c4190b7d7cdcc891beeb8546803e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 15:25:41 2015 +0100 tempcommit: Forget to change id also for atomInsertionDelayed. Merge with 2df80cf5 commit 7825d1e926534817c504ca4c8d11dd30fcc424fd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 15:25:06 2015 +0100 FIX: We did not check for status of identifier change in QtObservedInstanceBoard. commit 3944f4ad9190b7967cbdad05cab0ce97b751f39e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 15:23:09 2015 +0100 Extracted common code out of Molecule/AtomObserver into EntityObserver. - also all channels are generated as a static vector via boost::assign. commit 68046a88f814a8c567da09151090a56df88f993f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Dec 29 15:22:06 2015 +0100 tempcommit: Merge with d7a4cc7bb1 commit 53f11445f7d82dc3b3c34adbfa7cb78876d243e1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 21:10:33 2015 +0100 tempcommit: Merge with 9bdc30e commit bb0a2b836c413b7275b8a2be7b5d762aedaa6d78 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:24:17 2015 +0100 tempcommit: Merge with d7a4cc7b commit 3d0c8b30610f17285a317080851d9336bdc61c3a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:20:43 2015 +0100 Removed QtSelectionChangedAgent. - it is no longer used. We either listen to molecule/atom's selection changes directly or to all of them via the respective relay, i.e. MoleculeObserver. commit 9cee1c7bc51140782c0a5d355943042911f0b292 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:20:00 2015 +0100 tempcommit: Merge with 7d9de99 commit 46836ac8075ec7699d17d0c1af39aacd924ea26c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:14:32 2015 +0100 Removed QtSelectionAgent usage in QtMoleculeListView. - instead we subscribe to MoleculeObserver directly. commit e3bfff68f39c14624901c6d26cfced4402cdc58a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 20:04:29 2015 +0100 tempcommit: Merge with 54dba3bc - its unit test now has NotifactionObservers for all AtomObservable's channels. commit 7d9de99be2b7eed95bb9b49405f5b170f5accd37 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 18:12:08 2015 +0100 Removed QtSelectionUsage in GLWorldView and related. - instead GLMoleculeObject_.. directly use observedvalue to get notified when they have been (un)selected. commit d7a4cc7bb19e3e42672d55790eee6563fff79a23 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 16:10:47 2015 +0100 Added MoleculeObserver as pendant to AtomObserver for molecules. commit 54dba3bcb986874a7f6ca5eccedfc0a7e758a25d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 16:09:49 2015 +0100 FIX: AtomObserver was not up-to-date with respect to atom's channels. commit 35ef43cb741160b28ec2e458e97d57564e410ddc Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 13:55:00 2015 +0100 tempcommit: Merge with 1e7b36c8 commit 2c83658e75c3ce622f50c1f73966a442b120426d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 12:43:34 2015 +0100 Added ObservedValue for selection status of atoms and molecules to QtObserved... commit 1e7b36c893acbf9ca5ad6c4be72fd5abf3798193 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 12:43:28 2015 +0100 tempcommit: Added getSelected(). Merge with e6b6869 commit d3e4fe624daf76b20b270e668cfe6a53ee77cc50 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 11:27:48 2015 +0100 tempcommit: Merge with 35263d2 commit de786b0a29b35bec4e79ade66a20736483a881c0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 11:27:31 2015 +0100 tempcommit: Merge with e6b68698 commit 35263d2f4d8f8ad0c81e4594cbb854e3b99f6a63 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:28:10 2015 +0100 Added template functions to (un)set vector of instances in a row. commit e6b68698280450e664581a05840810e4b7502c28 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:18:42 2015 +0100 Added select() and unselect() functions to atom and molecule, also SelectionChanged channel. - this allows for more specific selection changs to be signalled. - this extends the current World's SelectionChanged channel that informs about selection changes by a more fine-grained/instance-specific change signalling. commit b49bd2dbdcea884a28bcc4ced55601791976e169 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 28 07:15:14 2015 +0100 Removed molecule's AboutToBeRemoved channel. commit 9bdc30ea6b9d1015f27cfea2d815b9c05b7657e1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 27 22:08:26 2015 +0100 FIX: Fixed wrong paths for adjacency and trianglematcher in regression and GuiChecks tests. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch Fix_QtGui_Testmode_not_showing_atoms updated. v1.5.0-165-ga35ec4c
by git＠ins.uni-bonn.de 18 Dec '15

18 Dec '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 "". The branch, Fix_QtGui_Testmode_not_showing_atoms has been updated via a35ec4c8e5faf96b7ba725efe7b25ad23853df09 (commit) via cc163a44c3213da4172f9eac182a2c4b77bb5226 (commit) via 6a366d88afe5d51f42e39e081d50d1ec7d62f442 (commit) via 9bdf8f710bd3dee90258ea0c6be46f9f82019da0 (commit) via 66af5c7f14336bb1bf7843eb9d2d058e05db3402 (commit) via 3789e5d955cbaf2a86326e41a3e54348b9cdc57a (commit) via fbe233acd73d4ac19771827a192112c7c0762cbf (commit) via 909b3019f6d522d645d5b5db7768a9c4274e6f19 (commit) via ec10453d494606aa5bc3c427760d44e3c563ef66 (commit) via dd2912c01d2770a1765d392c822480ed5c29ce42 (commit) via 2d2e8b0da3370a1f5f651826d4036bf0ae396df4 (commit) via 8c00fadd6b2922050417f3542335475c30f6e425 (commit) via d19c12eb09c6037d099d3a65e707db0070ad8597 (commit) via d640e59ff241b76b4166fc9f82aa877899d3bec3 (commit) via 6d21ce0aa38039fbc7559e86c69aab704600ebe5 (commit) via e4b7df4922b60b752fca67cf2a0fbb1a45c77482 (commit) from 65a73184853e7894f8c1ba485eb4be5aeadc8673 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit a35ec4c8e5faf96b7ba725efe7b25ad23853df09 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Dec 14 10:57:37 2015 +0100 MODIFYME: World's ObservedContainer no longer observe. - TODO: This requires CodePatterns 1.3.1 but we haven't changed the version there, yet. - I had misunderstood what Till had planed with these ObservedContainers for a long time: I though they would cause an OBSERVE signal for every iterator step but this is not the case. Rather they accumulate all OBSERVE signals to have them fire AFTER the loop is done. This is achieved through the depth count of the observer protectors. - Sadly, this runs against what we do with the lastchangedatom. We need the information right away as we the Observer/Observable stuff does not transport any information and always updating all is way too costly. - Hence, in CodePatterns we have implemented an UnobservedIterator which is used in ObservedContainer and does not cause any OBSERVE signals. - The source of the problem was createAtom() in a loop over selectedAtoms and these atoms not getting created (w.r.t QtInstanceBoard) before the molecule's got note of it (cause they are at depth 1). commit cc163a44c3213da4172f9eac182a2c4b77bb5226 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 17:06:18 2015 +0100 FIX: QtObservedInstanceBoard needs to allow delayed atomInserted from World. - we may get the notification from molecule before we get the insertion from the World. Hence, we store any ids obtained from molecule insertion if the set of the new atom's observed values have not been generated yet. commit 6a366d88afe5d51f42e39e081d50d1ec7d62f442 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 16:19:00 2015 +0100 tempcommit: Merge with b775b7ab commit 9bdf8f710bd3dee90258ea0c6be46f9f82019da0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 16:18:44 2015 +0100 tempcommit: Merge with 8c00fadd commit 66af5c7f14336bb1bf7843eb9d2d058e05db3402 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 16:18:06 2015 +0100 tempcommit: Merge with d19c12eb commit 3789e5d955cbaf2a86326e41a3e54348b9cdc57a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 16:17:54 2015 +0100 tempcommit: Merge with 08f75432 commit fbe233acd73d4ac19771827a192112c7c0762cbf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 16:16:32 2015 +0100 tempcommit: Merge with 6d21ce0 commit 909b3019f6d522d645d5b5db7768a9c4274e6f19 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 16:16:25 2015 +0100 tempcommit: Merge with 2f158c56 commit ec10453d494606aa5bc3c427760d44e3c563ef66 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 16:14:13 2015 +0100 tempcommit: Merge with 6d21ce0 commit dd2912c01d2770a1765d392c822480ed5c29ce42 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:22:39 2015 +0100 tempcommit: QtInfoBox disconnects signals. commit 2d2e8b0da3370a1f5f651826d4036bf0ae396df4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:22:16 2015 +0100 TEMP: Decreased waiting times in QtGUI's test mode. commit 8c00fadd6b2922050417f3542335475c30f6e425 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:22:06 2015 +0100 tempcommit: Merge with ad571e28 commit d19c12eb09c6037d099d3a65e707db0070ad8597 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:21:45 2015 +0100 tempcommit: Merge with 5a7b4a23 commit d640e59ff241b76b4166fc9f82aa877899d3bec3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:19:45 2015 +0100 tempcommit: QtObservedAtom::recieveNotification wrongly checked cast to atom. Merge with 92a780aa commit 6d21ce0aa38039fbc7559e86c69aab704600ebe5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 13 15:15:58 2015 +0100 FIX: ObservedValue need to be removed with a bit of delay. - ObservedValue has higher priority than e.g. QtObservedAtom. Hence, will also receive subjectKilled() before QtObservedAtom does. But right after all of these are received(), ObservedValueContainer will remove the instance which drops the shared ptr's count to zero (because Observer/Observables do not store shared_ptr but only ptrs!) and its dstor is called. Therefore, QtObservedAtom cannot access the ObservedValue any longer and this is against how the design was meant to be (ObservedValue lives at least as long as respective side in Qt needs access to its information). commit e4b7df4922b60b752fca67cf2a0fbb1a45c77482 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Dec 12 09:05:38 2015 +0100 Revert "Revert "DROPME: Removed logging into QtLogBox for debugging."" This reverts commit 73fcc4d0eb85a7339453cb79a5421a0bd595b392. ----------------------------------------------------------------------- Summary of changes: .../Qt4/InstanceBoard/ObservedValuesContainer.hpp | 25 +++++++- .../InstanceBoard/ObservedValuesContainer_impl.hpp | 62 +++++++++++++++++--- .../Qt4/InstanceBoard/QtObservedAtom.cpp | 66 +++++++++++----------- .../Qt4/InstanceBoard/QtObservedInstanceBoard.cpp | 39 +++++++++++-- .../Qt4/InstanceBoard/QtObservedInstanceBoard.hpp | 6 ++ .../Qt4/InstanceBoard/QtObservedMolecule.cpp | 12 ++-- src/UIElements/Qt4/QtUIFactory.cpp | 6 +- src/UIElements/Views/Qt4/QtInfoBox.cpp | 2 + src/UIElements/Views/Qt4/QtInfoBox.hpp | 6 ++ src/UIElements/Views/Qt4/QtLogBox.cpp | 4 +- src/UIElements/Views/Qt4/QtLogBox.hpp | 2 +- src/World.cpp | 4 +- src/World.hpp | 4 +- 13 files changed, 173 insertions(+), 65 deletions(-) hooks/post-receive --

1 0

[SCM] branch Fix_QtGui_Testmode_not_showing_atoms created. v1.5.0-149-g65a7318
by git＠ins.uni-bonn.de 31 Oct '15

