#
# ChangeLog for /
#
# Generated by Trac 1.6
# Dec 10, 2025, 7:34:00 AM

Thu, 14 Jan 2010 13:49:42 GMT Tillmann Crueger <crueger@…> [931903]
	* molecuilder/src/menu.cpp (modified)

	Made embeddMolecules menu-point use the new dialog framework


Wed, 13 Jan 2010 11:05:17 GMT Tillmann Crueger <crueger@…> [1630ce]
	* molecuilder/src/menu.cpp (modified)

	Used new Query Infrastructure for SimpleAdd menupoint


Wed, 13 Jan 2010 11:05:02 GMT Tillmann Crueger <crueger@…> [3896fc]
	* molecuilder/src/UIElements/Dialog.cpp (modified)
	* molecuilder/src/UIElements/Dialog.hpp (modified)
	* molecuilder/src/UIElements/TextDialog.cpp (modified)
	* molecuilder/src/UIElements/TextDialog.hpp (modified)

	Added infrastructure to query molecules from MoleculeList


Wed, 13 Jan 2010 10:22:29 GMT Tillmann Crueger <crueger@…> [f89c1c]
	* molecuilder/src/UIElements/Dialog.cpp (modified)
	* molecuilder/src/UIElements/Dialog.hpp (modified)
	* molecuilder/src/UIElements/TextDialog.cpp (modified)
	* molecuilder/src/UIElements/TextDialog.hpp (modified)
	* molecuilder/src/builder.cpp (modified)

	Changed dialog structure to  use objects for queries.


Mon, 11 Jan 2010 10:40:20 GMT Tillmann Crueger <crueger@…> [c489d9]
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Removed some unessecary methods from oldMenu


Sat, 09 Jan 2010 12:02:13 GMT Tillmann Crueger <crueger@…> [1120b7]
	* molecuilder/doc/menu classes.uxf (modified)

	Updated UML-Diagramm of all UI-Classes


Sat, 09 Jan 2010 11:30:49 GMT Tillmann Crueger <crueger@…> [d97af9]
	* molecuilder/src/Actions/ActionRegistry.cpp (modified)
	* molecuilder/src/UIElements/MainWindow.hpp (modified)
	* molecuilder/src/UIElements/TextUIFactory.cpp (modified)
	* molecuilder/src/UIElements/TextUIFactory.hpp (modified)
	* molecuilder/src/UIElements/TextWindow.cpp (modified)
	* molecuilder/src/UIElements/TextWindow.hpp (modified)
	* molecuilder/src/UIElements/UIFactory.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Seperated building of mainWindow and contained Menus

	- Moved code ...


Thu, 07 Jan 2010 14:46:34 GMT Tillmann Crueger <crueger@…> [3e8325]
	* molecuilder/src/Actions/Action.cpp (modified)
	* molecuilder/src/Actions/Action.hpp (modified)
	* molecuilder/src/Actions/ActionRegistry.cpp (added)
	* molecuilder/src/Actions/ActionRegistry.hpp (added)
	* molecuilder/src/Actions/ErrorAction.cpp (modified)
	* molecuilder/src/Actions/ErrorAction.hpp (modified)
	* molecuilder/src/Actions/MakroAction.cpp (modified)
	* molecuilder/src/Actions/MakroAction.hpp (modified)
	* molecuilder/src/Actions/MethodAction.cpp (modified)
	* molecuilder/src/Actions/MethodAction.hpp (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/UIElements/TextUIFactory.cpp (modified)
	* molecuilder/src/UIElements/TextUIFactory.hpp (modified)
	* molecuilder/src/UIElements/TextWindow.cpp (modified)
	* molecuilder/src/UIElements/UIFactory.cpp (modified)
	* molecuilder/src/UIElements/UIFactory.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/unittests/ActionSequenceTest.cpp (modified)

	Added a central registry that allows access to actions by name.


Thu, 07 Jan 2010 13:24:06 GMT Tillmann Crueger <crueger@…> [34ff5e6]
	* molecuilder/src/UIElements/MainWindow.cpp (added)
	* molecuilder/src/UIElements/MainWindow.hpp (added)
	* molecuilder/src/UIElements/TextWindow.cpp (added)
	* molecuilder/src/UIElements/TextWindow.hpp (added)

	Added support for creating a main window using the UIFactory.


Tue, 05 Jan 2010 15:34:52 GMT Tillmann Crueger <crueger@…> [6d21bd]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/UIElements/Dialog.cpp (added)
	* molecuilder/src/UIElements/Dialog.hpp (added)
	* molecuilder/src/UIElements/TextDialog.cpp (added)
	* molecuilder/src/UIElements/TextDialog.hpp (added)
	* molecuilder/src/UIElements/TextUIFactory.cpp (added)
	* molecuilder/src/UIElements/TextUIFactory.hpp (added)
	* molecuilder/src/UIElements/UIFactory.cpp (added)
	* molecuilder/src/UIElements/UIFactory.hpp (added)

	Added Basis for creating globally accessible and compatible ...


