- Molecuilder-devel

[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules created. v1.4.9-27-g65550d8
by git＠ins.uni-bonn.de 11 Jan '15

11 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been created at 65550d858d4c18ea86fba70e93129adfcf2b20a0 (commit) - Log ----------------------------------------------------------------- commit 65550d858d4c18ea86fba70e93129adfcf2b20a0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Jan 9 12:24:22 2015 +0100 FIX: World::SetTime() erased molecules twice. - once in SetTime() and then again in DFS.Update...(). commit be7317df86cdcf7df57a40c82b31ee2ccf0ade9a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Dec 20 21:09:50 2014 +0100 TranslateAtoms now has extra option position. - this is preparatory for translate-molecules where we need to fill in this option. commit 710e95c8989e4ed2c92d757fd34b4dee0f6322c2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:37:33 2014 +0100 Added TranslateMolecule action. - added translate-molecule to userguide. - added translate-miolecule regression tests. commit 094b32830d79a8c2fbee334fcac5ec3c20e17aea Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:45:44 2014 +0100 Added Push/PopMolecules selection action. - added push-molecule to userguide. - added regression tests to Push/PopMoleculeSelection. commit 5c0292f5f303fa29532c6b18de91f7506050bcef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:37:06 2014 +0100 Added Push/PopAtom selection actions. - added push-atom to userguide. - added regression tests to Push/PopAtomsSelection. commit 7c81c794cf1cf4699aeb057b4f34ecb47d460a74 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 20:32:31 2014 +0100 Added push/pop[Atoms|Molecules]Selection to World. - this is mostly convenience for MakroActions to use selections and still keep the selection from the user. commit 27554da98b22f86d918faa0bc53e6be63af8399e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 20:10:19 2014 +0100 EDITME: FIX: ActionQueue is no longer cleared when Action fails. - we only remove the present and all following Actions. - also cleaned up threaded/non-threaded parts of ActionQueue: CurrentAction, tempQueue is solely used in threaded part. - EDITME: clearTempQueue() should be in threaded only but I did not want to recompile the whole thing (due to header change). commit 4ae214783b53e3d69cbea0c4ceb6e77a697f3a30 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 19:15:47 2014 +0100 FIX: Failing Actions do not clear ActionQueue/History anymore. commit dc1a845623c807829df2205c648c55f086665443 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 21:38:29 2014 +0100 FIX: Bonds from new molecules are instantiated, too. - when filling in molecules, initially empty molecules are created and atoms added lateron. Added atoms would not add their already present atoms but only new ones via an Observer update. Now when an atom is inserted, all bonds if any are added. commit 1cf4ae6f168457477a3fd0c1614f799cdce4d35a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 19:41:27 2014 +0100 Undo/Redobuttons are grayed out when respective Action not possible. commit add4b1ae0a62b37fd99f82b311047f99c3619338 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 18:29:46 2014 +0100 Added new RemoveAction for molecules. - also add regression test. - added remove-molecule to userguide. commit c73a14327ac84582acc3e2b69cba8d87cab652c3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 09:28:58 2014 +0100 Extended UndoRedoHelpers by AddingMultipleMoleculesfromAtomicInfo. commit 90d1ad28a516c44354e10e1f7ffba3f15bd6d0e9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 21:05:41 2014 +0100 tempcommit: New update scheme for QtMoleculeList requires changing flag to prevent VisibilityChanged() trigger. commit a2b40c62e44b11ed86e1efe99679a4acd88cb78d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 20:43:05 2014 +0100 tempcommit: Extracted add/removeItem in QtMoleculeList, no more complete refilling on update. - this is unfinished as we can't find the item to a molecule that is about to be removed. commit d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 09:28:30 2014 +0100 Extended selection action for Molecule ids to multiple ids. commit b6d92e374e7b56b8a8b8399faf64a7363294d1b4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Dec 6 00:06:53 2014 +0100 GLWorldView's view may be changed via keyboard (especially zoom). - Zoom and keys distance change scaled by eye-center distance. commit f115ccd1f9b646866bddc9583360ebb5e27593b9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 3 23:15:42 2014 +0100 For GLMoleculeObject_atom element and position are only reset..