31 Oct '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 "". The branch, Fix_QtGui_Testmode_not_showing_atoms has been created at 65a73184853e7894f8c1ba485eb4be5aeadc8673 (commit) - Log ----------------------------------------------------------------- commit 65a73184853e7894f8c1ba485eb4be5aeadc8673 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 19:56:03 2015 +0100 Revert "Added mutex to QtObservedInstanceBoard." This reverts commit d6047811a42782cb37d49830bc6e17d3b3344f68. commit 9f3f9e56a581dc70fb89d4d5c805a1b9133fa9b1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 19:55:42 2015 +0100 Revert "tempcommit: QtObservedInstanceBoard uses mutex only for subjectKilled(). Merge with d6047811" This reverts commit 039eb1d53b41317c75d39a6563658582140d83d2. commit 039eb1d53b41317c75d39a6563658582140d83d2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 18:43:21 2015 +0100 tempcommit: QtObservedInstanceBoard uses mutex only for subjectKilled(). Merge with d6047811 commit 08f75432db31263ed75f1e0313881f79ad1d3669 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:41:51 2015 +0100 tempcommit: Merge with e228f3 commit 1832dcfa09ffeb5afd0995ea16cd9f9184e55c80 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:26:57 2015 +0100 tempcommit: Merge with 5aa1f2b7 commit 8d7fd984e57ad3b7f731ae516575b5d5d6c07f11 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:18:41 2015 +0100 tempcommit: Merge with e228f3 commit d6047811a42782cb37d49830bc6e17d3b3344f68 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:17:46 2015 +0100 Added mutex to QtObservedInstanceBoard. commit e228f3ba9206ecc217c85ae73ee38e5d4c708fc5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:15:30 2015 +0100 TODO: QtObservedAtom, ..Molecule, and ObservedValue_wCallback have flag to indicate invalid callback. - due to Qt's signal/slot destruction, which follows no proper order, we need to invalidate callback when their owners are destroyed. Each has a note-function() that flips the boolean to show the callbacks invalidity. - TODO: So far this is not nice, especially w.r.t to ObservedValue_wCallback because of templatization. We cannot place them in a loop and this makes this very error-prone once more Values are added ... commit d96f9a55c651a1c31a14cdd2b670739c244a4ef2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:14:57 2015 +0100 tempcommit: Need to split signedOn maps for atoms and molecule due to different number of channels. Merge with ...? commit dc05d81bfe40be3c1ebfc4fec8f0305adce08217 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:13:33 2015 +0100 tempcommit: merge with eda203c3 commit b47afb72fab6df9dcd5f84cae5ac3d29800413bf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 17:07:39 2015 +0100 FIX: Qt's parent properly set from QtMainWindow's point of view. commit 73fcc4d0eb85a7339453cb79a5421a0bd595b392 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 16:58:50 2015 +0100 Revert "DROPME: Removed logging into QtLogBox for debugging." This reverts commit 57b9cd365da71ff1d62c3ce6c112e331b086289f. commit 6e03cac48ca5729cfedfe279432bada76497baf6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 15:14:07 2015 +0100 tempcommit: merge with a8c9551b commit eda203c3214c9cbf233c4820cd727a0f39a8d658 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 15:07:55 2015 +0100 tempcommit: Equipped QtInfoBox with mutex and split clearTabs(). - this avoids a memory corruption with signal/slots as the first atomRemoved() signal also removes the molecule and hence the QtObservedMolecule ptr who is the recipient of the subsequent moleculeRemoved() signal. commit e54456aae6e9d661d577a0d9c7f05cef7b339b51 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 15:07:41 2015 +0100 tempcommit: merge with 70c61bd4+ commit 571fcbfee2a325e073fcd5a0547bb3ade866c384 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:54:29 2015 +0100 FIX: All ObservedValue getters now return const references. - this should avoid some unnecessary copying. commit 271060fcd1c1de868a06b88d8f1e34baece52521 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:36:21 2015 +0100 FIX: molecuilder.py is now loaded after GUI is done initializing. - otherwise consequences of loaded session (atoms, ...) are not displayed. - originally, this was done on purpose as it is quicker to just load stuff into the world and then tell the GUI to show what's there. However, now, due to constraints with different threads, this is no longer possible. commit 95a757bd9e1a5660ed590dc64a0503195ee32596 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:35:53 2015 +0100 tempcommit: Merge with 7a8832d4 commit 12ecc9a464e868e2095278c8287986ee5b0f9b4d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:06:30 2015 +0100 QtInfoBox now obtains information completely from QtObservedInstanceBoard and ObservedValues. commit 785fde32fe13558ebf6870591ef8b9152f0a93bf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 12:06:14 2015 +0100 tempcommit: merge with 7a8832d4 commit 5aa1f2b7ccecfee7e1238002ab0885590c9d3791 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 11:49:06 2015 +0100 xtended QtObservedMolecule by Center, NonHydrogenCount, and BondCount. - added Cacheable MoleculeCenter to molecule which is cleverly updated. commit 7a8832d4d20ecc2d2ff1aed5d2ca5f66be24695a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 11:48:16 2015 +0100 Extended QtObservedAtom by Name and Molecule. - added extra signal MoleculeChaned to AtomObservable. commit 834ff2cd2cd7749afa723eb22f681f2722b342ff Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 30 00:11:39 2015 +0100 tempcommit: Merge with 087563d29 commit abc9ea4cdbe2032f5fe794618b80a6a7d9513b91 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 23:52:15 2015 +0100 tempcommit: merge with 74d1bd0 commit 087563d292ebfaff5e237b4898d8a1fce4023cdb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 23:22:53 2015 +0100 QtMoleculeList takes InstanceBoard and listens to its molecule signals. commit 74d1bd00b1401eb63c10b46a6a2b67f7132db9f4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 23:21:30 2015 +0100 All QtMoleculeItem now heed QtObservedMolecule. - QtMoleculeItems no longer use Observer/Observable but get updates via signal/slot from QtObservedMolecule. commit 6356a6059f318b7bd416858a363d7a283b456aa1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 22:55:51 2015 +0100 Added AtomCount and FormulaChanged to QtObservedMolecule. commit 3b881145335c6ff16050bf12b91a96fe28d29684 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 19:45:46 2015 +0100 tempcommit: merge with 1c293cec commit 672945f5568c3592c37bee33145d3a62a7d0e091 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 19:45:22 2015 +0100 tempcommit: merge with 0fb2d3c3 commit 7d8b8b43517de6849f3bb430ad05db0059e990c6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 19:38:02 2015 +0100 FIX: ObservedValue_wCallback needs to call callback() only on last channel's signOff(). commit 0fb2d3c39f1eab131b6ee8cfcc9fca9f9f7ced38 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 19:31:07 2015 +0100 Revert "QtObserved..::AllSignedOnChannels is needed statically." This reverts commit 080cc49c388944e7782fa8e00e79b58a16b75974. commit 8bc85f6767371493ec33741f717bb09f9d89fbde Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 19:30:33 2015 +0100 tempcommit: Merge with 70c61bd4 commit a345227a313fe74b7e6b9f511ca909664fe97b2a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 17:22:46 2015 +0100 tempcommit: Merge with a8c9551b commit 9e007daf870bfbcf45ef770c4621e818439e3585 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 17:20:24 2015 +0100 tempcommit: Fixing signals of QtObservedMolecule. Check and merge with 92a780a commit 6c6d3c2df81a2c98c86f7475b5131dc955d5187c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 17:17:34 2015 +0100 tempcommit: activateObserver needs to be called after insertion into ObservedValuesContainer. Merge with c0943f48 commit 9881c3b93ce026abf818cdb1eb54905ac2bd65f2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 17:16:49 2015 +0100 tempcommit: Added again check on lastremoved.. to InstanceBoard. commit 080cc49c388944e7782fa8e00e79b58a16b75974 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 17:15:40 2015 +0100 QtObserved..::AllSignedOnChannels is needed statically. - this is used to check whether all ObservedValues already had their subjectKilled() called. commit b775b7ab9e68e656ce1078acbca5bd80429d9829 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 16:26:13 2015 +0100 tempcommit: Merge with ad571e28 commit f50b98a0d968216c12648ab5b3d71845dc55df6c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 16:26:02 2015 +0100 tempcommit: Merge with 5a7b4a23 commit 8b16324d3cf9be7dbdf92a601c4c3a67c3297b0d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 16:24:15 2015 +0100 tempcommit: Merge with c0943f48 commit ad571e284a59bf54e939d7a4a3025466f30381f5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 16:23:18 2015 +0100 tempcommit: Merge with a8c9551b commit 5a7b4a23d77105c2b2ad6d3cf83663c33cd8834a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 16:22:44 2015 +0100 tempcommit: Merge with 92a780aa commit 70c61bd41e1e139d3f3e552ed794aa741c736325 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 16:12:34 2015 +0100 No more ObservedValues_t from QtObservedInstanceBoard. - we now work with QtObserved..::ptr directly everywhere. commit 89a166473561b51e254c1cb815611d71c4726d11 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 15:46:17 2015 +0100 tempcommit: merge with e6d34be3 commit c0943f48129c534587407d263d59cb56aa9a836d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 15:41:13 2015 +0100 ObservedValuesContainer now stores QtObserved.. instances directly. - we need this as QtObservedAtom and ..Molecule must signOn() to World's instance right away. If later requests to ObservedValuesContainer::get() cause new signOn()s, then these might fail. commit e6d34be30f840209719f7a0075f29dfbbca6529c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 15:02:35 2015 +0100 Moved countSubjectKilled related code from QtObservedInstanceBoard into ObservedValuesContainer. - this avoids some more duplicated code. commit a8c9551b45087863cb04b87bdf54ffd64ded6f08 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 13:52:29 2015 +0100 Extracted all ObservedValue functionality out of GLMoleculeObject_molecule. - see previous commit for explanations. commit 92a780aa795996a1d3bd79a2083b2794115b3782 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 11:46:45 2015 +0100 Extracted all ObservedValue functionality out of GLMoleculeObject_atom. - i.e. GLMoleculeObject_atom is reduced to simple displaying, updated via Qt signals. These signals are connected to a QtObservedAtom which in turn now contains all the ObservedValue functionality. - this is preparatory for having a single (Observed)Atom as representer of its associated World's atom in the QtGui part of the code. commit 2f158c56623234be6ebfbc278761bd440773f715 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 29 10:52:10 2015 +0100 Extracted functions handling refcounting of ObservedValues into ObservedValuesContainer. - this avoids a lot of code duplication. commit 76d18f39134465d8a544751f9e36f6cc11e3cbed Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:57:10 2015 +0100 Added rudimentary getter and returner for ObservedAtom/..Molecule() to InstanceBoard. commit 6a50bb20ea7ea1b24f4ffac1990bc37d9078d426 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:24:10 2015 +0100 Added QtObservedAtom and ..Molecule() instances. commit 1c293cecf80bebccd7bd90664c05f0aae700e3c9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 14:23:09 2015 +0100 Moved and renamed QtInstanceInformationBoard -> QtObservedInstanceBoard. - this is preparatory for adding ObservedAtom and ObservedMolecule classes that combine all observed information on either type. commit 066f19447803d0bf7000ac80c17ecbfe55c290e0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 13:09:43 2015 +0100 AddAction and UndoRedoHelpers' AddAtomsFromAtomicInfo use recreate..