Tue, 05 Jan 2010 13:48:05 GMT Tillmann Crueger <crueger@…> [53f5e6]
	* molecuilder/src/Actions/ErrorAction.cpp (modified)
	* molecuilder/src/Actions/ErrorAction.hpp (modified)
	* molecuilder/src/menu.cpp (modified)

	Transitioned MergeMolecule Menu to new menu structure


Tue, 05 Jan 2010 10:11:52 GMT Tillmann Crueger <crueger@…> [70c4aa6]
	* molecuilder/src/Actions/ErrorAction.cpp (added)
	* molecuilder/src/Actions/ErrorAction.hpp (added)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Extracted all methods from MergeMolecules Menu

	- Added new action ...


Tue, 05 Jan 2010 09:23:25 GMT Tillmann Crueger <crueger@…> [538744]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Moved saveConfig method from oldmenu to a method inside config class


Sat, 02 Jan 2010 15:53:39 GMT Tillmann Crueger <crueger@…> [16f86d]
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Removed unecessary method stubs from oldmenu class


Sat, 02 Jan 2010 15:49:40 GMT Tillmann Crueger <crueger@…> [f48622]
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Moved several Methods from Menu to MoleculeListClass


Sat, 02 Jan 2010 15:28:29 GMT Tillmann Crueger <crueger@…> [c7dcff]
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Made EditMoleculesMenu a Submenu inside the MainMenu


Sat, 02 Jan 2010 15:18:00 GMT Tillmann Crueger <crueger@…> [1f137d]
	* molecuilder/src/Menu/TextMenu.cpp (modified)
	* molecuilder/src/menu.cpp (modified)

	Transitioned EditMoleculesMenu to new menu structure


Tue, 29 Dec 2009 12:56:55 GMT Tillmann Crueger <crueger@…> [077f6e]
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Extracted several methods from the EditMolecules Submenu.


Tue, 29 Dec 2009 12:20:20 GMT Tillmann Crueger <crueger@…> [aa117c]
	* molecuilder/src/Menu/DisplayMenuItem.cpp (modified)
	* molecuilder/src/Menu/DisplayMenuItem.hpp (modified)
	* molecuilder/src/Menu/MenuItem.cpp (modified)
	* molecuilder/src/Menu/MenuItem.hpp (modified)
	* molecuilder/src/Menu/SeperatorItem.cpp (modified)
	* molecuilder/src/Menu/SeperatorItem.hpp (modified)
	* molecuilder/src/Menu/TextMenu.cpp (modified)
	* molecuilder/src/Menu/TextMenu.hpp (modified)

	Added possibility to add default Items to textMenus


Tue, 29 Dec 2009 11:57:09 GMT Tillmann Crueger <crueger@…> [fab853]
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Moved flipChosen method from oldmenu to MoleculeListClass


Tue, 29 Dec 2009 11:47:57 GMT Tillmann Crueger <crueger@…> [8d24e2]
	* molecuilder/src/unittests/ActionSequenceTest.cpp (modified)
	* molecuilder/src/unittests/ActionSequenceTest.hpp (modified)

	Added more tests for Actionsequence

	- Test if every included object ...


Thu, 17 Dec 2009 16:56:06 GMT Tillmann Crueger <crueger@…> [93df03f]
	* molecuilder/src/unittests/ActionSequenceTest.cpp (added)
	* molecuilder/src/unittests/ActionSequenceTest.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)

	Added unittest for ActionSequence.


Thu, 17 Dec 2009 14:50:06 GMT Tillmann Crueger <crueger@…> [99bf23]
	* molecuilder/doc/menu classes.uxf (modified)

	Update of class diagram for menu classes.


Thu, 17 Dec 2009 14:40:16 GMT Tillmann Crueger <crueger@…> [f3dd95]
	* molecuilder/src/menu.cpp (modified)

	Removed legacy code from old menu structure.


Thu, 17 Dec 2009 14:38:29 GMT Tillmann Crueger <crueger@…> [32df34]
	* molecuilder/src/Actions/Action.hpp (modified)
	* molecuilder/src/Actions/ActionSequence.cpp (modified)
	* molecuilder/src/Actions/MakroAction.cpp (added)
	* molecuilder/src/Actions/MakroAction.hpp (added)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/menu.cpp (modified)

	Added an action that allows grouping and grouped execution of several ...


Thu, 17 Dec 2009 14:21:47 GMT Tillmann Crueger <crueger@…> [425da9]
	* molecuilder/src/Actions/ActionSequence.cpp (added)
	* molecuilder/src/Actions/ActionSequence.hpp (added)
	* molecuilder/src/Makefile.am (modified)

	Added mechanism that allow to store and later execute sequences of ...


Thu, 17 Dec 2009 13:49:27 GMT Tillmann Crueger <crueger@…> [38546d]
	* molecuilder/doc/menu classes.uxf (modified)

	Minimal Changes to the UML-Diagram of menu classes.