() on hook'ed in draw(). - similarly as with GLMoleculeObject_molecule, we check in draw() when need to reset..() and do it before the actual drawing. This speeds up a lot. commit a7aebd81a7ffd4f46af11dbf5e777b8833c831cf Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 3 20:20:31 2014 +0100 World removes empty molecules. - on destroyAtom() of molecule's last atom, destroyMolecule() is called. - FIX: destroyMolecule(molecule *) did use OBSERVE unncessarily. This caused seg'fault. - extracted removeAtomsinMolecule from molecule class. This is necessary since World will automatically remove empty molecules. commit 7b93f9dad1f3a6bad5e0303472273227cebbcc50 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Nov 18 20:52:44 2014 +0100 Added MeshFreeType to GLMoleculeObject. commit 3eb91c4b2479f25056f44fbdb7275387992fccea Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Nov 16 17:31:35 2014 +0100 Molecule's Visibility can be changed "group-wise". - FIX: Removed this funny clear() on update() signal. Also using notifications now, which appear less often. commit 9a7ef90a4cc774b21092647cb1d743b0a756dbb6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 23:35:35 2014 +0100 Molecules can be (un)selected by clicking on the tesselation hull. commit 2b596f94d8d4eaae7f603d8c5e7e9546cc3cfe3f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 23:26:05 2014 +0100 Hovering over molecules is working including update of QtInfoBox. - SelectionBox is drawn again when molecule is fully shown. commit 7b59843c6e0fcf96629146aac977053a6deaab43 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 20:01:33 2014 +0100 GLMoleculeObject_molecule listens to AtomMoved signal to update hull only when necessary. commit c32d21acd3e47b463b8a5f9dc56fe34113509f73 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 19:14:17 2014 +0100 Molecule relays atom's PositionChanged as AtomMoved signal. - this allows to update tesselation hull only when something changed. commit 34e7fdbe244fe3d4cc7ffaf1162683ab8c7eff45 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Nov 6 00:22:55 2014 +0100 GLMoleculeObject_molecule display tesselated surface in m_visible case. - set TesselationHull radius to 2., independent of mol's bounding sphere. - added bool to indicate when subjectKilled() had been called. commit 739ee9365702db570a88ff6eecfa0f87be1ec93b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 5 23:00:40 2014 +0100 GLMoleculeObject have m_visible, settable in QtMoleculeList. - is connected via QtMainWindow an GLWorldView, GLWorldScene. - i.e. molecule's atoms and bond display can now be switched on and off. commit 8c001aeb40538cff3bf30540d0cc0b8359472d75 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 5 20:19:42 2014 +0100 GLMoleculeObject_atoms and .._bonds are now children of .._molecule. - GLMoleculeObject::initialize() is now virtual. - .._molecule is now draw()ing its children, i.e. initialize() of .._molecule calls in turn those of .._atom and .._bond. Similarly with draw. - molecule has a lastchangedatom member variable now. - FIX: molecule::getBoundingSphere() did not check for no atoms. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules deleted. v1.4.9-43-g99b1759
by git＠ins.uni-bonn.de 11 Jan '15

11 Jan '15

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been deleted was 99b1759cc8e41e6df7fbdf41b40c5c6ff40ad5b1 ----------------------------------------------------------------------- 99b1759cc8e41e6df7fbdf41b40c5c6ff40ad5b1 Added Push/PopMolecules selection action. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules updated. v1.4.9-43-g99b1759
by git＠ins.uni-bonn.de 19 Dec '14