(). commit a869e049c07be3cf8a6950d3b1bf73b71c6cdf7a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 13:08:04 2015 +0100 Added recreateAtom() and recreateMolecule() to World. - in order to overcome problems with Qt signals being delayed so much that in between sending and receiving the id of a newly instantiated atom has changed, we need to set the right id (after undo/redo commands) right away. For this, these two new functions are well-suited. commit e8cb76a185c93938c78d43387229180d20fe6e07 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 10:20:53 2015 +0100 GLMoleculeObject_molecule does not listen directly to molecule::AtomInserted/Removed. - this is done by QtInstanceInformationBoard instead. commit 0e8af80722e2f47e6b65e77c8cb0ad1abc12b91d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 10:20:09 2015 +0100 QtInstanceInformationBoard has now unique maps for either set of ObservedValues. commit 97bb26d4907d865970184db65245b6070b7da9d7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 28 10:13:15 2015 +0100 FIX: GLMoleculeObject_atom and .._molecule need to account for multiple subjectKilled(), one per channel. commit 338e3a86a7595d963f667cbaef3c44f38063e4e1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 20:51:05 2015 +0200 Revert "tempcommit: Removed a lot of now unused signal/slots from World, Scene and _molecule." This reverts commit 61b8538c5cad80c1af7db190009b1406dcb696f9. Conflicts: src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp - readded MissedStateMap in GLWorldScene. commit 9d7f587da43870b91b2e6990586cb2c461b42126 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 20:28:45 2015 +0200 tempcommit: QtInstanceInformationBoard informs about AtomRemoved, AtomInserted via molecule. commit 7547a3be8fd2121c65b2ddeb5df6d377924c8cfa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 20:28:23 2015 +0200 tempcommit: Selection uses direct connection. commit 4445f7735e8e685a8e8b404e73ce91f85bda383f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 20:27:50 2015 +0200 tempcommit: Removed resetAtoms() and PresentAtoms from GLMoleculeObject_molecule. - this information must come from instanceboard. commit 4c6952672301696fa7fc10a169afa9a97e67fc2c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 19:20:40 2015 +0200 QtInstanceInformationBoard also informs about index changes. commit 2b65b4846cdb14011409001d8870719c72973a77 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 19:20:13 2015 +0200 tempcommit: GLMoleculeObject_atom uses resetBonds() to add initial bonds. commit e962bf24ac918adb591a550e600008d9efa4ccfa Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 18:48:19 2015 +0200 tempcommit: .._atom and .._molecule now return ObservedValue to QtInstanceInformationBoard. - this way we can transfer these from one GLMoleculeObject_atom to another. commit 61b8538c5cad80c1af7db190009b1406dcb696f9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 18:47:31 2015 +0200 tempcommit: Removed a lot of now unused signal/slots from World, Scene and _molecule. - basically all replaced by QtInstanceInformationBoard connections. commit 58737c96ffae94195696088c0a78976c1aaa8451 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 18:46:36 2015 +0200 tempcommit: Removed countSubjectKilled() and deprecator cstors from .._molecule. commit dc5c8f72db61ba5a149ede2a997a1a3c40528e63 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 18:45:21 2015 +0200 tempcommit: Removed countSubjectKilled() and deprecated cstors from .._atom. commit 8fd310cf6a723b7458fb7aa2e46c971fb3cefb7a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 18:03:53 2015 +0200 tempcommit: QtInstanceInformationBoard signOn maps need to store ref, not id. Merge with ... - we cannot access atom's id as only AtomObservable is left. commit 664d3ee7336ae4219f5826083bc628b676796504 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:21:37 2015 +0200 tempcommit: not using const ref in binding updateBoundingBox() for molecule. commit 57b9cd365da71ff1d62c3ce6c112e331b086289f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:21:16 2015 +0200 DROPME: Removed logging into QtLogBox for debugging. commit 9e0a33ac8bdd6947c0a04fd73187cea4b68a2722 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:20:56 2015 +0200 tempcommit: Additions to DROPME: debugging output. Merge with ... commit ca20d7b996c43666281013354bd200c6451dea86 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:20:34 2015 +0200 tempcommit: Fixes to QtInstanceInformationBoard. Merge with ... commit 2a1fa1f4859c41480232bbf66ef1af0a0031927b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:19:46 2015 +0200 tempcommit: Merge with e84e2c80 commit d77744bf3b3c4edca89a7d4346166d0e9fcd01e4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:18:13 2015 +0200 DROPME: Added debugging output to QtInstanceInformationBoard. commit 72cd6215eed6def5c3c4d89e5df800e7684d088f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:17:43 2015 +0200 FIX: QtInfoBox only updatePage() when ref still present (no subjectKilled() yet). commit e0ff31fa724d04612bcaa4b652b1bfbb80ba9ad1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:17:19 2015 +0200 tempcommit: resetTesselationHull() only called when owner still present. commit 44d90cfbf4c0582186c8158941c0d02978b92f08 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:16:53 2015 +0200 Changed connections between GLWorldScene, GLWorldView and GLMoleculeObject_molecule. commit ce326e15d9e99bbab30b4772cb336a3c5d2fa7a7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:16:30 2015 +0200 GLMoleculeObject_atom, _bond, _molecule all use QtInstanceInformationBoard passed via GLWorldScene. commit a7a81684ba0cf49e1bd43c0272a542de73424dce Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:13:14 2015 +0200 FIX: QtMoleculeItem not signing off after subjectKilled(). commit 36f72a26eff131507efec4b9d4668ab086fd7d8a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 23 17:12:42 2015 +0200 tempcommit: QtInstanceBoard lifetime managed by parent QtMainWindow. Merge with ... commit 1c50baf9829a26f204938f7c6f0db62ccf17c719 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 21:46:52 2015 +0200 tempcommit: Replaced connections GLWorldView with QtInstanceInformationBoard. commit bf1de432c42165753bd9c996bd2b5e4b5cfb6205 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 21:08:44 2015 +0200 tempcommit: Enhanced ObservedValue_wCallback to take a bound getIndex function(). - additionally, we route internally to ObservedValue::get() and this gets us out of the painful situation where we need to supply an index getter to the ObservedValue that monitors the index (and hence must be present already to bind to its get function). commit e84e2c80597cedd0d64825fb5cef8b951359c789 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 19:03:48 2015 +0200 tempcommit: Final version of QtInstanceInformationBoard. commit cc861e0f1fcce8aaf29d231e672495d718a48949 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 19:01:09 2015 +0200 Changed GLMoleculeObject_...:countSubjectKilled() to taking id parameter. - this is a precursor for when the ObservedValues reside with QtInstanceInformationBoard. commit 57d3ae2e8eb2070b76bae18e2b6c05b89b6cf2c4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 18:59:19 2015 +0200 tempcommit: Merge with f6e0c328 commit 0a0cbe536dd01a4864f68d9b4cb39942f20c4ff1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 18:58:32 2015 +0200 tempcommit: Merge with 96d38bf commit 33bdeff78e8289331e8eea760bb818e6fd13ab17 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 18:57:48 2015 +0200 tempcommit: Merge with af7a33c5 commit 59c1c6f8b33a2deceab5c6d8263f5e9fd8744c9f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 18:47:35 2015 +0200 temcommit: Merge with f6e0c328 commit 2683c18da13ba37c11a576121ca65c72bfa4944a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 17:42:17 2015 +0200 Added QtInstanceInformationBoard that handles ObservedValues through the QtGui interface. - this is meant as a instantiator of all ObservedValue's needed by QtGui for representing information from the World. The ObservedValue's are instantiated separately w.r.t. to the instance for the visual representation. This is light-weight and can be performed in the same thread, while the visual representation's instantiation can be done elsewhere and there we just need to access the ready ObservedValue's that exist as long as they are needed by the QtGui. commit 085a87610d66db8fb9e578b0a11501791051478c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 17:41:24 2015 +0200 tempcommit: Merge with f6e0c328 commit ed08e1426da5dcaaf57c69953f8349e21fe4999f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 17:41:01 2015 +0200 tempcommit: Merge with af7a33c5f commit 96d38bfd524a4e0eaa1d48ca99c0bb32673fcf61 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 15:28:19 2015 +0200 GLMoleculeObject_bond's ObservedValues is now all static. - again, the same change as with .._molecule and .._atom. commit af7a33c5f26d7efcc83ad69bd3f59333751ca04e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:55:30 2015 +0200 GLMoleculeObject_atom's ObservedValues is now all static. - this is equivalent to the changes to GLMoleculeObject_molecule. commit e9c2370056ed4e15d17f470f44487b1b4300be62 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:42:13 2015 +0200 FIX: World needs to first destroy the molecule, then release its ids. - this is similar to the change for the atom. commit f6e0c32812b93f7790837a0e033ab7be689ede42 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:40:14 2015 +0200 GLMoleculeObject_molecule's ObservedValues is now all static. - this is preparatory for extracting their instantation to an external class InstanceInformationBoard that keeps track of the lives of instances in the World that are needed inside QtGui (e.g. for visual representation). commit 190990ab5eb8412c3ce3d49cbdde37d18de10e19 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 14:18:30 2015 +0200 FIX: GLMoleculeObject_molecule::updateAtoms() used DisplayAtoms directly. - we need an old and a new set, i.e. the difference needs to be discernable between updates. However, so far we updated the old set directly, too. commit c6f7d851f7c828041d233968209abd07c53b0eb2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 17 11:09:07 2015 +0200 DROPME: Switching to log tab in worldTab for test-single. commit cfcbd701acc2c2d72b56189edae70c870bce4819 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 21:48:20 2015 +0200 FIX: World::destroy..() did not emit SelectionChanged signal. commit 01ee257b96b3aa8d62e48dfae817ae0ab653c9c7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 13:51:16 2015 +0200 FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule wrapped into vector. - the idea is that a GLMoleculeObject may only remove itself _after_ each and every contained Observer has gotten the subjectKilled() signal from the Observables. Only then will destroying the Object and its members thereby not cause any signOff() which try to access Observables or their channels which are no longer present. This can be imagined as a graph where we have to start destroying object at the very bottom. - This is the avoid the following conflict: A superior object gets note of a molecule to be removed. It sends the visual representation a signal to remove itself, which causes it to use signOff(). On a parallel track (in another thread) we have the observed object calling subjectKilled() to inform any Observer about its immediate destruction. These two tracks collide. Now, we let first pass all subjectKilled() and when the last Observable has gotten its signal, we begin destroying the visual rep. - rerouted signal/slots accordingly. commit d0225f4933595168bf533fabce90f7d419db754a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:59:22 2015 +0200 FIX: GLMoleculeObject_molecule::subjectKilled() should not call deactivateObserver(). - we just take note that we are signedOff. commit 568a2ce22f8ef6124b26c0e1d410ebc7af6cff91 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:58:31 2015 +0200 FIX: GLWorldScene has additional moleculePrepared... slots and signals. - i.e. we first insert into MoleculesInMap via direct connection and then signal is emitted (queued) to construct the actual GLMoleculeObject_molecule. commit 5e96c742ba17709d74218898f5f708dbbf5228bb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 16 10:56:48 2015 +0200 FIX: GLMoleculeObject_molecule still contained hack to get upper bound on molecule's bounding box. - we don't longer need the hack as we have the molecule cleverly updating the box and an ObservedValue. commit d9ca9621d208e1af1fdaf75e5e2c1b5022e8e459 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 15 11:08:37 2015 +0200 QtFavoriteActions uses ObservedValue for checking last queued action's name. commit 35ccc012ef350e6eb15b273b40f361af989bc6ae Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 15 11:08:09 2015 +0200 tempcommit: FIX: ActionQueue was setting lastchangedaction twice. Put into Fix_ActionQueue... branch