Wed, 16 Dec 2009 14:40:09 GMT Tillmann Crueger <crueger@…> [da09909]
	* molecuilder/src/Actions/Action.cpp (modified)
	* molecuilder/src/Actions/Action.hpp (modified)
	* molecuilder/src/Actions/MethodAction.hpp (modified)
	* molecuilder/src/Menu/ActionMenuItem.hpp (modified)
	* molecuilder/src/Menu/DisplayMenuItem.hpp (modified)
	* molecuilder/src/Menu/Menu.hpp (modified)
	* molecuilder/src/Menu/MenuItem.cpp (modified)
	* molecuilder/src/Menu/MenuItem.hpp (modified)
	* molecuilder/src/Menu/SeperatorItem.hpp (modified)
	* molecuilder/src/Menu/TextMenu.cpp (modified)
	* molecuilder/src/Menu/TextMenu.hpp (modified)
	* molecuilder/src/Views/MethodStringView.hpp (modified)
	* molecuilder/src/Views/StreamStringView.hpp (modified)
	* molecuilder/src/Views/StringView.hpp (modified)
	* molecuilder/src/Views/View.hpp (modified)

	Improved documentation for menu framework.


Wed, 16 Dec 2009 13:58:12 GMT Tillmann Crueger <crueger@…> [c2c893]
	* molecuilder/doc/class structure.uxf (modified)
	* molecuilder/doc/menu classes.uxf (added)

	Added class diagram to document structure of menu framework


Wed, 16 Dec 2009 12:58:40 GMT Frederik Heber <heber@…> [a5eee6]
	* Makefile.am (modified)
	* molecuilder/Makefile.am (modified)
	* molecuilder/doc/Doxyfile (modified)
	* molecuilder/doc/class structure.uxf (added)
	* molecuilder/src/Actions/Action.cpp (added)
	* molecuilder/src/Actions/Action.hpp (added)
	* molecuilder/src/Actions/MethodAction.cpp (added)
	* molecuilder/src/Actions/MethodAction.hpp (added)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/Menu/ActionMenuItem.cpp (added)
	* molecuilder/src/Menu/ActionMenuItem.hpp (added)
	* molecuilder/src/Menu/DisplayMenuItem.cpp (added)
	* molecuilder/src/Menu/DisplayMenuItem.hpp (added)
	* molecuilder/src/Menu/Menu.cpp (added)
	* molecuilder/src/Menu/Menu.hpp (added)
	* molecuilder/src/Menu/MenuItem.cpp (added)
	* molecuilder/src/Menu/MenuItem.hpp (added)
	* molecuilder/src/Menu/SeperatorItem.cpp (added)
	* molecuilder/src/Menu/SeperatorItem.hpp (added)
	* molecuilder/src/Menu/SubMenuItem.cpp (added)
	* molecuilder/src/Menu/SubMenuItem.hpp (added)
	* molecuilder/src/Menu/TextMenu.cpp (added)
	* molecuilder/src/Menu/TextMenu.hpp (added)
	* molecuilder/src/Views/MethodStringView.cpp (added)
	* molecuilder/src/Views/MethodStringView.hpp (added)
	* molecuilder/src/Views/StreamStringView.cpp (added)
	* molecuilder/src/Views/StreamStringView.hpp (added)
	* molecuilder/src/Views/StringView.cpp (added)
	* molecuilder/src/Views/StringView.hpp (added)
	* molecuilder/src/Views/View.cpp (added)
	* molecuilder/src/Views/View.hpp (added)
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/atom_graphnode.cpp (modified)
	* molecuilder/src/atom_trajectoryparticle.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/defs.hpp (modified)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/src/errorlogger.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)
	* molecuilder/src/menu.cpp (added)
	* molecuilder/src/menu.hpp (added)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_dynamics.cpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/vector.cpp (modified)

	Merge branch 'MenuRefactoring' into JansCluster_water


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [212c827]
	* molecuilder/src/Menu/MenuItem.cpp (modified)
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Finished transformation of main menu. Signed-off-by: Tillmann Crueger ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [62e23d]
	* molecuilder/src/Menu/SubMenuItem.cpp (modified)
	* molecuilder/src/Menu/SubMenuItem.hpp (modified)

	Rebuilt SubMenuItem to use inclusion (Strategy pattern) instead of ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [f00f02]
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)

	Added method to flip ActiveFlag for single molecules. Signed-off-by: ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [2309fa]
	* molecuilder/src/Menu/DisplayMenuItem.cpp (modified)
	* molecuilder/src/Menu/DisplayMenuItem.hpp (modified)
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Added Title to DisplayMenuItems. Signed-off-by: Tillmann Crueger ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [057b77]
	* molecuilder/src/menu.cpp (modified)

	Small fix to delete the complete menu.