19 Dec '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been updated via 99b1759cc8e41e6df7fbdf41b40c5c6ff40ad5b1 (commit) via 0f2e30633c636c0cccb1e31b38bfa7bc743ce630 (commit) via 0bda4554bfa598ae892d665e5afa95d7a682393b (commit) via 2122ad01dba5a4567eafce075beb89f7d50d61a6 (commit) via 5d9b8641f43b319ff2a5b7453d5ff9bb2f3555ee (commit) via 7315986e2f2bd37ded044dd495b6d2b890696080 (commit) via f7ffa9816725f66a38e9311eae206b41ea09145f (commit) via 2c21102b9c991c3977d061f7eab6bf4c195cab78 (commit) via 9c602744180737b258d8a92605021afb88cdc500 (commit) via f763f34ab6077c50b53ca2d1df19de17bd7b9d77 (commit) via 6c74c06c3ba093a18bcbd07a1282da2b3edc6e7d (commit) via 94c17043166ec2d8b4cf369029351dedcbda86f9 (commit) from 71ec5f12bad3f9ca07448c022d49cd6cf4cba571 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 99b1759cc8e41e6df7fbdf41b40c5c6ff40ad5b1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:45:44 2014 +0100 Added Push/PopMolecules selection action. commit 0f2e30633c636c0cccb1e31b38bfa7bc743ce630 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:37:33 2014 +0100 Added TranslateMolecule action. commit 0bda4554bfa598ae892d665e5afa95d7a682393b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:37:06 2014 +0100 Added Push/PopAtom selection actions. commit 2122ad01dba5a4567eafce075beb89f7d50d61a6 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:36:38 2014 +0100 tempcommit: World Queue fixes. commit 5d9b8641f43b319ff2a5b7453d5ff9bb2f3555ee Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 19 17:36:18 2014 +0100 tempcommit: clearTempQueue() fixes. commit 7315986e2f2bd37ded044dd495b6d2b890696080 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 20:32:31 2014 +0100 Added push/pop[Atoms|Molecules]Selection to World. - this is mostly convenience for MakroActions to use selections and still keep the selection from the user. commit f7ffa9816725f66a38e9311eae206b41ea09145f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 20:32:19 2014 +0100 tempcommit: Fixing clearTempQueue(). commit 2c21102b9c991c3977d061f7eab6bf4c195cab78 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 20:27:35 2014 +0100 tempcommit: Fixing SelectionBox drawing, was not scaled nor translated. Merge with ... commit 9c602744180737b258d8a92605021afb88cdc500 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 20:10:19 2014 +0100 EDITME: FIX: ActionQueue is no longer cleared when Action fails. - we only remove the present and all following Actions. - also cleaned up threaded/non-threaded parts of ActionQueue: CurrentAction, tempQueue is solely used in threaded part. - EDITME: clearTempQueue() should be in threaded only but I did not want to recompile the whole thing (due to header change). commit f763f34ab6077c50b53ca2d1df19de17bd7b9d77 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 19:17:01 2014 +0100 tempcommit: Merge with 94c1704 commit 6c74c06c3ba093a18bcbd07a1282da2b3edc6e7d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 19:15:47 2014 +0100 FIX: Failing Actions do not clear ActionQueue/History anymore. commit 94c17043166ec2d8b4cf369029351dedcbda86f9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Dec 14 19:11:47 2014 +0100 tempcommit: Zoom and keys distance change scaled by eye-center distance. Merge with ... ----------------------------------------------------------------------- Summary of changes: src/Actions/Action.cpp | 10 +- src/Actions/ActionQueue.cpp | 82 +++++++++------- src/Actions/ActionQueue.hpp | 36 +++++-- src/Actions/ActionRegistry.cpp | 14 +++ src/Actions/GlobalListOfActions.hpp | 5 + .../GraphAction/SubgraphDissectionAction.cpp | 26 +---- src/Actions/Makefile.am | 27 ++++- src/Actions/MoleculeAction/TranslateAction.cpp | 103 ++++++++++++++++++++ src/Actions/MoleculeAction/TranslateAction.def | 33 ++++++ src/Actions/MoleculeAction/TranslateAction.hpp | 22 ++++ .../SelectionAction/Atoms/PopAtomsAction.cpp | 72 ++++++++++++++ .../SelectionAction/Atoms/PopAtomsAction.def | 33 ++++++ .../SelectionAction/Atoms/PopAtomsAction.hpp | 22 ++++ .../SelectionAction/Atoms/PushAtomsAction.cpp | 73 ++++++++++++++ .../SelectionAction/Atoms/PushAtomsAction.def | 33 ++++++ .../SelectionAction/Atoms/PushAtomsAction.hpp | 22 ++++ .../Molecules/PopMoleculesAction.cpp | 72 ++++++++++++++ .../Molecules/PopMoleculesAction.def | 33 ++++++ .../Molecules/PopMoleculesAction.hpp | 22 ++++ .../Molecules/PushMoleculesAction.cpp | 73 ++++++++++++++ .../Molecules/PushMoleculesAction.def | 33 ++++++ .../Molecules/PushMoleculesAction.hpp | 22 ++++ src/UIElements/CommandLineUI/CommandLineParser.cpp | 1 + src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp | 3 +- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 17 +++- src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp | 10 ++- src/World.cpp | 30 ++++++- src/World.hpp | 7 ++ 28 files changed, 849 insertions(+), 87 deletions(-) create mode 100644 src/Actions/MoleculeAction/TranslateAction.cpp create mode 100644 src/Actions/MoleculeAction/TranslateAction.def create mode 100644 src/Actions/MoleculeAction/TranslateAction.hpp create mode 100644 src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp create mode 100644 src/Actions/SelectionAction/Atoms/PopAtomsAction.def create mode 100644 src/Actions/SelectionAction/Atoms/PopAtomsAction.hpp create mode 100644 src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp create mode 100644 src/Actions/SelectionAction/Atoms/PushAtomsAction.def create mode 100644 src/Actions/SelectionAction/Atoms/PushAtomsAction.hpp create mode 100644 src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp create mode 100644 src/Actions/SelectionAction/Molecules/PopMoleculesAction.def create mode 100644 src/Actions/SelectionAction/Molecules/PopMoleculesAction.hpp create mode 100644 src/Actions/SelectionAction/Molecules/PushMoleculesAction.cpp create mode 100644 src/Actions/SelectionAction/Molecules/PushMoleculesAction.def create mode 100644 src/Actions/SelectionAction/Molecules/PushMoleculesAction.hpp hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules updated. v1.4.9-31-g71ec5f1
by git＠ins.uni-bonn.de 13 Dec '14

13 Dec '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been updated via 71ec5f12bad3f9ca07448c022d49cd6cf4cba571 (commit) via 94444b5f4bd072f57b46989474a7407caf6a75c4 (commit) via 98e539ae2870958646d3af1faf75d84de2de0941 (commit) via 475d81cdae13f55cb3ab1a22ec9ea5784cec122d (commit) via 655f68de8bef7d0db47490198f9ddcc88ed29267 (commit) via e84c92bda5070ea442b1bbec14dafcf8fc69587f (commit) via 5a93de00c8f02283320b822aec6504f20d0822c3 (commit) via 3d33f4c3066f85982c6ed23a84bd8e9693f27cdb (commit) via c5a4e7f18f1f16913e26e27f9a919f933ee9e468 (commit) via 5df432a62c45c377195b2c1799e3122e1f2a25ee (commit) via 50c306d9853a916d7ca381740c48dcd24e72f602 (commit) via f84ff5bcec8b1dfcb0149eae79795d53ffa866ea (commit) via 0d1c15e4d7f98048440c8168616f255654632a55 (commit) from 197e264ced646aa6c0bc234550e7c76006790bef (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 71ec5f12bad3f9ca07448c022d49cd6cf4cba571 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Dec 13 09:09:40 2014 +0100 tempcommit: SelectionBox is drawn again when molecule is fully shown. - SelectionBox is not correctly updated. commit 94444b5f4bd072f57b46989474a7407caf6a75c4 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 21:38:29 2014 +0100 FIX: Bonds from new molecules are instantiated, too. - when filling in molecules, initially empty molecules are created and atoms added lateron. Added atoms would not add their already present atoms but only new ones via an Observer update. Now when an atom is inserted, all bonds if any are added. commit 98e539ae2870958646d3af1faf75d84de2de0941 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 21:05:41 2014 +0100 tempcommit: New update scheme for QtMoleculeList requires changing flag to prevent VisibilityChanged() trigger. commit 475d81cdae13f55cb3ab1a22ec9ea5784cec122d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 20:43:05 2014 +0100 tempcommit: Extracted add/removeItem in QtMoleculeList, no more complete refilling on update. - this is unfinished as we can't find the item to a molecule that is about to be removed. commit 655f68de8bef7d0db47490198f9ddcc88ed29267 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 19:41:27 2014 +0100 Undo/Redobuttons are grayed out when respective Action not possible. commit e84c92bda5070ea442b1bbec14dafcf8fc69587f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 19:22:55 2014 +0100 Extracted removeAtomsinMolecule from molecule class. - this is necessary since World will automatically remove empty molecules. commit 5a93de00c8f02283320b822aec6504f20d0822c3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 19:13:18 2014 +0100 tempcommit: Fixes due to molecules being automatically removed. commit 3d33f4c3066f85982c6ed23a84bd8e9693f27cdb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 