commit f7a37da6c306abfadb52abc833485cdeedf65874 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Oct 14 11:18:05 2015 +0200 FIX: Fitting domain to window on QtMainWindow's init. commit 405dc5ea68d53a7ed220e143bb0dfe7082866028 Merge: 14a618b 62d092e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 13 22:14:45 2015 +0200 Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.2 commit 62d092e08dbdb67e4f00547587c38322bf8bb828 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 9 00:12:20 2015 +0200 Rewrote ChargeSmearer to use visitor pattern. - this is used for going over the bspline domain. - we need it when the support does not fit onto grid and when we need to recalculate the normalization. commit 17e4fde191dda907bf7bd206803886c13e02d440 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 7 21:03:37 2015 +0200 Added new option DoSmearElectronicCharges to FragmentationAutomationAction. - this uses ChargeSmearer: is prepared in InterfaceVMGJob and used in WindowGrid_converter. - VMGJob and VMGFragmentController need to pass along the DoSmearCharges option from the command-line. commit 445ce6d3846182eaf130a6a73ea863d0a443e6f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 7 08:25:28 2015 +0200 Modified WindowGrid_converter::addWindowOntoGrid(): first reset, then write values. - this is required for smearing electronic charge distributions as we then write also neighboring values. commit cceb8cfe148cf346613694b5f15bde9f95e63393 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 2 11:16:58 2015 +0200 Added ChargeSmearer that is only compiled for CONDVMG. - we store the spline values in a singleton such that they are calculated only once. commit 92232f71902106c7de16c1208aa802471f88fbb1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 11 16:14:00 2015 +0200 Adding warning when inter-distance is given less then minimum required rcut. commit cee9e8b8d814bc0aaefacaf9bdc81d5ca2f2876b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 1 15:47:28 2015 +0200 Added Interfragmenter::findLargestCutoff() to find largest Rcut not causing additional inter-fragments. - so far, the function is only used in FragmentationAction by merely printing the distance. commit b1c5f46c2e8356c3a5cb7319f77fe3e21793f787 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 1 15:46:05 2015 +0200 Interfragmenter now combines two fragments up to (in sum) till MaxOrder. - before only fragments of each MaxOrder were allowed, now the sum of their bond order must not exceed maxOrder, i.e. MaxOrder of 4 means 1+1, 1+2, 1+3, 2+2, 3+1, 2+1, 1+1 (with order of left and right fragment that are joined). commit 0d90534c2cfcca7121d5161e6f235225bdb4c0df Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 1 10:31:54 2015 +0200 Exracted several functions out of Interfragmenter::operator(). - extracted Interfragmenter::getAtomKeysetMap(), ::getNeighborsOutsideMolecule(), ::getAtomSpecificKeySetMap(), ::combineFragments(). - this is preparatory for enhancing the Interfragmenter to automatically ascertaining a certain "distance" between fragments for long-range interactions. That is, we may afterwards smear out nuclear and electronic charge distributions up to said distance without them overlapping outside of a present fragments (i.e. without capturing their short-range interactions elsewhere). commit 7537d191a569f0b72f4ef6db9b9ae70d575a463f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Mar 16 17:05:28 2015 +0100 Removing setting net force to zero and setting hasForce to true. commit 00d815ca595052983db7c34a5f62e31c775c680e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 14 12:58:32 2015 +0100 FIX: Need to divide by global number of particles, when summing later, in ExportSolution. commit 6e73f5af95ffb4eb1a979d776df10f17828e74f9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 26 00:01:51 2014 +0200 Added debugging changes to InterfaceVMGJob on force summation. commit ff347fc31ed5cd23e7ad30c79dd005ca9145acb2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 7 12:21:09 2015 +0100 Added gathering of full and longrange forces into extra file. - added new structs to VMGDataFusedMap for summation. - tempcommit: we do not have the full index set available, hence it just accumulated all indices from all fragments into a sorted set and use this in lieu of the full index set. We need to check how the full solution is constructed and how indices to the particles and their force vectors can be assigned. - extended printFullSolution() by another table with short- and long-range forces. commit 20bb3b83b5704876159d8aeede5c88f78cb27559 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 26 00:00:30 2014 +0200 MPQCData now also uses FragmentForces (instead of typedef forcevector). - required small changes to MPQCCommandJob due to changed typedef. - we need to maintain the old code which used vector of forces. Therefore, the serialization version of MPQCData is increased and a simple conversion routine added. commit 94db134a7b8bcdb17a2134fe1c6ca1aed4aded49 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 23:56:32 2014 +0200 Again changes to obtain correct longrange forces, also forces are optional. - renamed particle_forces -> forces to make it consistent with MPQCData_Fused. - MPQCData_Fused and VMGData_Fused are structs and no longer namespace as the latter cannot serve as template arguments. - split off forces in VMGData into VMGDataForceMap_t and VMGDataForceVector_t. - changed ConvertMPQCDataToForceMap() into template function ConvertDataToForceMap(), working also on VMGDataForceMap_t. - this required changes in FragmentationShortRangeResults. - FragmentationLongRangeResults now also converts the longrange forces correctly. - AnalyseFragmentResults now prints also a ..VMGForces.dat file. - VMGData's forces are now optional to some degree and analysis chain can deal with it. - introducing forces we must still maintain working code when results without forces are calculated (e.g. as in the regression tests). Hence, a boolean im VMGData and FragmentationLongRangeResults states whether forces have been found or not and whether these should be summed up or not subsequently. commit 14a618bda4c5471ea8d26d9429a8c964bd366dff Merge: b19f280 b61bd5e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 13 22:10:12 2015 +0200 Merge branch 'Fix_debianpackage' into Candidate_v1.5.2 commit b19f2801b7152275a338f8cc95c051ccd1679bb7 Merge: 18f47f8 24f4251 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 13 22:10:00 2015 +0200 Merge branch 'Fix_ActionQueue_lastchangedaction' into Candidate_v1.5.2 commit 18f47f88da033fc8b97a339b874684f5aba29199 Merge: 0a3449a dace6c7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 13 22:09:38 2015 +0200 Merge branch 'Fix_molecuilderguitest_with_valgrind' into Candidate_v1.5.2 commit 0a3449a7a998a2d08cf2b499e980ab657da627b8 Merge: dcff593 2f429ef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 13 22:09:22 2015 +0200 Merge branch 'Better_HBondDistances' into Candidate_v1.5.2 commit dcff593de06c56b6b49d074d77955a90c552aaa2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 31 14:38:50 2015 +0200 Implemented more efficient per-molecule bounding box information. - molecule now has internal bimaps to know the extent of itself in a cheap way, right map needs to be multiset_of to allow for non-unique values. - moved BoundingBoxInfo from GLMolObject to molecule. - is itself a Cacheable and is requested from GLMoleculeObject_molecule on new channel BoundingBoxChanged. - Cacheable listens to AtomInserted, AtomRemoved, and AtomMoved. - in molecule::changeAtomId() we also change BoundingBoxSweepingAxis entry. commit a06378771ff430b3ce4652d680ae761a08426668 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Aug 31 14:38:30 2015 +0200 FIX: Removed double coding in molecule::erase(). commit 59e799680d2829d1437a7c22cb6820332ca100a5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Oct 13 16:33:52 2015 +0200 FIX: World needs to first destroy the atom, then release its ids. commit ceaab1dbd47046505deba359f3a96512689de872 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 29 09:40:52 2015 +0200 AddAtom now adds a molecule (atom always associated with a molecule). - also by default, constructs a new molecule if none has been selected. - we missed changing the atom id on redo (new ones have different ids) and especially now telling the associated molecule about it. This is changed with a new molecule::changeAtomId(). commit b61bd5e8f51d73a916f0e0a2fcd4dcadcf84dfd8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 2 23:10:12 2015 +0200 Fixed levmar m4 to use pkgconfig and locate. - we don't need to give with-levmar which allows debuild to make use of the installed package. commit 6227207a85bc7078c5be7985f12def5bac3f8287 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 2 23:09:53 2015 +0200 Added all required libboost.. to Build-depends. commit 3c6b4067162cb45d4e7ac87de102c3c8683d0a5b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 28 12:41:00 2015 +0200 Changed debian files to heber(a)molecuilder.com and changed boost dep. - we now just depend on libboost-dev (i.e. on all). commit 2f429ef69adf29a1bf0267338e9cecd1fb5b238c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 22 20:02:47 2015 +0200 Elements are now parsed as string (and tried for being int). - this allows to parse both "He" and "2", i.e. both symbol and atomic number. - this works for both command-line and Python. commit 3b1c369fabf5039957cb70e0059346c668d0eebf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 11 08:40:03 2015 +0200 Entered HBondDistance results from VSpeShape into elements_db. - we now have single bond distances for all elements from 1 to 37. They are mostly consistent with the old values (but some are not, e.g. for element no 20, but they look like copied). commit c85c2e7c1a8f696987bf232998d8eef09d386b99 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 11 03:33:54 2015 +0200 FIX: Element's HBondDistance and HBondAngle were not initialized as -1. - this causes faulty behavior with saturate-atoms (e.g. Li) which showed the bug. - TESTFIX: ElementUnitTest adapted to new default behavior. commit 4f8079f804337514271581f8a67c750b656f2fbb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 10 17:16:57 2015 +0200 Added Hbonddistance and -angle for sodium (Na). commit e3c4c532b457c1d83d8ac94e74300e037b757ace Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 10 16:41:24 2015 +0200 MpqcParser additionally allows to save optimization jobs. - this is enabled via a new flag "jobtype" that can be either Default or Optimization. - also storing "checkpoint = no" per default for all mpqc input files. This is a safety measures such that no old checkpoint files are used that reside in the same folder accidentally. This is especially important for fragment files. - TESTFIX: changed all regression tests comparing against .in files, added new checkpoint statement. - TESTFIX: changed unit test ParserMpqcUnitTest in the same manner. commit 6c30ab3e28b74461e5739b1fae84da32b57c8642 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 10 16:19:41 2015 +0200 Assertion in SaturateBond now states element. commit d79ca1b812618b68d1781fb9ef48651c790f66f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 30 19:54:29 2015 +0200 FIX: SaturateAction would use double instead of single hydrogen bond length. commit 2a7dbe1527726bfd2bc8d6793a86c59deefc3fdf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 8 10:17:13 2015 +0200 FIX: Help on SetBoundaryConditionsAction did not have capitalized condition name. commit 83a425eb7c3e26118a81096a43c79ffe877b2113 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 12:49:02 2014 +0200 Split off sampled_potential im VMGDataMap_t into separate fusion container. - this should correct the output in ..._VMGEnergy.dat commit ce98747dfef7546f47996405283750bc34c9ad5d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 20 18:30:19 2014 +0100 Added extraction of long-range forces from VMGData's array f. commit d200ae2e4a4f8002d6ef527fd7bfa418be477b9c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 