	Signed-off-by: Tillmann ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [df55a0]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/Menu/DisplayMenuItem.cpp (added)
	* molecuilder/src/Menu/DisplayMenuItem.hpp (added)
	* molecuilder/src/Views/MethodStringView.cpp (added)
	* molecuilder/src/Views/MethodStringView.hpp (added)
	* molecuilder/src/Views/StreamStringView.cpp (added)
	* molecuilder/src/Views/StreamStringView.hpp (added)
	* molecuilder/src/Views/StringView.cpp (added)
	* molecuilder/src/Views/StringView.hpp (added)
	* molecuilder/src/Views/View.cpp (added)
	* molecuilder/src/Views/View.hpp (added)
	* molecuilder/src/menu.cpp (modified)

	Added basic View functionality. - Added DisplayMenuItem to show ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [7cb300]
	* molecuilder/src/Menu/MenuItem.cpp (modified)
	* molecuilder/src/Menu/MenuItem.hpp (modified)
	* molecuilder/src/Menu/SeperatorItem.cpp (modified)
	* molecuilder/src/Menu/SeperatorItem.hpp (modified)
	* molecuilder/src/Menu/SubMenuItem.cpp (modified)
	* molecuilder/src/Menu/SubMenuItem.hpp (modified)
	* molecuilder/src/Menu/TextMenu.cpp (modified)
	* molecuilder/src/Menu/TextMenu.hpp (modified)
	* molecuilder/src/defs.hpp (modified)

	Changed formating of menus and added protection to keep MenuItems ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [45ff42]
	* molecuilder/src/Menu/TextMenu.cpp (modified)

	Fixed memory leak in TextMenu Signed-off-by: Tillmann Crueger ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [381df6]
	* molecuilder/src/Actions/MethodAction.cpp (modified)
	* molecuilder/src/Actions/MethodAction.hpp (modified)
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Rebuild the main menu using the new structure as far as possible. ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [d20ed5]
	* molecuilder/src/Actions/Action.cpp (added)
	* molecuilder/src/Actions/Action.hpp (added)
	* molecuilder/src/Actions/MethodAction.cpp (added)
	* molecuilder/src/Actions/MethodAction.hpp (added)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/Menu/ActionMenuItem.cpp (added)
	* molecuilder/src/Menu/ActionMenuItem.hpp (added)
	* molecuilder/src/Menu/Menu.cpp (added)
	* molecuilder/src/Menu/Menu.hpp (added)
	* molecuilder/src/Menu/MenuItem.cpp (added)
	* molecuilder/src/Menu/MenuItem.hpp (added)
	* molecuilder/src/Menu/SeperatorItem.cpp (added)
	* molecuilder/src/Menu/SeperatorItem.hpp (added)
	* molecuilder/src/Menu/SubMenuItem.cpp (added)
	* molecuilder/src/Menu/SubMenuItem.hpp (added)
	* molecuilder/src/Menu/TextMenu.cpp (added)
	* molecuilder/src/Menu/TextMenu.hpp (added)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/menu.cpp (modified)
	* molecuilder/src/menu.hpp (modified)

	Added basic menu and action framework

	- Added action base class
	- ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [eb3538]
	* Makefile.am (modified)
	* molecuilder/Makefile.am (modified)

	Added capability to build doc from anywhere in the tree. Signed-off- ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [f2904c]
	* molecuilder/doc/class structure.uxf (added)

	Added class diagramm to documentation directory Signed-off-by: ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [1b4d9f]
	* molecuilder/src/menu.cpp (modified)

	Minor changes to menu::SaveConfig() Signed-off-by: Tillmann Crueger ...


Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber <heber@…> [7df43b]
	* molecuilder/doc/Doxyfile (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/menu.cpp (added)
	* molecuilder/src/menu.hpp (added)

	Started refactoring of the menu. - Created new menu class - moved all ...


Thu, 26 Nov 2009 11:45:04 GMT Frederik Heber <heber@…> [b61c30]
	* molecuilder/tests/Tesselations/defs.in (added)

	Forgot to add molecuilder/tests/Tesselations/defs.in


Mon, 23 Nov 2009 19:09:42 GMT Frederik Heber <heber@…> [7d1ad9]
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/errorlogger.cpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

	bugfix to errorLogger and some error verbosity changes.

	- BUGFIX: ...


Mon, 23 Nov 2009 18:51:50 GMT Frederik Heber <heber@…> [3d4969]
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule_dynamics.cpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

	Fixing ticket #18.

	- each eLog() << Verbose(0) is now followed by ...


Mon, 23 Nov 2009 18:22:33 GMT Frederik Heber <heber@…> [418117a]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/atom_graphnode.cpp (modified)
	* molecuilder/src/atom_trajectoryparticle.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule_dynamics.cpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/vector.cpp (modified)

	Verbosity corrected for ERROR and WARNING

	- present ERROR and ...


Tue, 10 Nov 2009 20:59:00 GMT Frederik Heber <heber@…> [09d3b8]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

	Attempt to fix tesselation for case 1_2-dimethylbenzene.

	- The ...