19:03:06 2014 +0100 tempcommit: Fixes to RemoveAction. commit c5a4e7f18f1f16913e26e27f9a919f933ee9e468 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 18:50:58 2014 +0100 tempcommit: Fixes to World destroying empty molecules. commit 5df432a62c45c377195b2c1799e3122e1f2a25ee Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 18:43:03 2014 +0100 tempcommit: Fixes to extension of MoleculeIdAction. commit 50c306d9853a916d7ca381740c48dcd24e72f602 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 18:29:46 2014 +0100 Added new RemoveAction for molecules. - also add regression test. commit f84ff5bcec8b1dfcb0149eae79795d53ffa866ea Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 09:28:58 2014 +0100 Extended UndoRedoHelpers by AddingMultipleMoleculesfromAtomicInfo. commit 0d1c15e4d7f98048440c8168616f255654632a55 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Dec 12 09:28:30 2014 +0100 Extended selection action for Molecule ids to multiple ids. ----------------------------------------------------------------------- Summary of changes: src/Actions/ActionQueue.cpp | 10 + src/Actions/ActionQueue.hpp | 12 + src/Actions/GlobalListOfActions.hpp | 1 + src/Actions/Makefile.am | 3 + src/Actions/MoleculeAction/RemoveAction.cpp | 122 +++++++++++ .../RemoveAction.def} | 24 ++- .../RemoveAction.hpp | 8 +- .../SelectionAction/Atoms/NotAtomByIdAction.def | 1 - .../Molecules/MoleculeByIdAction.cpp | 65 +++++-- .../Molecules/MoleculeByIdAction.def | 16 +- .../Molecules/NotMoleculeByIdAction.cpp | 64 +++++-- .../Molecules/NotMoleculeByIdAction.def | 16 +- src/Actions/UndoRedoHelpers.cpp | 39 ++++- src/Actions/UndoRedoHelpers.hpp | 9 +- src/Actions/WorldAction/RepeatBoxAction.cpp | 8 +- src/Fragmentation/Exporters/ExportGraph.cpp | 3 +- src/Graph/unittests/AdjacencyListUnitTest.cpp | 3 +- src/MoleculeLeafClass.cpp | 7 +- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 77 +++++--- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp | 6 + src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp | 10 +- src/UIElements/Views/Qt4/QtMoleculeList.cpp | 216 +++++++++++++------- src/UIElements/Views/Qt4/QtMoleculeList.hpp | 6 + src/UIElements/Views/Qt4/QtToolBar.cpp | 59 +++++- src/UIElements/Views/Qt4/QtToolBar.hpp | 19 ++- .../Views/Qt4/QtToolBar_QtFavoriteActions.cpp | 1 - src/World.cpp | 1 + src/molecule.cpp | 6 +- src/molecule.hpp | 7 +- tests/regression/Makefile.am | 1 + .../Molecules/Remove/post/id0_2_missing.pdb | 38 ++++ .../regression/Molecules/Remove/post/water_box.pdb | 44 ++++ .../regression/Molecules/Remove/pre/water_box.pdb | 50 +++++ .../testsuite-molecules-remove.at} | 48 +++-- tests/regression/Molecules/testsuite-molecules.at | 3 + .../post/{id4_missing.xyz => id2_4_missing.xyz} | 5 +- .../post/{water_id4.xyz => water_id2_4.xyz} | 5 +- .../testsuite-selection-select-molecule-by-id.at | 10 +- .../testsuite-selection-unselect-molecule-by-id.at | 10 +- 39 files changed, 812 insertions(+), 221 deletions(-) create mode 100644 src/Actions/MoleculeAction/RemoveAction.cpp copy src/Actions/{GraphAction/DestroyAdjacencyAction.def => MoleculeAction/RemoveAction.def} (59%) copy src/Actions/{AtomAction => MoleculeAction}/RemoveAction.hpp (61%) create mode 100644 tests/regression/Molecules/Remove/post/id0_2_missing.pdb create mode 100644 tests/regression/Molecules/Remove/post/water_box.pdb create mode 100644 tests/regression/Molecules/Remove/pre/water_box.pdb copy tests/regression/Molecules/{ChangeBondAngle/testsuite-molecules-change-bond-angle.at => Remove/testsuite-molecules-remove.at} (53%) rename tests/regression/Selection/Molecules/MoleculeById/post/{id4_missing.xyz => id2_4_missing.xyz} (99%) rename tests/regression/Selection/Molecules/MoleculeById/post/{water_id4.xyz => water_id2_4.xyz} (65%) hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules updated. v1.4.9-18-g197e264
by git＠ins.uni-bonn.de 12 Dec '14

12 Dec '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been updated via 197e264ced646aa6c0bc234550e7c76006790bef (commit) from 174c199165b1533ce15955e80eb49c9a501761eb (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 197e264ced646aa6c0bc234550e7c76006790bef Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Dec 6 00:06:53 2014 +0100 GLWorldView's view may be changed via keyboard (especially zoom). ----------------------------------------------------------------------- Summary of changes: src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp | 27 +++++++++++++++++++++++++ 1 files changed, 27 insertions(+), 0 deletions(-) hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules updated. v1.4.9-17-g174c199