20 18:31:42 2014 +0100 Added new SetValues FragmentForces. - struct is particle_forces used in fusion maps and vectors. commit 057c8a49f208862ececbcb5c1adeaf0566d89313 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Feb 7 12:18:59 2015 +0100 FIX: When there's just a single fragment, don't remove the fullsolution. - this usually causes some assert to hit when we test the long-range calculation on a single water molecule where there's only a single fragment and it conincides with the full molecule. Hence, the full solution calculation does not cause an extra fragment job. commit 9593d16ae241f82c256733f785601e2e0cfb9b29 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 17 19:29:19 2014 +0200 FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob. - note that so far domains needs to be cubic. commit c20839bcb1af30decfbda10a56579a6b43c683be Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 09:54:37 2014 +0200 FIX: Shared libraries's Makefile.am rules are now consistent. - pkgconfig is just given once (in src/Makefile.am). - all have version information, including now pyMoleCuilder.so. commit 24f425178ef9717a191dfb42f15da6fc45bbc899 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 23 18:14:18 2014 +0200 FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad. - causes segfault when notification informs about change and _lastchangeaction is still NULL (as the very first Action failed). - we now only notify when action succeeded. commit dace6c77620134a6d8c643e895a7d94794d97f13 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 4 14:26:53 2015 +0200 FIX: tests/GuiChecks/atlocal lacked valgrind variable. - note that running molecuilder through valgrind currently produces loads of error messages all connected to the Qt and/or python parts and have in the vast majority nothing to do with molecuilder. We will use our own memory debugger until suitable suppression files can be found. Until that not sensible debugging of memory leaks is possible in the GUI part of the code. commit 08d9df7e636ea0df65e73df162455c8f47deb448 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 2 11:59:44 2015 +0200 FIX: Rename codepatterns -> libcodepatterns. - updated makeDebianPackage.sh to compile with multiple cores. commit ba353982fb33936c0b6e4c92a14dba221dc08c56 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 29 13:47:45 2015 +0200 Package CodePatterns is now called libcodepatterns. - updated m4 file. - also updated .pc files. ----------------------------------------------------------------------- hooks/post-receive --

1 0

[SCM] branch stable updated. v1.5.0
by git＠ins.uni-bonn.de 15 Aug '15

15 Aug '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 "". The branch, stable has been updated via bff5e273091c20e062b35677796d4f022e572385 (commit) via 5284fffa7f4365151a666b79f37c046f73411a9e (commit) via 57c25368aae2779cf2545bd715d92847c1f853a0 (commit) via 196702d9c311b2871aef6cff534ecf5e37661227 (commit) via 65ca735893cc3cd45422991765fad3175ed57b57 (commit) via 66b092e089b4fe741dc1a5497ad61222883e30c0 (commit) via 8fbd7b3b947194c7f2e32d92bbfeb47a1ca108b0 (commit) via b8b2e63323e4a8a49765e237e34a436191f9a532 (commit) via d68514266b1d90ca4e9774dc1ebdf195a18c5c02 (commit) via b8f0a8d46d1cb0c1dc07f2d6a783b8cf0fd1f067 (commit) via 399571102f903dadaa8e99db9e4f4be3e8d34fb0 (commit) via d07a38beef13fba24ae491f74c049ef04179ac35 (commit) via 6fe4f7657cee7b53f89f832e3948f7fa4bbbe4ba (commit) via ec84716c2318851ba3564aff1286a259ca46df4d (commit) via b9e47e05b980c2d1717a7e44831434a551b3a246 (commit) via 7e2adcdacc44d805e377ada69a708f7d564f4498 (commit) via a9161db25c69419446f0371e9ca3b69d3d4daac1 (commit) via 07136ae14d7826fc7287ec37e92157cd61721c87 (commit) via 369cb1be7527ef62fee18c457e912c21b1b698eb (commit) via 92ee4137bc23814e0da4f5dc268c7ec9f06e392f (commit) via ca4b63bb2e6c328401c4597bf9a2d00d25f055e2 (commit) via 68989c020a48fae01762aa4040fb603221d5e981 (commit) via 25a81dcb5ee7c2436679aa4784523a95b0e90fb6 (commit) via 5b61e5e3ff8d5a18604de0315358ab7a74c40a48 (commit) via 07b8001035a112557377b6b6205094bc48f53c8e (commit) via a39d72c6d5edf5fa534720d234e4a54c6dcfc17a (commit) via 015f8c18d74c335a5af0741c3ff7f82dfcbfa0d1 (commit) via e5a47740179fa6bd45778ad5a4caea81fde92864 (commit) via cc297688a2f09a635ccb45323617573684f51f9d (commit) via b9680b48b3c408eb08fa28771d7f329859cf047b (commit) via f02b53a6f30feeb1be573eceaad0edfb9dbcac71 (commit) via 5be7988b41312420dd9335d53345f61a79a43f07 (commit) via 54bdaae692392765ace3b38c8635806888d0c8b5 (commit) via fb95a5645025c4f145cfcbf9ef41a1f12c86a506 (commit) via f714763c1502a8d2a462b4e01ad3c708f9fa17cf (commit) via 3d5b5bdeb158f9612295a4adbb43add240c21bd9 (commit) via 52c5d4c7c4ecce1343353bae76e18959dd8d2d1a (commit) via fcdf0553321b79c267b07b0d50decd2bd4fd4a2d (commit) via 95f49f80844c3103ded5d5940874d5342ce246a6 (commit) via 88846bef6d3c0a61836ca4125b1bd6c2ee80ef95 (commit) via 20f9b5ca3d0b9027b2885d6239e5b48b8dea45a5 (commit) via 6c16a02ecd71315045f7522510b3807789050e4b (commit) via 3e52834b600d16813f5a1e262cafdbdc7586571d (commit) via 009e2e2d372810a555a452769338209c68591479 (commit) via 53437425e2d51ca59e9a3ab458b6f636927987ee (commit) via b3a33d2dc647c629f4efa8e07674f19b1af1740f (commit) via 574d377d6df9c61b2d15b880404e8bb7d6d2fff0 (commit) via 0ea4ddbf6833adf1a4a2ada1981935715775879f (commit) via c307ba4e4b46954d39964089972d5cb1f29a6f40 (commit) via 10aee4386f0c1b8e07b3a74e7d97d99ef2622bc8 (commit) via 94232b82bf9b20300fb870881f38c94ce0857bdd (commit) via 725a1da23441218ebfe802d5508feedc1a4a8b46 (commit) via 3532b77102b83baecdd39fade5a59f5aaf230ed0 (commit) via 8e790ebd981dac78daa03f5e06560ba8ea84a21a (commit) via c66ae6684084ff864820af9b907d9f3b9725530d (commit) via f7054cab5c6c0b7c73d7b4866501383e989b50da (commit) via 80f678157992ab9328be5ba384216ae6e1548684 (commit) via c569220c375bbffdf838cc2cfd11de122bf57a86 (commit) via 024c65bc14cdcf98c86fcf1892e8bc3b3c0c6764 (commit) via 7a0456949e5c8efe51fc75d2a5902483c296feec (commit) via 42b40a4b4a9210b1ed60a0be93acd12541dedde9 (commit) via a82f61a466e15715e16f9470a56c3bdadfcb3895 (commit) via 143263bb92532b8d3e50535a2c7cfae698a6ab6d (commit) via fe0ddfc870329d8adcaf7269129b4690ddd98db4 (commit) via f5452477d87da2369a118585276d5b6793a46480 (commit) via c6719db9d555d7c3f1b43c5cd90b1ccc2a8df1c8 (commit) via df3f2f34f6c9dbddae6f42d32b7a644c3b756eb8 (commit) via a963cf91fe5fac81f5a6c9c3e2c5d8100868fea3 (commit) via 883ea068fbdbd4af0bcd8dfb11919f5f24ecb781 (commit) via 561b94558bc3dbfbf79f15bb042f3376517efa4c (commit) via f27c2c5f268ff6d130b9e9d54bc176a6377242d0 (commit) via 7d146a387231de6a2198a250dbdbab1f1e9076bd (commit) via d4c8694f2cbd423faa6c19ddec88eeb7e5f118a3 (commit) via 9a48804bc9927b9c662e2653a5f08e7a1b65538b (commit) via a87d1e2e1fdd4b7739a97a917c411937f941852d (commit) via 9ec4b8fd1c0781bcd20ad52c2755ad52ae89d518 (commit) via bcf0561c44a090831a61ab4b4118c79b38750317 (commit) via 9fb2137ff4183dfa58b9083f255c8037873fb5ba (commit) via 92df042994f7c0a88d2ebb7c6506fd351ed68a39 (commit) via ea73ce1f1f7bfca1ca449bed235f03c42b10b58b (commit) via 7d0ddb4a2c0b433b55ce0a432f64c21bde6c9535 (commit) via 9d4f964574dae09a31c613751f654551f61f308a (commit) via 7d0a4e076689218b5c7275f30d0ca5ee9341af8b (commit) via 9ad4d612899bb1547d6400f43c8330480c78d103 (commit) via 2a4b054470c32d7dfd7235c070c54dcdde1a99a0 (commit) via 9b56f0a18eb8b397e931302e9b49b96672885279 (commit) via 73b13cdd45329e4acbf0a0ca9dd9b780dac892d7 (commit) via 9737db9c0d2798f3bb61807cda1a59701dc33939 (commit) via 4965922285cce1bd99002053cab2e8913e7fd819 (commit) via 2f76d207662ae0c1e550c622a0d53f769646a691 (commit) via f759e5f2aa47178e7225d67a127028ed62570fdc (commit) via 9c259e4ccaa1f9c8cabd00d1c1ca8e22e40a8199 (commit) via 8923ad833541d0d5da649e21cb7b6537558a282b (commit) via 28864c30d2f893d3d3b12899626e0d2defa2da74 (commit) via d619338ee65ee4df303696fa8a82dbf27e594f44 (commit) via 8d3ee64e6d4d84d033921af0895634eccaec7466 (commit) via 084304e6dfbb4c6567df7dac36d3cb925b2a0b8e (commit) via e7341ec2716284e96e58763befbd8fa9e68b27df (commit) via f3b5971ec8cc96538608d12dd2998861f1e187db (commit) via fac58f919238a82bc5d6cab2eb5c9621c85c941c (commit) via 99db9baca1782e208fb17d2cc6ace3f4cadb568b (commit) via a58c16f47065e9446b7916a407271c6544180022 (commit) via f01769bf04baacedde88443ce16ab2f2dd809f30 (commit) via 1259df9500410b59c3a56d9cf8d54624b53f97da (commit) via 63fb7a963007e0f94b955d96ca949cd435eacb2a (commit) via 795c0fbd35ce4d14a5986636e88a0fe5fcc53381 (commit) via 97445f1edda30c6d17472c562f9832a49df3e644 (commit) via 270bdface47b2d970089daba2ed78dc3f90395a7 (commit) via 9b3262b2e3b9296a0c5ea340ffa6b8b38a694615 (commit) via d12d818e7c101fa705af778bca10771e52c18690 (commit) via 599b3232e65ac3b245869d9dd63c45d7e8f162f4 (commit) via a4dee7ca90a18a6be133d405f7a0b0f5e8181d6d (commit) via 6b69594bcabc35afd7ab6ba170e610a1588c1df4 (commit) via 74831898be603d80e0fe28f09943254aee55e893 (commit) via 6b474e1aa04d153d6d0b68b8cf8de9ed806ef258 (commit) via 69b434b1d1a5180a87c3d669024542593104c8e0 (commit) via 704d59ccf5f2559ab48b197552d1bea827b92ad2 (commit) via 34641b910ee6b9ce05b01bd6c5aa2e558ef54466 (commit) via eac542d5b19b04687918ad9252e1d9cb4adfc4cd (commit) via 2520ccbe1eb2cf5456bd770eedc0656bcef7846f (commit) via ec6abc5fcbede9d754e9e8267ef3dc93f92ab49a (commit) via 4669341c36fbec6d4f4114ed868a2c6ca3c34085 (commit) via ef3013cd854f882cf600cfb78dc0c9cd4f78897b (commit) via c13b913f78b416eebfc6ff8ac0031329a4944e78 (commit) via 068a852341119fad16f4f312d9ab6289fe0edd65 (commit) via 7774f7e70f2ae517967d41e9125f5dba0adf1dbe (commit) via 23110a4092c457be30e89f88181ea2df46c504e5 (commit) from 2fc697b743f39b710d3866f7ce2c17542470e39f (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit bff5e273091c20e062b35677796d4f022e572385 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 25 15:07:28 2015 +0200 Set version to 1.5.0. - MoleCuilder library is now 15:0:0. - Codename "GUI" (the GUI has tests and is fully working). commit 5284fffa7f4365151a666b79f37c046f73411a9e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 13 22:31:22 2015 +0200 FIX: This prevent crash of molecuildergui in debian package. - somehow QGLView hiccups in the parsed arguments although they should be safe to use via QApplication. I have not idea but this solves the issue and does no no harm. Hence, we proceed. commit 57c25368aae2779cf2545bd715d92847c1f853a0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 12 23:11:10 2015 +0200 TESTFIX: for source builds we need to exclude all moc'ed files from codechecks. commit 196702d9c311b2871aef6cff534ecf5e37661227 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 13 23:51:14 2015 +0200 FIX: Qt can now be found even without --with-Qtbin... commit 65ca735893cc3cd45422991765fad3175ed57b57 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 4 21:51:55 2015 +0200 DISTFIX: EXTRA_DIST in tests/../Makefile.ams depended on not yet set variables. - it would use TESTSCRIPT but the variable would be set afterwards. commit 66b092e089b4fe741dc1a5497ad61222883e30c0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 13 09:31:41 2015 +0200 Added debugging package molecuilder-dbg and source package molecuilder-dev - debug information is stripped into extra file. All is handled by CDBS. - needed .install files for stating where to install what file in source tree in debian/.. commit 8fbd7b3b947194c7f2e32d92bbfeb47a1ca108b0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Aug 12 23:38:07 2015 +0200 Enabled GUI compilation for debian package. commit b8b2e63323e4a8a49765e237e34a436191f9a532 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 21:04:44 2015 +0200 Added script for creating debian package. commit d68514266b1d90ca4e9774dc1ebdf195a18c5c02 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 11:26:47 2015 +0200 Added debian/.. files for debian packaging. - added all dependencies (without JobMarket, QtGui, QWT, or vmg). commit b8f0a8d46d1cb0c1dc07f2d6a783b8cf0fd1f067 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 20:32:37 2015 +0200 FIX: bash_completion was accidentally removed by clean target. - also Python/boxmaker was not contained in EXTRA_DIST. commit 