Tue, 10 Nov 2009 20:58:31 GMT Frederik Heber <heber@…> [2fbbc96]
	* molecuilder/src/builder.cpp (modified)

	Only biggest molecule is tesselated for now in ...


Tue, 10 Nov 2009 20:57:58 GMT Frederik Heber <heber@…> [f28e0c]
	* molecuilder/configure.ac (modified)
	* molecuilder/tests/Makefile.am (modified)
	* molecuilder/tests/Tesselations/1_2-dimethoxyethane.test (added)
	* molecuilder/tests/Tesselations/1_2-dimethoxyethane/1_2-dimethoxyethane.xyz (added)
	* molecuilder/tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (added)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene.test (added)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene/1_2-dimethylbenzene.xyz (added)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (added)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (added)
	* molecuilder/tests/Tesselations/2-methylcyclohexanone.test (added)
	* molecuilder/tests/Tesselations/2-methylcyclohexanone/2-methylcyclohexanone.xyz (added)
	* molecuilder/tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (added)
	* molecuilder/tests/Tesselations/C16_0-Torus.test (added)
	* molecuilder/tests/Tesselations/C16_0-Torus/C16_0-Torus.xyz (added)
	* molecuilder/tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (added)
	* molecuilder/tests/Tesselations/Makefile.am (added)
	* molecuilder/tests/Tesselations/N_N-dimethylacetamide.test (added)
	* molecuilder/tests/Tesselations/N_N-dimethylacetamide/N_N-dimethylacetamide.xyz (added)
	* molecuilder/tests/Tesselations/N_N-dimethylacetamide/NonConvexEnvelope-N_N-dimethylacetamide.dat (added)
	* molecuilder/tests/Tesselations/cholesterol.test (added)
	* molecuilder/tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (added)
	* molecuilder/tests/Tesselations/cholesterol/cholesterol.xyz (added)
	* molecuilder/tests/Tesselations/cluster.test (added)
	* molecuilder/tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (added)
	* molecuilder/tests/Tesselations/cluster/cluster.dbond (added)
	* molecuilder/tests/Tesselations/cluster/cluster.xyz (added)
	* molecuilder/tests/Tesselations/cycloheptane.test (added)
	* molecuilder/tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (added)
	* molecuilder/tests/Tesselations/cycloheptane/cycloheptane.xyz (added)
	* molecuilder/tests/Tesselations/dimethyl_bromomalonate.test (added)
	* molecuilder/tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (added)
	* molecuilder/tests/Tesselations/dimethyl_bromomalonate/dimethyl_bromomalonate.xyz (added)
	* molecuilder/tests/Tesselations/glucose.test (added)
	* molecuilder/tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (added)
	* molecuilder/tests/Tesselations/glucose/glucose.xyz (added)
	* molecuilder/tests/Tesselations/heptan.test (added)
	* molecuilder/tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (added)
	* molecuilder/tests/Tesselations/heptan/heptan.xyz (added)
	* molecuilder/tests/Tesselations/isoleucine.test (added)
	* molecuilder/tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (added)
	* molecuilder/tests/Tesselations/isoleucine/isoleucine.xyz (added)
	* molecuilder/tests/Tesselations/neohexane.test (added)
	* molecuilder/tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (added)
	* molecuilder/tests/Tesselations/neohexane/neohexane.xyz (added)
	* molecuilder/tests/Tesselations/proline.test (added)
	* molecuilder/tests/Tesselations/proline/NonConvexEnvelope-proline.dat (added)
	* molecuilder/tests/Tesselations/proline/proline.xyz (added)
	* molecuilder/tests/Tesselations/putrescine.test (added)
	* molecuilder/tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (added)
	* molecuilder/tests/Tesselations/putrescine/putrescine.xyz (added)
	* molecuilder/tests/Tesselations/round_cluster.test (added)
	* molecuilder/tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (added)
	* molecuilder/tests/Tesselations/round_cluster/round_cluster.dbond (added)
	* molecuilder/tests/Tesselations/round_cluster/round_cluster.xyz (added)
	* molecuilder/tests/Tesselations/tartaric_acid.test (added)
	* molecuilder/tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (added)
	* molecuilder/tests/Tesselations/tartaric_acid/tartaric_acid.xyz (added)

	Added Tesselation testsets as TESTS to molecuilder.

	- defs.in with ...


Tue, 10 Nov 2009 20:53:33 GMT Frederik Heber <heber@…> [548cbf]
	* molecuilder/src/errorlogger.cpp (modified)
	* molecuilder/src/logger.cpp (modified)
	* molecuilder/src/verbose.hpp (modified)

	BUGFIX: Output is again indented, errorLogger prefixes according to ...


Sat, 07 Nov 2009 12:27:15 GMT Frederik Heber <heber@…> [e960b1]
	* molecuilder/src/unittests/bondgraphunittest.cpp (modified)
	* molecuilder/src/unittests/bondgraphunittest.hpp (modified)

	BUGFIX: unnecessary include in header, file not closed in definition ...