by git＠ins.uni-bonn.de 03 Dec '14

03 Dec '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been updated via 174c199165b1533ce15955e80eb49c9a501761eb (commit) via 51434cab019b5c476aad17eeaa7c454f7ba1a5f8 (commit) via b0d664acd7255e191d084c1a7308c53818ec56ac (commit) via d9c271d6f3a4c76cd320838b4f400ba74ef20576 (commit) from 108652894fc66605c48fd9dc0d85960c03a107eb (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 174c199165b1533ce15955e80eb49c9a501761eb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 3 23:15:42 2014 +0100 For GLMoleculeObject_atom element and position are only reset..() on hook'ed in draw(). - similarly as with GLMoleculeObject_molecule, we check in draw() when need to reset..() and do it before the actual drawing. This speeds up a lot. commit 51434cab019b5c476aad17eeaa7c454f7ba1a5f8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 3 21:07:53 2014 +0100 tempcommit: updateTesselationHull() was not called in GLMoleculeObject_molecule::draw(). - this caused no update despite atoms having been moved. commit b0d664acd7255e191d084c1a7308c53818ec56ac Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 3 20:30:54 2014 +0100 FIX: In QtMoleculeList group is no longer selectable. commit d9c271d6f3a4c76cd320838b4f400ba74ef20576 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Dec 3 20:20:31 2014 +0100 World removes empty molecules. - on destroyAtom() of molecule's last atom, destroyMolecule() is called. - FIX: destroyMolecule(molecule *) did use OBSERVE unncessarily. This caused seg'fault. ----------------------------------------------------------------------- Summary of changes: .../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp | 28 ++++++++++++++++--- .../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp | 5 +++ .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 2 + src/UIElements/Views/Qt4/QtMoleculeList.cpp | 4 +- src/World.cpp | 8 +++++- 5 files changed, 39 insertions(+), 8 deletions(-) hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules updated. v1.4.9-13-g1086528
by git＠ins.uni-bonn.de 18 Nov '14

18 Nov '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been updated via 108652894fc66605c48fd9dc0d85960c03a107eb (commit) via 63025a47676250073220ed79c30da598cf6419b1 (commit) via 1b8e58c02badd91cbfdfd06656878d7d0e623808 (commit) via fd4077208fecdc6637f3c62c34907d9ab2c4b8eb (commit) from 9152f55e9acb1ec1bcddd08248af17fe193f3d5c (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 108652894fc66605c48fd9dc0d85960c03a107eb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Nov 18 20:53:47 2014 +0100 tempcommit: Merge with d5eea21 commit 63025a47676250073220ed79c30da598cf6419b1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Nov 18 20:53:12 2014 +0100 GLMoleculeObject_molecule's UpdateBoundingBox() only called when necessary. commit 1b8e58c02badd91cbfdfd06656878d7d0e623808 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Nov 18 20:52:44 2014 +0100 Added MeshFreeType to GLMoleculeObject. commit fd4077208fecdc6637f3c62c34907d9ab2c4b8eb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Nov 16 17:31:35 2014 +0100 Molecule's Visibility can be changed "group-wise". - FIX: Removed this funny clear() on update() signal. Also using notifications now, which appear less often. ----------------------------------------------------------------------- Summary of changes: src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp | 14 ++- src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp | 5 + .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 22 ++-- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp | 1 + src/UIElements/Views/Qt4/QtMoleculeList.cpp | 127 +++++++++++++++----- src/UIElements/Views/Qt4/QtMoleculeList.hpp | 14 ++- 6 files changed, 143 insertions(+), 40 deletions(-) hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules updated. v1.4.9-9-g9152f55
by git＠ins.uni-bonn.de 13 Nov '14