399571102f903dadaa8e99db9e4f4be3e8d34fb0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 20:32:01 2015 +0200 DOCU: Described workaround for missing pyconfig.h. commit d07a38beef13fba24ae491f74c049ef04179ac35 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat May 23 16:23:14 2015 +0200 FIX: AllPotentialHealder.hpp not excluded from CodeCheck config_h. - this only causes an error when not doing an out-of-source bild (which debuild does and that's why it came up). commit 6fe4f7657cee7b53f89f832e3948f7fa4bbbe4ba Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 4 15:53:52 2015 +0200 FIX: updateBoundingBox() must not call molecule::getBoundingBox() on every update. - this is O(N^2). We now update by using the current center and radius and looking at the last changed atom's position. This diverges with respect to the radius after some time. Hence, a true getBoundingBox() should be called after a while. commit ec84716c2318851ba3564aff1286a259ca46df4d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Jul 25 15:06:15 2015 +0200 FIX: QtLogBox is again included and working thread-safe. - QDebugStream is now appending text to QtLogBox in a thread-safe manner by using signal/slots. This code is taken from qt-forum.de. commit b9e47e05b980c2d1717a7e44831434a551b3a246 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 23:54:14 2015 +0200 TESTFIX: Marked molecule translation guicheck tests as XFAIL. - so far, we cannot use a MakroAction as a python function except if not arguments are required. Hence, for the moment we mark it as XFAIL. - The problem is with the boost::python::def function. We need to fill its arguments during compile-time but that would require some weird preprocessor magic going through all Actions contained in the MakroAction's sequence. commit 7e2adcdacc44d805e377ada69a708f7d564f4498 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 22:47:41 2015 +0200 FIX: GLMoleculeObject_bond had both flipped ids and the side. - in essence, both do the same thing. We removed all switches that check the sides as flipped ids are actually nice and look good in the observerLog. We keep the side variable as it might come handy for checking which one we are. commit a9161db25c69419446f0371e9ca3b69d3d4daac1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 22:22:53 2015 +0200 FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more. commit 07136ae14d7826fc7287ec37e92157cd61721c87 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 20 11:16:27 2015 +0200 FIX: Fixing display of shapes in GLWorldView. - we propagate shape name via S/S system such that we may lookup the name in ShapeRegistry and do not have to rely on probably already deallocated lastchanged() shape. This affects ShapeAdded() and ShapeRemoved(). - GLMoleculeObject_shape now copies the shape, ensuring that its present while its surface is tesselated. commit 369cb1be7527ef62fee18c457e912c21b1b698eb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 15:47:57 2015 +0200 GLWorldScene lacked assert of Walker in atomClicked(). commit 92ee4137bc23814e0da4f5dc268c7ec9f06e392f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 15:47:19 2015 +0200 Asserted that GLMoleculeObject_molecule::update() is never called. commit ca4b63bb2e6c328401c4597bf9a2d00d25f055e2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 15:46:41 2015 +0200 AddAtomBonds() now uses just id not ptr as param. commit 68989c020a48fae01762aa4040fb603221d5e981 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 15:46:02 2015 +0200 Avoided use of getId() on molecules and atoms in Qt code where possible. - it is ok if we are inside O/O functions or functions called from these functions. commit 25a81dcb5ee7c2436679aa4784523a95b0e90fb6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 15:29:37 2015 +0200 GLMoleculeObject_molecule does not use getAtomCount() anymore. - this removes any usage of getAtomCount() apart from ObservedValue's. commit 5b61e5e3ff8d5a18604de0315358ab7a74c40a48 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 15:25:40 2015 +0200 GLMoleculeObject_molecule also has ObservedValue for name. - this removes any (uncached) molecule::getName() from Qt code part. commit 07b8001035a112557377b6b6205094bc48f53c8e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 14:01:14 2015 +0200 FIX: Setting molecule's name via QtMoleculeList item is again possible. - this is similar to checkForVisibilityChange(), only now for the name. - we required four Actions, i.e. this cannot be undone in a single step but needs four. However, right now it is not easily possible to construct MakroActions from inside the code at compile-time as we do not have access to modify parameters via their tokens. - using constructed MakroAction in QtMoleculeList for name change. commit a39d72c6d5edf5fa534720d234e4a54c6dcfc17a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 13:35:26 2015 +0200 Fixed formula usage in Qt part of code. - formula of a molecule is only access through ObservedValue or directly within the World's O/O system. - Molecule may disappear before selection event. - Atoms may disappear before selection event. commit 015f8c18d74c335a5af0741c3ff7f82dfcbfa0d1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 09:08:38 2015 +0200 QtMainWindow uses QtSelectionChangedAgent. - QtMoleculeListView and GLWorldView receive its signals. The latter passes it on to GLWorldScene. - QtMoleculeList has new MoleculeIdToIndex to allow QtMoleculeListView to (un)select specific rows on a given index. - GLWorldScene passes atom and molecule selection to GLMoleculeObject_molecule. - GLMoleculeObject_molecule passes atom selection to respective GLMoleculeObject_atom. commit e5a47740179fa6bd45778ad5a4caea81fde92864 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 08:36:38 2015 +0200 Added QtSelectionChangedAgent to transform O/O to S/S system. - also this will be far more effective, as e.g. not all GLMoleculeOBject_molecule will receive SelectionChanged from World if just a single molecule has been selected. - Atom might not yet have a molecule, i.e. it is not drawn yet. We do nothing then. - recieveNotification allows for vanished atom (due to removal). We do nothing then. commit cc297688a2f09a635ccb45323617573684f51f9d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 19 08:30:51 2015 +0200 QtMoleculeItem_.. now shout when they receive subjectKilled(). - this way we do not have this double system of both QtMoleculeList (in a lazy fashion) and each QtMoleculeList listens for moleculeRemoved (one through the Observer channel, the other through subjectKilled()). - we simply count the number of QtMoleculeItems that received subjectKilled() and if max is reached, the row is removed. - to prevent molecule id clash, insertion (of same id) after removal is ok. This works cause we first remove and then insert new item. Hence, having the same id is possible. commit b9680b48b3c408eb08fa28771d7f329859cf047b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 16 10:29:09 2015 +0200 FIX: Fixing "pure virtual function called" in QtMoleculeItem. - as a matter of fact this should not be a problem: Inside QtMoleculeItem's dstor body while signing off from the channels, it is no problem to receive a notification for a channel we have not signed off yet. The vtable has not been touched with respect to QtMoleculeItem. I really do not understand this issue. I have tried to reproduce it with a few mock classes that have the very same inheritance pattern and used locks to force the same case of a virtual function being called while inside the dstor's body but it does not reproduce the error. - the same holds for the cstor and again the vtable is created before the code pointer enters the cstor body, hence it should be no problem ... - the solution is to signOn..() and signOff..() on the highest level, i.e. on the most derived classes. This causes some code duplication but at least it works. commit f02b53a6f30feeb1be573eceaad0edfb9dbcac71 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 16 01:26:09 2015 +0200 World now first releases id and then destroys the atom/molecule. - this prevents any access to atoms/molecules in the phase of destruction. commit 5be7988b41312420dd9335d53345f61a79a43f07 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jul 31 11:20:51 2015 +0200 Removed molecule::lastChanged(). - we have lastChangedAtomId() and ids are safer to use than ptrs. commit 54bdaae692392765ace3b38c8635806888d0c8b5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 16 01:25:22 2015 +0200 Qt4 instance use new lastChanged..Id() in place of lastChanged(). - also changed in FormatParser_common. commit fb95a5645025c4f145cfcbf9ef41a1f12c86a506 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Jul 16 01:23:30 2015 +0200 Added lastChanged..Id() to both World and molecule. commit f714763c1502a8d2a462b4e01ad3c708f9fa17cf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 15 17:22:04 2015 +0200 GLWorldView no longer listens to WorldTime::TimeChanged. - molecules are re-created when the time changes anyway so the world view is informed about the change. - removed all commented-out lines. commit 3d5b5bdeb158f9612295a4adbb43add240c21bd9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 15 16:01:41 2015 +0200 GLWorldView does not emit changed() on each general update() from the World and others. commit 52c5d4c7c4ecce1343353bae76e18959dd8d2d1a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Jul 15 15:56:58 2015 +0200 DOCU: Updated documentation on Qt Gui construct. commit fcdf0553321b79c267b07b0d50decd2bd4fd4a2d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jul 14 15:55:47 2015 +0200 Fixing QtMoleculeList with list containing only formulas and ids. - COLUMNTYPE now belongs to QtMoleculeItem not QtMoleculeItemFactory. - callback function in QtMoleculeItem signature changed to molid and column. - QtMoleculeItem::getType() for obtaining the type to be used as argument in the callback. commit 95f49f80844c3103ded5d5940874d5342ce246a6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jul 7 03:10:10 2015 +0200 QtMoleculeList::informDirtyState() does not need to lock refill_mutex anymore. - we simply write the QtMoleculeItem to the ToBeMoved list and convert it to the very first item in the row in updateItemStates(). commit 88846bef6d3c0a61836ca4125b1bd6c2ee80ef95 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Jul 7 03:08:58 2015 +0200 Fixing QtElementList::updateElement(). commit 20f9b5ca3d0b9027b2885d6239e5b48b8dea45a5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Jul 20 10:35:41 2015 +0200 GLWorldScene propagates changed mol id to GLMoleculeObject_molecule. - GLWorldScene must emit MoleculeRemoved on last subjectKlled(). - GLWorldScene has internal RemovalMolecule in case moleculeRemoved comes prior to moleculeInserted. commit 6c16a02ecd71315045f7522510b3807789050e4b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 14:16:19 2015 +0200 GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state. commit 3e52834b600d16813f5a1e262cafdbdc7586571d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 06:49:13 2015 +0200 QtMoleculeItem_... use ObservedValue for internally representing atom's state. - this affects atomcount, formula, and name. visibility depends on clicked state and occurrence is changed elsewhere. commit 009e2e2d372810a555a452769338209c68591479 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 06:46:32 2015 +0200 GLMoleculeObject_bond uses ObservedValue for internally representing atom's state. commit 53437425e2d51ca59e9a3ab458b6f636927987ee Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jun 19 19:37:50 2015 +0200 GLMoleculeObject_atom uses ObservedValue for internally representing atom's state. - we use internal owner as ref to Observable. commit b3a33d2dc647c629f4efa8e07674f19b1af1740f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jun 21 14:16:57 2015 +0200 Removed init() and signal WorldSelectionChanged() from GLWorldScene. commit 574d377d6df9c61b2d15b880404e8bb7d6d2fff0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Jul 5 09:55:15 2015 +0200 Using static