Sat, 07 Nov 2009 12:25:32 GMT Frederik Heber <heber@…> [e462b3]
	* molecuilder/src/analysis_bonds.cpp (modified)
	* molecuilder/src/analysis_bonds.hpp (modified)
	* molecuilder/src/unittests/analysisbondsunittest.cpp (modified)
	* molecuilder/src/unittests/analysisbondsunittest.hpp (modified)

	Two new bond analysis functions.

	- GetMaxMinMeanBondCount() - ...


Sat, 07 Nov 2009 12:17:55 GMT Frederik Heber <heber@…> [1fcedd]
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)

	New function bond::GetDistance...()

	- bond::GetDistance() and ...


Sat, 07 Nov 2009 12:16:57 GMT Frederik Heber <heber@…> [486aa5]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Added config::SavePDB() and config::SaveMPQC().

	- note: for CODICE ...


Sat, 07 Nov 2009 09:46:08 GMT Frederik Heber <heber@…> [341850]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analysis_bonds.cpp (added)
	* molecuilder/src/analysis_bonds.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/analysisbondsunittest.cpp (added)
	* molecuilder/src/unittests/analysisbondsunittest.hpp (added)

	Added initial analysis_bonds.cpp and unit test for Analysis of bonds. ...


Sat, 07 Nov 2009 09:44:11 GMT Frederik Heber <heber@…> [fc420f]
	* molecuilder/src/boundary.cpp (modified)

	LEAKFIX: FillBoxWithMolecule() had mismatch delete/delete[]

	- ...


Thu, 05 Nov 2009 18:14:08 GMT Frederik Heber <heber@…> [4ef101]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)

	LEAKFIX: ReturnFullMatrixForSymmetric() and InverseMatrix() have ...


Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber <heber@…> [543ce4]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/atom_bondedparticle.hpp (modified)
	* molecuilder/src/atom_graphnode.cpp (modified)
	* molecuilder/src/atom_graphnode.hpp (modified)
	* molecuilder/src/atom_trajectoryparticle.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/bondgraph.hpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/datacreator.cpp (modified)
	* molecuilder/src/element.cpp (modified)
	* molecuilder/src/element.hpp (modified)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/src/ellipsoid.hpp (modified)
	* molecuilder/src/errorlogger.cpp (moved)
	* molecuilder/src/errorlogger.hpp (moved)
	* molecuilder/src/graph.cpp (modified)
	* molecuilder/src/graph.hpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/log.cpp (modified)
	* molecuilder/src/log.hpp (modified)
	* molecuilder/src/logger.cpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_dynamics.cpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/molecule_pointcloud.cpp (modified)
	* molecuilder/src/molecule_template.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)
	* molecuilder/src/test/ActOnAlltest.hpp (modified)
	* molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/bondgraphunittest.cpp (modified)
	* molecuilder/src/unittests/logunittest.cpp (modified)
	* molecuilder/src/unittests/memoryallocatorunittest.cpp (modified)
	* molecuilder/src/unittests/stackclassunittest.cpp (modified)
	* molecuilder/src/unittests/tesselationunittest.cpp (modified)
	* molecuilder/src/unittests/vectorunittest.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/verbose.cpp (modified)

	Huge change from ofstream * (const) out --> Log().

	- first shift ...


Wed, 04 Nov 2009 18:25:42 GMT Frederik Heber <heber@…> [ec70ec]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/errorLogger.cpp (added)
	* molecuilder/src/errorLogger.hpp (added)
	* molecuilder/src/log.cpp (added)
	* molecuilder/src/log.hpp (added)
	* molecuilder/src/logger.cpp (added)
	* molecuilder/src/logger.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/logunittest.cpp (added)
	* molecuilder/src/unittests/logunittest.hpp (added)
	* molecuilder/src/verbose.cpp (modified)
	* molecuilder/src/verbose.hpp (modified)

	Merge branch 'CodeRefactoring' of ...


Wed, 04 Nov 2009 18:15:10 GMT Frederik Heber <heber@…> [5f1d021]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* molecuilder/src/vector.cpp (modified)

	Periodic variants of AnalysisPair...() implemented.

	- BUGFIX: ...


Wed, 04 Nov 2009 17:34:05 GMT Frederik Heber <heber@…> [20895b]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	Extension to the periodic boundary case for analysis_correlation.cpp
 ...


Wed, 04 Nov 2009 15:08:11 GMT Frederik Heber <heber@…> [c1b76e]
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	config::Load() refactored: Dissection into connected subgraphs -> ...


Wed, 04 Nov 2009 14:54:31 GMT Frederik Heber <heber@…> [e1900f]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified)

	Closed ticket #48 (AnalysisCorrelation...() take MoleculeListClass ...


Wed, 04 Nov 2009 14:51:02 GMT Frederik Heber <heber@…> [4efdad]
	* molecuilder/src/config.cpp (modified)

	BUGFIX: Allocated one molecule too much in config::Load().