13 Nov '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been updated via 9152f55e9acb1ec1bcddd08248af17fe193f3d5c (commit) via 975cd086d8fb7bebc6f153ed2929294c650ca974 (commit) via 6c1a9867afae698c9960d65a071636ad8750cb70 (commit) via 16de4ab3a020c943a28442b0f393209522e02e81 (commit) via 5fb01183e168093637148acd51d1a44b9cf4ae54 (commit) from a6663c4c6a601e59af979e8f8b82299069ccf653 (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 9152f55e9acb1ec1bcddd08248af17fe193f3d5c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 23:35:35 2014 +0100 Molecules can be (un)selected by clicking on the tesselation hull. commit 975cd086d8fb7bebc6f153ed2929294c650ca974 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 23:26:05 2014 +0100 Hovering over molecules is working including update of QtInfoBox. commit 6c1a9867afae698c9960d65a071636ad8750cb70 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 20:01:33 2014 +0100 GLMoleculeObject_molecule listens to AtomMoved signal to update hull only when necessary. commit 16de4ab3a020c943a28442b0f393209522e02e81 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 19:59:51 2014 +0100 tempcommit: Set TesselationHull radius to 2., independent of mol's bounding sphere. commit 5fb01183e168093637148acd51d1a44b9cf4ae54 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 12 19:14:17 2014 +0100 Molecule relays atom's PositionChanged as AtomMoved signal. - this allows to update tesselation hull only when something changed. ----------------------------------------------------------------------- Summary of changes: src/Atom/atom.cpp | 10 ++- src/UIElements/Qt4/QtMainWindow.cpp | 3 +- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp | 84 +++++++++++++++++--- .../Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp | 9 ++- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp | 17 ++++- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp | 4 +- src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp | 10 ++- src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp | 6 +- src/UIElements/Views/Qt4/QtInfoBox.cpp | 37 ++++++++- src/UIElements/Views/Qt4/QtInfoBox.hpp | 6 +- src/molecule.cpp | 38 +++++++++ src/molecule.hpp | 5 + 12 files changed, 202 insertions(+), 27 deletions(-) hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules created. v1.4.9-4-ga6663c4
by git＠ins.uni-bonn.de 06 Nov '14

06 Nov '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been created at a6663c4c6a601e59af979e8f8b82299069ccf653 (commit) - Log ----------------------------------------------------------------- commit a6663c4c6a601e59af979e8f8b82299069ccf653 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Nov 6 00:22:55 2014 +0100 GLMoleculeObject_molecule display tesselated surface in m_visible case. commit e658f1476c231eb0bfaed2af32df3d60ef6eee91 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 5 23:00:40 2014 +0100 GLMoleculeObject have m_visible, settable in QtMoleculeList. - is connected via QtMainWindow an GLWorldView, GLWorldScene. - i.e. molecule's atoms and bond display can now be switched on and off. commit d5eea2183811d1e7905ba2f05253516661f33d58 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 5 20:19:42 2014 +0100 GLMoleculeObject_atoms and .._bonds are now children of .._molecule. - GLMoleculeObject::initialize() is now virtual. - .._molecule is now draw()ing its children, i.e. initialize() of .._molecule calls in turn those of .._atom and .._bond. Similarly with draw. commit 15c75f81c6cdda2f09bf5dfdbf24c513d58ada80 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Nov 5 21:49:45 2014 +0100 molecule has a lastchangedatom member variable now. - FIX: molecule::getBoundingSphere() did not check for no atoms. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_TesselatedLargeMolecules deleted. v1.4.9-4-gb618fd3
by git＠ins.uni-bonn.de 06 Nov '14

06 Nov '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, GUI_TesselatedLargeMolecules has been deleted was b618fd3708b8333749937ec3b3292deb7b55754c ----------------------------------------------------------------------- b618fd3708b8333749937ec3b3292deb7b55754c GLMoleculeObject_molecule display tesselated surface in m_visible case. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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