[Molecuilder-devel] [SCM] branch stable updated. v1.5.0
git at ins.uni-bonn.de
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Sat Aug 15 11:15:15 CEST 2015
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- Log -----------------------------------------------------------------
commit bff5e273091c20e062b35677796d4f022e572385
Author: Frederik Heber <heber at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at ins.uni-bonn.de>
Date: Tue Jul 7 03:08:58 2015 +0200
Fixing QtElementList::updateElement().
commit 20f9b5ca3d0b9027b2885d6239e5b48b8dea45a5
Author: Frederik Heber <heber at 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 at 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 at 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 at 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 at 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 at 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 at 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%)
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