	- ...


Wed, 04 Nov 2009 12:57:24 GMT Frederik Heber <heber@…> [a3ffb44]
	* molecuilder/src/builder.cpp (modified)

	Closing ticket #47, case 'C' uses biggest molecule as surface for ...


Tue, 03 Nov 2009 16:34:31 GMT Frederik Heber <heber@…> [c1b4a4]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/bondgraph.hpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

	"not working parsed molecule into subgraph splitting"-BUG fixed, ...


Tue, 03 Nov 2009 14:34:02 GMT Frederik Heber <heber@…> [08b88b]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/bondgraph.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Fixing not created adjacency list, partially fixing subgraph ...


Tue, 03 Nov 2009 12:38:08 GMT Frederik Heber <heber@…> [5f9f8b]
	* molecuilder/src/unittests/Makefile.am (modified)

	Removed libmolecuilder linking from unit tests where only some few ...


Tue, 03 Nov 2009 12:37:55 GMT Frederik Heber <heber@…> [8bc524]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule_dynamics.cpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/unittests/memoryallocatorunittest.cpp (modified)

	Several memory bugfixes (thx valgrind).

	- main() - shortened case ...


Mon, 02 Nov 2009 12:50:57 GMT Frederik Heber <heber@…> [df0520]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Small changes.

	- VolumeOfConvexEnvelope() - setprecision corrected ...


Fri, 30 Oct 2009 16:09:29 GMT Frederik Heber <heber@…> [245826]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

	BondGraph is initialized within config::Load(), as it has to happen ...


Fri, 30 Oct 2009 15:49:38 GMT Frederik Heber <heber@…> [b84ab4]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/unittests/bondgraphunittest.cpp (modified)

	BondGraph is parsed if command line switch '-g' is given.

	- ...


Fri, 30 Oct 2009 11:04:50 GMT Saskia Metzler <metzler@…> [96d8dc]
	* molecuilder/src/errorLogger.cpp (added)
	* molecuilder/src/errorLogger.hpp (added)
	* molecuilder/src/log.cpp (added)
	* molecuilder/src/log.hpp (added)
	* molecuilder/src/logger.cpp (added)
	* molecuilder/src/logger.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/logunittest.cpp (added)
	* molecuilder/src/unittests/logunittest.hpp (added)
	* molecuilder/src/verbose.cpp (modified)
	* molecuilder/src/verbose.hpp (modified)

	Ticket 43 Create a logging class

	The verbosity level can now be ...


Fri, 30 Oct 2009 09:05:30 GMT Frederik Heber <heber@…> [5f697c]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/atom_bondedparticle.hpp (modified)
	* molecuilder/src/bondgraph.cpp (added)
	* molecuilder/src/bondgraph.hpp (added)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/bondgraphunittest.cpp (added)
	* molecuilder/src/unittests/bondgraphunittest.hpp (added)

	New class BondGraph.

	- BondGraph parses a file containing bond ...


Fri, 30 Oct 2009 08:29:31 GMT Frederik Heber <heber@…> [bc8155]
	* molecuilder/src/test/ActOnAlltest.hpp (modified)
	* molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified)
	* molecuilder/src/unittests/ActOnAllUnitTest.hpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)

	Test code is moved to its own source subdirectory: test.

	- ...


Fri, 30 Oct 2009 08:29:07 GMT Frederik Heber <heber@…> [92fc40]
	* molecuilder/src/test/ActOnAlltest.hpp (moved)
	* molecuilder/src/unittests/stackclassunittest.cpp (added)
	* molecuilder/src/unittests/stackclassunittest.hpp (added)

	Added Unit test for StackClass.

	- was former ...


Thu, 29 Oct 2009 10:09:05 GMT Frederik Heber <heber@…> [dbc152]
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)

	Refactored StackClass with respect to tickets #38, #4.

	- #38 make ...


Tue, 27 Oct 2009 17:41:12 GMT Frederik Heber <heber@…> [6d7651]
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)

	Refactored tesselationhelpers.cpp with respect to ticket #38 (make ...


Tue, 27 Oct 2009 17:16:31 GMT Frederik Heber <heber@…> [069034]
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/periodentafel.hpp (modified)
	* molecuilder/src/vector.hpp (modified)

	class config, ConfigFileBuffer, periodentafel and Vector are ...


Tue, 27 Oct 2009 16:11:22 GMT Frederik Heber <heber@…> [a9b2a0a]
	* molecuilder/configure.ac (modified)
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/src/leastsquaremin.cpp (modified)
	* molecuilder/src/leastsquaremin.hpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/linkedcell.hpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/molecule_pointcloud.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)
	* molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	Huge refactoring to make const what is const (ticket #38), continued. ...


Tue, 27 Oct 2009 11:51:52 GMT Frederik Heber <heber@…> [55a71b]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/molecule.hpp (modified)

	analyzer.cpp and boundary.cpp refactored.

	- ticket #39 is done with ...