Observable::..NotificationsChannel() functions. - requiring now CodePatterns 1.3.0 due to ObservedValue. - also we purge the GlobalObservablesInfo in cleanUp(). ----------------------------------------------------------------------- Summary of changes: Makefile.am | 10 +- configure.ac | 65 +- debian/changelog | 6 + debian/compat | 1 + debian/control | 53 + debian/copyright | 29 + debian/molecuilder-dev.install | 2 + debian/molecuilder.install | 6 + debian/rules | 12 + debian/source/format | 1 + doc/userguide/userguide.xml | 5439 +++++++++----------- makeDebianPackage.sh | 46 + src/Actions/Action.cpp | 2 +- src/Actions/Action.hpp | 19 +- src/Actions/ActionQueue.cpp | 42 +- src/Actions/ActionQueue.hpp | 37 +- src/Actions/ActionRegistry.cpp | 85 +- src/Actions/ActionRegistry.hpp | 3 +- src/Actions/ActionSequence.cpp | 47 +- src/Actions/ActionSequence.hpp | 3 +- src/Actions/ActionStatusList.cpp | 2 +- src/Actions/Action_impl_header.hpp | 2 + src/Actions/Action_impl_pre.hpp | 23 +- .../DipoleAngularCorrelationAction.cpp | 16 +- .../AnalysisAction/DipoleCorrelationAction.cpp | 3 +- .../AnalysisAction/PairCorrelationAction.cpp | 6 +- .../AnalysisAction/PointCorrelationAction.cpp | 3 +- .../AnalysisAction/SurfaceCorrelationAction.cpp | 3 +- src/Actions/AtomAction/ChangeElementAction.cpp | 23 +- .../AtomAction/RotateAroundOriginByAngleAction.cpp | 2 +- src/Actions/AtomAction/SaturateAction.cpp | 8 +- src/Actions/Calculation.hpp | 2 + src/Actions/Calculation_impl.hpp | 4 + src/Actions/CommandAction/HelpAction.cpp | 4 +- src/Actions/FillAction/FillRegularGridAction.cpp | 3 +- src/Actions/FillAction/FillSurfaceAction.cpp | 6 +- src/Actions/FillAction/FillVolumeAction.cpp | 4 +- src/Actions/FillAction/SuspendInMoleculeAction.cpp | 7 +- .../AnalyseFragmentationResultsAction.cpp | 4 +- .../FragmentationAction/FragmentationAction.cpp | 10 +- .../FragmentationAutomationAction.cpp | 2 +- .../MolecularDynamicsAction.cpp | 24 +- .../StructuralOptimizationAction.cpp | 24 +- .../GraphAction/CorrectBondDegreeAction.cpp | 12 +- src/Actions/GraphAction/CreateAdjacencyAction.cpp | 17 +- src/Actions/GraphAction/DestroyAdjacencyAction.cpp | 12 +- .../GraphAction/SubgraphDissectionAction.cpp | 16 +- src/Actions/GraphAction/UpdateMoleculesAction.cpp | 24 +- src/Actions/MakroAction.cpp | 11 +- src/Actions/MakroAction.hpp | 5 +- src/Actions/MakroAction_impl_pre.hpp | 6 +- src/Actions/ManipulateAtomsProcess.cpp | 3 + src/Actions/ManipulateAtomsProcess.hpp | 2 + src/Actions/MethodAction.cpp | 3 + src/Actions/MethodAction.hpp | 1 + src/Actions/MoleculeAction/RemoveAction.cpp | 4 +- .../MoleculeAction/SaveTemperatureAction.cpp | 5 +- src/Actions/MoleculeAction/StretchBondAction.cpp | 15 +- src/Actions/MoleculeAction/TranslateAction.cpp | 12 +- .../SaveSelectedAtomsAsExtTypesAction.cpp | 5 +- .../SelectionAction/Atoms/AllAtomsAction.cpp | 5 +- .../SelectionAction/Atoms/AllAtomsAction.def | 2 +- .../Atoms/AllAtomsInsideVolumeAction.cpp | 5 +- .../Atoms/AllAtomsInsideVolumeAction.def | 2 +- .../Atoms/AllAtomsOfMoleculeAction.cpp | 5 +- .../Atoms/AllAtomsOfMoleculeAction.def | 2 +- .../SelectionAction/Atoms/AtomByElementAction.cpp | 5 +- .../SelectionAction/Atoms/AtomByElementAction.def | 2 +- .../SelectionAction/Atoms/AtomByIdAction.cpp | 15 +- .../SelectionAction/Atoms/AtomByOrderAction.cpp | 9 +- .../SelectionAction/Atoms/ClearAllAtomsAction.cpp | 5 +- .../SelectionAction/Atoms/ClearAllAtomsAction.def | 2 +- .../SelectionAction/Atoms/NotAllAtomsAction.cpp | 5 +- .../SelectionAction/Atoms/NotAllAtomsAction.def | 2 +- .../Atoms/NotAllAtomsInsideVolumeAction.cpp | 5 +- .../Atoms/NotAllAtomsInsideVolumeAction.def | 2 +- .../Atoms/NotAllAtomsOfMoleculeAction.cpp | 5 +- .../Atoms/NotAllAtomsOfMoleculeAction.def | 2 +- .../Atoms/NotAtomByElementAction.cpp | 5 +- .../Atoms/NotAtomByElementAction.def | 2 +- .../SelectionAction/Atoms/NotAtomByIdAction.cpp | 15 +- .../SelectionAction/Atoms/NotAtomByOrderAction.cpp | 9 +- .../SelectionAction/Atoms/PopAtomsAction.cpp | 16 +- .../SelectionAction/Atoms/PopAtomsAction.def | 4 +- .../Molecules/AllMoleculesAction.cpp | 5 +- .../Molecules/AllMoleculesAction.def | 2 +- .../Molecules/ClearAllMoleculesAction.cpp | 5 +- .../Molecules/ClearAllMoleculesAction.def | 2 +- .../Molecules/MoleculeByFormulaAction.cpp | 8 +- .../Molecules/MoleculeByFormulaAction.def | 2 +- .../Molecules/MoleculeByIdAction.cpp | 9 +- .../Molecules/MoleculeByNameAction.cpp | 7 +- .../Molecules/MoleculeByNameAction.def | 2 +- .../Molecules/MoleculeByOrderAction.cpp | 3 +- .../Molecules/MoleculeOfAtomAction.cpp | 5 +- .../Molecules/MoleculeOfAtomAction.def | 2 +- .../Molecules/NotAllMoleculesAction.cpp | 5 +- .../Molecules/NotAllMoleculesAction.def | 4 +- .../Molecules/NotMoleculeByFormulaAction.cpp | 10 +- .../Molecules/NotMoleculeByFormulaAction.def | 2 +- .../Molecules/NotMoleculeByIdAction.cpp | 9 +- .../Molecules/NotMoleculeByNameAction.cpp | 7 +- .../Molecules/NotMoleculeByNameAction.def | 2 +- .../Molecules/NotMoleculeByOrderAction.cpp | 3 +- .../Molecules/NotMoleculeOfAtomAction.cpp | 7 +- .../Molecules/NotMoleculeOfAtomAction.def | 4 +- .../Molecules/PopMoleculesAction.cpp | 16 +- .../Molecules/PopMoleculesAction.def | 4 +- .../TesselationAction/ConvexEnvelopeAction.cpp | 3 +- src/Actions/WorldAction/BoundInBoxAction.cpp | 28 +- src/Actions/WorldAction/CenterInBoxAction.cpp | 28 +- src/Actions/WorldAction/RepeatBoxAction.cpp | 7 +- src/Actions/unittests/ActionSequenceUnitTest.cpp | 56 +- src/Analysis/analysis_bonds.cpp | 4 +- src/Analysis/analysis_correlation.cpp | 73 +- src/Analysis/analysis_correlation.hpp | 89 +- .../AnalysisCorrelationToPointUnitTest.cpp | 2 +- .../AnalysisCorrelationToPointUnitTest.hpp | 2 +- .../AnalysisCorrelationToSurfaceUnitTest.cpp | 2 +- .../AnalysisCorrelationToSurfaceUnitTest.hpp | 2 +- .../unittests/AnalysisPairCorrelationUnitTest.cpp | 3 +- src/Atom/AtomObserver.cpp | 2 +- src/Atom/AtomSet.hpp | 12 +- src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp | 6 +- src/Atom/atom.cpp | 5 +- src/Atom/atom.hpp | 2 +- src/Atom/atom_atominfo.cpp | 18 +- src/Atom/atom_bondedparticle.cpp | 40 +- src/Atom/atom_bondedparticle.hpp | 14 +- src/Atom/atom_observable.cpp | 2 +- src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp | 8 +- src/AtomIdSet.cpp | 16 +- src/AtomIdSet.hpp | 8 +- src/Bond/AdjacencyMatcher/Adjacency.hpp | 149 + src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp | 193 + src/Bond/AdjacencyMatcher/Makefile.am | 33 + src/Bond/BondInfo.cpp | 4 +- src/Bond/bond_observable.cpp | 2 +- src/Box.cpp | 6 +- src/Descriptors/AtomDescriptor.cpp | 53 +- src/Descriptors/AtomDescriptor.hpp | 15 +- src/Descriptors/AtomDescriptor_impl.hpp | 37 +- src/Descriptors/AtomIdDescriptor.cpp | 13 +- src/Descriptors/AtomIdDescriptor_impl.hpp | 4 +- ...ulePtrDescriptor.cpp => AtomNameDescriptor.cpp} | 31 +- src/Descriptors/AtomNameDescriptor.hpp | 22 + src/Descriptors/AtomNameDescriptor_impl.hpp | 25 + src/Descriptors/AtomOfMoleculeDescriptor.cpp | 2 +- src/Descriptors/AtomOfMoleculeDescriptor_impl.hpp | 2 +- .../AtomOfMoleculeSelectionDescriptor.cpp | 28 +- .../AtomOfMoleculeSelectionDescriptor_impl.hpp | 7 +- src/Descriptors/AtomOrderDescriptor.cpp | 43 +- src/Descriptors/AtomOrderDescriptor_impl.hpp | 5 +- src/Descriptors/AtomSelectionDescriptor.cpp | 22 +- src/Descriptors/AtomSelectionDescriptor_impl.hpp | 7 +- src/Descriptors/AtomShapeDescriptor.cpp | 24 +- src/Descriptors/AtomShapeDescriptor_impl.hpp | 6 +- src/Descriptors/AtomTypeDescriptor.cpp | 2 +- src/Descriptors/AtomTypeDescriptor_impl.hpp | 2 +- .../AtomsWithinDistanceOfDescriptor.cpp | 17 +- .../AtomsWithinDistanceOfDescriptor_impl.hpp | 6 +- src/Descriptors/DescriptorBase.hpp | 11 + src/Descriptors/DescriptorBase_impl.hpp | 34 +- src/Descriptors/MoleculeDescriptor.cpp | 67 +- src/Descriptors/MoleculeDescriptor.hpp | 12 + src/Descriptors/MoleculeDescriptor_impl.hpp | 37 +- src/Descriptors/MoleculeFormulaDescriptor.cpp | 2 +- src/Descriptors/MoleculeFormulaDescriptor_impl.hpp | 2 +- src/Descriptors/MoleculeIdDescriptor.cpp | 14 +- src/Descriptors/MoleculeIdDescriptor_impl.hpp | 4 +- src/Descriptors/MoleculeNameDescriptor.cpp | 2 +- src/Descriptors/MoleculeNameDescriptor_impl.hpp | 2 +- .../MoleculeOfAtomSelectionDescriptor.cpp | 47 +- .../MoleculeOfAtomSelectionDescriptor_impl.hpp | 7 +- src/Descriptors/MoleculeOrderDescriptor.cpp | 45 +- src/Descriptors/MoleculeOrderDescriptor_impl.hpp | 5 +- src/Descriptors/MoleculePtrDescriptor.cpp | 6 +- src/Descriptors/MoleculePtrDescriptor.hpp | 2 +- src/Descriptors/MoleculePtrDescriptor_impl.hpp | 6 +- src/Descriptors/MoleculeSelectionDescriptor.cpp | 22 +- .../MoleculeSelectionDescriptor_impl.hpp | 7 +- .../unittests/AtomDescriptorUnitTest.cpp | 94 +- .../unittests/MoleculeDescriptorUnitTest.cpp | 78 +- src/Filling/unittests/ClusterUnitTest.cpp | 15 +- src/Filling/unittests/FillerUnitTest.cpp | 4 +- .../Automation/VMGFragmentController.cpp | 5 +- src/Fragmentation/Exporters/SaturatedFragment.cpp | 7 +- src/Fragmentation/Fragmentation.cpp | 20 +- src/Fragmentation/Graph.cpp | 3 +- .../Homology/HomologyGraph_getFromKeyset.cpp | 10 +- src/Fragmentation/Interfragmenter.cpp | 2 +- src/Graph/AdjacencyList.cpp | 3 +- src/Graph/BuildInducedSubgraph.cpp | 2 +- src/Graph/BuildInducedSubgraph.hpp | 4 +- src/Graph/DepthFirstSearchAnalysis.cpp | 13 +- src/Helpers/helpers.hpp | 9 +- .../unittests/stubs/AtomObserverStub.cpp | 2 +- src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp | 2 +- src/LinkedCell/unittests/stubs/WorldTimeStub.cpp | 2 +- src/Makefile.am | 8 +- src/Parameters/Makefile.am | 2 + src/Parameters/Specifics/Value_atom.cpp | 20 +- src/Parameters/Specifics/Value_elements.cpp | 99 + .../{Value_element.hpp => Value_elements.hpp} | 0 src/Parameters/Specifics/Value_molecule.cpp | 21 +- src/Parameters/StreamOperators.hpp | 14 +- .../Validators/Specific/AtomIdValidator.cpp | 2 +- .../Validators/Specific/MoleculeIdValidator.cpp | 2 +- .../Specific/TimeStepPresentValidator.cpp | 8 +- src/Parser/FormatParser.hpp | 2 +- src/Parser/FormatParserInterface.hpp | 2 +- src/Parser/FormatParserStorage.cpp | 24 +- src/Parser/FormatParserStorage.hpp | 2 +- src/Parser/FormatParser_common.cpp | 7 +- src/Parser/MpqcParser.cpp | 7 +- src/Parser/MpqcParser.hpp | 2 +- src/Parser/PcpParser.cpp | 22 +- src/Parser/PcpParser.hpp | 15 +- src/Parser/PdbParser.cpp | 32 +- src/Parser/PdbParser.hpp | 8 +- src/Parser/Psi3Parser.cpp | 11 +- src/Parser/Psi3Parser.hpp | 4 +- src/Parser/TremoloParser.cpp | 39 +- src/Parser/TremoloParser.hpp | 13 +- src/Parser/XmlParser.cpp | 13 +- src/Parser/XmlParser.hpp | 2 +- src/Parser/XyzParser.cpp | 12 +- src/Parser/XyzParser.hpp | 2 +- src/Parser/unittests/ParserMpqcUnitTest.cpp | 3 +- src/Parser/unittests/ParserPcpUnitTest.cpp | 5 +- src/Parser/unittests/ParserPdbUnitTest.cpp | 5 +- src/Parser/unittests/ParserPsi3UnitTest.cpp | 8 +- src/Parser/unittests/ParserTremoloUnitTest.cpp | 27 +- src/Parser/unittests/ParserXmlUnitTest.cpp | 5 +- src/Parser/unittests/ParserXyzUnitTest.cpp | 23 +- src/Python/PythonScripting.cpp | 37 +- src/Shapes/BaseShapes.cpp | 6 +- src/Shapes/ShapeFactory.cpp | 3 +- src/Shapes/ShapeRegistry.cpp | 2 +- .../unittests/stubs/WorldSelectedMoleculesStub.cpp | 6 +- src/Tesselation/TriangleMatcher/Makefile.am | 34 + src/Tesselation/TriangleMatcher/Triangle.hpp | 145 + .../TriangleMatcher/TriangleMatcher.cpp | 203 + src/Tesselation/TriangleMatcher/types.hpp | 30 + src/Tesselation/boundary.cpp | 12 +- src/ThreadGuard.hpp | 34 + .../CommandLineUI/CommandLineUIFactory.cpp | 4 +- .../CommandLineUI/Query/AtomCommandLineQuery.cpp | 2 +- .../CommandLineUI/Query/AtomsCommandLineQuery.cpp | 2 +- .../Query/MoleculeCommandLineQuery.cpp | 2 +- .../Query/MoleculesCommandLineQuery.cpp | 3 +- src/UIElements/Makefile.am | 8 +- src/UIElements/Menu/TextMenu/ActionMenuItem.cpp | 6 +- src/UIElements/Menu/TextMenu/ActionMenuItem.hpp | 2 +- src/UIElements/Menu/TextMenu/MenuItem.cpp | 2 +- src/UIElements/Menu/TextMenu/MenuItem.hpp | 2 +- src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp | 3 + src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp | 1 + src/UIElements/Qt4/QtMainWindow.cpp | 14 +- src/UIElements/Qt4/QtMainWindow.hpp | 2 + src/UIElements/Qt4/QtUIFactory.cpp | 22 +- src/UIElements/Qt4/Query/AtomQtQuery.cpp | 7 +- src/UIElements/Qt4/Query/MoleculeQtQuery.cpp | 7 +- src/UIElements/TextUI/Query/AtomTextQuery.cpp | 2 +- src/UIElements/TextUI/Query/AtomsTextQuery.cpp | 4 +- src/UIElements/TextUI/Query/MoleculeTextQuery.cpp | 2 +- src/UIElements/TextUI/Query/MoleculesTextQuery.cpp | 4 +- src/UIElements/TextUI/TextUIFactory.cpp | 4 +- src/UIElements/TextUI/TextWindow.cpp | 2 +- src/UIElements/UIFactory.cpp | 2 + src/UIElements/UIFactory.hpp | 4 + .../Views/Qt4/MoleculeList/QtMoleculeItem.cpp | 86 +- .../Views/Qt4/MoleculeList/QtMoleculeItem.hpp | 48 +- .../Qt4/MoleculeList/QtMoleculeItemFactory.cpp | 34 +- .../Qt4/MoleculeList/QtMoleculeItemFactory.hpp | 9 +- .../Views/Qt4/MoleculeList/QtMoleculeList.cpp | 727 ++- .../Views/Qt4/MoleculeList/QtMoleculeList.hpp | 94 +- .../Views/Qt4/MoleculeList/QtMoleculeListView.cpp | 106 +- .../Views/Qt4/MoleculeList/QtMoleculeListView.hpp | 8 + .../SpecificItems/QtMoleculeItem_atomcount.hpp | 44 +- .../SpecificItems/QtMoleculeItem_formula.hpp | 44 +- .../SpecificItems/QtMoleculeItem_name.hpp | 44 +- .../SpecificItems/QtMoleculeItem_occurrence.hpp | 16 +- .../SpecificItems/QtMoleculeItem_visibility.hpp | 16 +- src/UIElements/Views/Qt4/QDebugStream.hpp | 139 +- .../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp | 347 +- .../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp | 69 +- .../Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp | 363 +- .../Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp | 77 +- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 726 ++- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp | 131 +- .../Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp | 1 - .../Views/Qt4/Qt3D/GLMoleculeObject_shape.hpp | 4 +- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp | 532 +- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp | 55 +- src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp | 148 +- src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp | 26 +- src/UIElements/Views/Qt4/QtElementList.cpp | 160 +- src/UIElements/Views/Qt4/QtElementList.hpp | 29 +- src/UIElements/Views/Qt4/QtFragmentList.cpp | 3 +- src/UIElements/Views/Qt4/QtHomologyList.cpp | 4 +- src/UIElements/Views/Qt4/QtHomologyList.hpp | 3 +- src/UIElements/Views/Qt4/QtInfoBox.cpp | 70 +- src/UIElements/Views/Qt4/QtInfoBox.hpp | 25 +- src/UIElements/Views/Qt4/QtLogBox.cpp | 5 +- src/UIElements/Views/Qt4/QtLogBox.hpp | 4 +- .../Views/Qt4/QtSelectionChangedAgent.cpp | 158 + .../Views/Qt4/QtSelectionChangedAgent.hpp | 58 + src/UIElements/Views/Qt4/QtShapeList.cpp | 3 +- src/UIElements/Views/Qt4/QtTimeLine.cpp | 12 +- src/UIElements/Views/Qt4/QtTimeLine.hpp | 2 + src/World.cpp | 112 +- src/World.hpp | 60 +- src/WorldTime.cpp | 2 +- src/builder.cpp | 6 + src/builder_init.cpp | 18 + src/builder_init.hpp | 1 - src/cleanUp.cpp | 2 + src/documentation/constructs/actions.dox | 49 +- src/documentation/constructs/qt-gui.dox | 275 +- src/documentation/install.dox | 11 + src/documentation/tests/tests.dox | 36 +- src/molecule.cpp | 70 +- src/molecule.hpp | 27 +- src/molecule_geometry.cpp | 16 +- src/moleculelist.cpp | 46 +- src/unittests/AtomIdSetUnitTest.cpp | 16 +- src/unittests/stubs/WorldStub.cpp | 2 +- tests/CodeChecks/testsuite-config_h.at | 9 +- tests/CodeChecks/testsuite-memdebug.at | 7 + tests/CodeChecks/testsuite-project-disclaimer.at | 7 + tests/Fragmentations/Makefile.am | 4 +- .../testsuite-bond-adjacencymatcher.at | 34 + tests/GuiChecks/Bond/testsuite-bond.at | 3 + .../FillSurface/testsuite-fill-surface-cube.at | 51 +- .../FillSurface/testsuite-fill-surface-cylinder.at | 51 +- .../testsuite-fill-surface-everywhere.at | 16 +- .../FillSurface/testsuite-fill-surface-micelle.at | 51 +- .../FillSurface/testsuite-fill-surface-nowhere.at | 16 +- .../FillSurface/testsuite-fill-surface-sphere.at | 51 +- .../FillVolume/testsuite-fill-volume-cube.at | 14 +- .../FillVolume/testsuite-fill-volume-cylinder.at | 45 +- .../FillVolume/testsuite-fill-volume-everywhere.at | 14 +- .../FillVolume/testsuite-fill-volume-nowhere.at | 14 +- .../FillVolume/testsuite-fill-volume-sphere.at | 14 +- ...suite-fragmentation-fragmentation-automation.at | 33 +- .../testsuite-graph-depth-first-search.at | 1 - .../testsuite-graph-subgraph-dissection.at | 1 - tests/GuiChecks/Makefile.am | 7 +- .../testsuite-molecules-save-adjacency.at | 2 +- .../testsuite-molecules-translation-periodic.at | 3 + .../Translation/testsuite-molecules-translation.at | 3 + .../testsuite-parser-set-parameters-mpqc-basis.at | 9 +- ...ite-parser-set-parameters-mpqc-maxiterations.at | 9 +- .../Mpqc/testsuite-parser-set-parameters-mpqc.at | 9 +- .../testsuite-potential-fit-potential.at | 90 +- ...ion-select-atoms-inside-cuboid-with-defaults.at | 6 +- ...stsuite-selection-select-atoms-inside-cuboid.at | 6 +- ...suite-selection-unselect-atoms-inside-cuboid.at | 6 +- ...stsuite-selection-select-atoms-inside-sphere.at | 6 +- ...te-selection-select-atoms-inside-tiny-sphere.at | 6 +- ...suite-selection-unselect-atoms-inside-sphere.at | 6 +- ...-selection-unselect-atoms-inside-tiny-sphere.at | 6 +- ...testsuite-selection-select-molecules-by-name.at | 6 +- ...stsuite-selection-unselect-molecules-by-name.at | 6 +- .../testsuite-tesselation-big-convex-envelope.at | 4 +- ...estsuite-tesselation-big-non-convex-envelope.at | 4 +- .../testsuite-tesselation-convex-envelope.at | 4 +- .../testsuite-tesselation-non-convex-envelope.at | 4 +- .../testsuite-tesselation-trianglematcher.at | 35 + .../GuiChecks/Tesselation/testsuite-tesselation.at | 3 + .../{molecuilder.in => adjacencymatcher.in} | 6 +- .../{molecuilder.in => trianglematcher.in} | 6 +- tests/JobMarket/Makefile.am | 24 +- .../CommandHelp/testsuite-python-commandhelp.at | 18 +- tests/Python/Makefile.am | 8 +- .../testsuite-1_2-dimethoxyethane.at | 4 +- .../testsuite-1_2-dimethylbenzene.at | 4 +- .../testsuite-2-methylcyclohexanone.at | 4 +- .../testsuite-N_N-dimethylacetamide.at | 4 +- .../Convex/amylose/testsuite-amylose.at | 4 +- .../Convex/benzene/testsuite-benzene.at | 4 +- .../Convex/cholesterol/testsuite-cholesterol.at | 4 +- .../Convex/cycloheptane/testsuite-cycloheptane.at | 4 +- .../testsuite-dimethyl_bromomalonate.at | 4 +- .../Convex/glucose/testsuite-glucose.at | 4 +- .../Tesselations/Convex/heptan/testsuite-heptan.at | 4 +- .../Convex/isoleucine/testsuite-isoleucine.at | 4 +- .../Convex/neohexane/testsuite-neohexane.at | 4 +- .../Convex/proline/testsuite-proline.at | 4 +- .../Convex/putrescine/testsuite-putrescine.at | 4 +- .../tartaric_acid/testsuite-tartaric_acid.at | 4 +- tests/Tesselations/Makefile.am | 9 +- .../testsuite-1_2-dimethoxyethane.at | 4 +- .../testsuite-1_2-dimethylbenzene.at | 4 +- .../testsuite-2-methylcyclohexanone.at | 4 +- .../testsuite-N_N-dimethylacetamide.at | 4 +- .../NonConvex/benzene/testsuite-benzene.at | 4 +- .../NonConvex/cholesterol/testsuite-cholesterol.at | 4 +- .../cycloheptane/testsuite-cycloheptane.at | 4 +- .../testsuite-dimethyl_bromomalonate.at | 4 +- .../NonConvex/glucose/testsuite-glucose.at | 4 +- .../NonConvex/heptan/testsuite-heptan.at | 4 +- .../NonConvex/isoleucine/testsuite-isoleucine.at | 4 +- .../NonConvex/neohexane/testsuite-neohexane.at | 4 +- .../NonConvex/proline/testsuite-proline.at | 4 +- .../NonConvex/putrescine/testsuite-putrescine.at | 4 +- .../tartaric_acid/testsuite-tartaric_acid.at | 4 +- .../trianglematcher.in} | 6 +- .../AdjacencyMatcher/pre/notequal.adj} | 6 +- .../AdjacencyMatcher/pre/notequal2.adj} | 6 +- .../post => Bond/AdjacencyMatcher/pre}/test.adj | 4 +- .../AdjacencyMatcher/pre/test2.adj} | 1 + .../testsuite-bond-adjacencymatcher.at | 34 + tests/regression/Bond/testsuite-bond.at | 3 + ...suite-fragmentation-fragmentation-automation.at | 8 +- .../testsuite-graph-depth-first-search.at | 3 +- .../testsuite-graph-subgraph-dissection.at | 3 +- tests/regression/Makefile.am | 13 +- .../testsuite-molecules-save-adjacency.at | 2 +- .../testsuite-parser-set-parameters-mpqc-basis.at | 9 +- ...ite-parser-set-parameters-mpqc-maxiterations.at | 9 +- .../Mpqc/testsuite-parser-set-parameters-mpqc.at | 9 +- ...ion-select-atoms-inside-cuboid-with-defaults.at | 6 +- ...stsuite-selection-select-atoms-inside-cuboid.at | 6 +- ...suite-selection-unselect-atoms-inside-cuboid.at | 6 +- ...stsuite-selection-select-atoms-inside-sphere.at | 6 +- ...te-selection-select-atoms-inside-tiny-sphere.at | 6 +- ...suite-selection-unselect-atoms-inside-sphere.at | 6 +- ...-selection-unselect-atoms-inside-tiny-sphere.at | 6 +- ...testsuite-selection-select-molecules-by-name.at | 6 +- ...stsuite-selection-unselect-molecules-by-name.at | 6 +- .../testsuite-tesselation-big-convex-envelope.at | 4 +- ...estsuite-tesselation-big-non-convex-envelope.at | 4 +- .../testsuite-tesselation-convex-envelope.at | 4 +- .../testsuite-tesselation-non-convex-envelope.at | 4 +- .../Tesselation/TriangleMatcher/pre/convex.dat | 5 + .../TriangleMatcher/pre/convex_none.dat | 5 + .../TriangleMatcher/pre/convex_other.dat | 5 + .../testsuite-tesselation-trianglematcher.at | 35 + .../Tesselation/testsuite-tesselation.at | 3 + .../adjacencymatcher.in} | 6 +- .../trianglematcher.in} | 6 +- utils/Bash/Makefile.am | 3 +- utils/Python/Makefile.am | 4 +- utils/developer/createGuiChecks.sh | 14 +- 446 files changed, 9387 insertions(+), 6334 deletions(-) create mode 100644 debian/changelog create mode 100644 debian/compat create mode 100644 debian/control create mode 100644 debian/copyright create mode 100644 debian/molecuilder-dev.install create mode 100644 debian/molecuilder.install create mode 100755 debian/rules create mode 100644 debian/source/format create mode 100755 makeDebianPackage.sh create mode 100644 src/Bond/AdjacencyMatcher/Adjacency.hpp create mode 100644 src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp create mode 100644 src/Bond/AdjacencyMatcher/Makefile.am copy src/Descriptors/{MoleculePtrDescriptor.cpp => AtomNameDescriptor.cpp} (60%) create mode 100644 src/Descriptors/AtomNameDescriptor.hpp create mode 100644 src/Descriptors/AtomNameDescriptor_impl.hpp create mode 100644 src/Parameters/Specifics/Value_elements.cpp copy src/Parameters/Specifics/{Value_element.hpp => Value_elements.hpp} (100%) create mode 100644 src/Tesselation/TriangleMatcher/Makefile.am create mode 100644 src/Tesselation/TriangleMatcher/Triangle.hpp create mode 100644 src/Tesselation/TriangleMatcher/TriangleMatcher.cpp create mode 100644 src/Tesselation/TriangleMatcher/types.hpp create mode 100644 src/ThreadGuard.hpp create mode 100644 src/UIElements/Views/Qt4/QtSelectionChangedAgent.cpp create mode 100644 src/UIElements/Views/Qt4/QtSelectionChangedAgent.hpp create mode 100644 tests/GuiChecks/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at create mode 100644 tests/GuiChecks/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at copy tests/GuiChecks/{molecuilder.in => adjacencymatcher.in} (72%) copy tests/GuiChecks/{molecuilder.in => trianglematcher.in} (71%) copy tests/{GuiChecks/molecuilder.in => Tesselations/trianglematcher.in} (71%) copy tests/regression/{Molecules/SaveAdjacency/post/test.adj => Bond/AdjacencyMatcher/pre/notequal.adj} (52%) copy tests/regression/{Molecules/SaveAdjacency/post/test.adj => Bond/AdjacencyMatcher/pre/notequal2.adj} (51%) copy tests/regression/{Molecules/SaveAdjacency/post => Bond/AdjacencyMatcher/pre}/test.adj (66%) copy tests/regression/{Molecules/SaveAdjacency/post/test.adj => Bond/AdjacencyMatcher/pre/test2.adj} (98%) create mode 100644 tests/regression/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at create mode 100644 tests/regression/Tesselation/TriangleMatcher/pre/convex.dat create mode 100644 tests/regression/Tesselation/TriangleMatcher/pre/convex_none.dat create mode 100644 tests/regression/Tesselation/TriangleMatcher/pre/convex_other.dat create mode 100644 tests/regression/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at copy tests/{GuiChecks/molecuilder.in => regression/adjacencymatcher.in} (72%) copy tests/{GuiChecks/molecuilder.in => regression/trianglematcher.in} (71%) hooks/post-receive --

1 0