Tue, 27 Oct 2009 11:45:23 GMT Frederik Heber <heber@…> [8b6ee4]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)

	Begun with ticket #4 (shorten constructors) on class atom and class ...


Tue, 27 Oct 2009 08:54:44 GMT Frederik Heber <heber@…> [94d0ad]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/atom_bondedparticle.hpp (modified)
	* molecuilder/src/atom_particleinfo.cpp (modified)
	* molecuilder/src/atom_particleinfo.hpp (modified)
	* molecuilder/src/atom_trajectoryparticle.cpp (modified)
	* molecuilder/src/atom_trajectoryparticle.hpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_template.hpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	Begun with ticket #38 (make const what is const).

	- basically all ...


Tue, 27 Oct 2009 08:53:25 GMT Frederik Heber <heber@…> [2e6aa1]
	* molecuilder/src/unittests/Makefile.am (modified)

	..._CPPFLAGS and ..._LDFLAGS in unittests/Makefile.am put into global ...


Tue, 20 Oct 2009 08:55:17 GMT Frederik Heber <heber@…> [2e2a70]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (modified)
	* molecuilder/src/atom_atominfo.cpp (added)
	* molecuilder/src/atom_atominfo.hpp (added)
	* molecuilder/src/atom_bondedparticle.cpp (added)
	* molecuilder/src/atom_bondedparticle.hpp (added)
	* molecuilder/src/atom_bondedparticleinfo.cpp (added)
	* molecuilder/src/atom_bondedparticleinfo.hpp (added)
	* molecuilder/src/atom_graphnode.cpp (added)
	* molecuilder/src/atom_graphnode.hpp (added)
	* molecuilder/src/atom_graphnodeinfo.cpp (added)
	* molecuilder/src/atom_graphnodeinfo.hpp (added)
	* molecuilder/src/atom_particleinfo.cpp (added)
	* molecuilder/src/atom_particleinfo.hpp (added)
	* molecuilder/src/atom_trajectoryparticle.cpp (added)
	* molecuilder/src/atom_trajectoryparticle.hpp (added)
	* molecuilder/src/atom_trajectoryparticleinfo.cpp (added)
	* molecuilder/src/atom_trajectoryparticleinfo.hpp (added)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

	Refactored atom.cpp into multiple files.

	After the class atom was ...


Tue, 20 Oct 2009 08:54:51 GMT Frederik Heber <heber@…> [3b0ba2]
	* molecuilder/src/vector.hpp (modified)

	iostream was missing in vector includes.


Mon, 19 Oct 2009 13:09:29 GMT Frederik Heber <heber@…> [6b937bd]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_template.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

	Huge Refactoring: class atom split up into several inherited classes. ...


Sun, 18 Oct 2009 19:58:38 GMT Frederik Heber <heber@…> [99bed3]
	* molecuilder/src/molecule_graph.cpp (modified)

	Added BFSAccounting and DFSAccounting structures and all functions ...


Sun, 18 Oct 2009 18:12:53 GMT Frederik Heber <heber@…> [e60069]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored molecule::BuildInducedSubgraph()

	- new functions ...


Sun, 18 Oct 2009 17:52:47 GMT Frederik Heber <heber@…> [9897787]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored molecule::BreadthFirstSearchAdd()

	- new function: ...


Sun, 18 Oct 2009 17:07:33 GMT Frederik Heber <heber@…> [312ba2]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored CheckAdjacencyFileAgainstMolecule().

	- new functions: ...


Sun, 18 Oct 2009 16:35:25 GMT Frederik Heber <heber@…> [6e250f]
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/molecule_template.hpp (modified)

	Removed ResetAllAtomNumbers(), replaced by templated ...


Sun, 18 Oct 2009 16:09:26 GMT Frederik Heber <heber@…> [f444ce]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

	Shifted molecuke::InitComponentNumbers() to atom::InitComponentNr.
 ...


Sun, 18 Oct 2009 16:01:57 GMT Frederik Heber <heber@…> [c9f639]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored molecule::CyclicStructureAnalysis()

	- new functions: ...


Sun, 18 Oct 2009 15:13:46 GMT Frederik Heber <heber@…> [77894f]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored molecule::DepthFirstSearchAnalysis()

	- new functions: ...


Sun, 18 Oct 2009 14:51:38 GMT Frederik Heber <heber@…> [872b51]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/lists.hpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/molecule_template.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/listofbondsunittest.cpp (added)
	* molecuilder/src/unittests/listofbondsunittest.hpp (added)

	Huge refactoring: molecule::ListOfBondsPerAtom and ...


Sat, 17 Oct 2009 19:47:58 GMT Frederik Heber <heber@…> [b0ee98]
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored CreateAdjacencyList().

	- new auxiliary functions: ...


Sat, 17 Oct 2009 19:46:28 GMT Frederik Heber <heber@…> [aec775]
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/linkedcell.hpp (modified)

	Extended class LinkedCell to handle a relative offset to current ...