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python-avogadro - Molecular Graphics and Modelling System (Python module)…  more info»

changelog.gz

2011-04-25  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/FindNumpy.cmake: Sync with FindNumPy from master.  The old
  version was susceptible to issues as it was dereferencing the variable
  explicitly. This is prone to error, and causes warnings with newer versions
  of CMake. 

2011-04-24  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * CMakeLists.txt, Doxyfile: Bumped to version 1.0.3 in preparation for
  release.

2011-04-23  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * avogadro/src/CMakeLists.txt, cmake/modules/FindLinguist.cmake,
  libavogadro/src/CMakeLists.txt: Actually set Linguist_FOUND to TRUE.  If the
  required executables are found, set Linguist_FOUND to true. This addresses
  bug #3292000. 

2011-04-22  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * CMakeLists.txt, Doxyfile: Version number bump to 1.0.2 for tagging.

  * cmake/modules/AvoCPack.cmake: Updated install rules for minimal Windows
  package.  No Python/extended dependencies.

2010-09-20  David C. Lonie <loniedavid@gmail.com>

  * avogadro/gl2ps/gl2ps.c: M_PI is not defined on windows, added a definition
  for gl2ps. 

2011-04-14  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/CMakeLists.txt: Add the zlib include directory
  for qtiocompressor.

2010-09-20  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/gamessinputdialog.cpp: Added an implementation
  of double round(double)  For the the gamess input reader when compiling on
  windows. 

2011-04-13  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/FindLinguist.cmake: Fixed FindLinguist to respect REQUIRED
  option.

2011-04-12  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/gamessinputdialog.cpp: Fixed bug #3285388,
  should be atomAdded and friends.  This input dialog was not being correctly
  updated when atoms were added, updated or removed. This is due to the
  specialization of the signals from molecule for the common cases of atoms and
  bonds. 

2011-04-11  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/surfaceextension.cpp: Fixed a crash when ESP
  cube is selected.  This was never implemented, if the user selects it then it
  falls through to ElectronDensity and can potentially crash if there is no
  electronic structure loaded. 

2011-04-11  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/tests/moleculetest.cpp: Test for crashes when removing atoms
  and bonds that do not belong to the molecule.

2011-02-25  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/molecule.cpp: Don't try to remove atom if it does not
  belong to this Molecule  The same for bonds, cubes, meshes, residues, rings 

2011-04-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-ca@valencia.po, i18n/avogadro-cs.po,
  i18n/avogadro-da.po, i18n/avogadro-de.po, i18n/avogadro-el.po,
  i18n/avogadro-en_AU.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-eu.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-gl.po, i18n/avogadro-he.po,
  i18n/avogadro-hr.po, i18n/avogadro-hu.po, i18n/avogadro-id.po,
  i18n/avogadro-it.po, i18n/avogadro-ja.po, i18n/avogadro-kn.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-oc.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sr.po, i18n/avogadro-sv.po, i18n/avogadro-th.po,
  i18n/avogadro-tr.po, i18n/avogadro-ug.po, i18n/avogadro-uk.po,
  i18n/avogadro-vi.po, i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-bs.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-ca@valencia.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-da.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_AU.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-eu.po,
  i18n/libavogadro-fi.po, i18n/libavogadro-fr.po, i18n/libavogadro-gl.po,
  i18n/libavogadro-he.po, i18n/libavogadro-hi.po, i18n/libavogadro-hu.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-kn.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-oc.po, i18n/libavogadro-pl.po,
  i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po,
  i18n/libavogadro-sk.po, i18n/libavogadro-sr.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-ug.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-vi.po, i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po:
  Updated translations from Launchpad.

2011-04-08  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/tools/autoopttool.cpp: Ensure there is an OBConversion for
  forcefield.  This is a patch suggested in a Fedora bug, 
  https://bugzilla.redhat.com/show_bug.cgi?id=680292  It is a copy of the patch
  in the forcefield extension, to ensure we can find a forcefield in the auto
  optimization tool. 

  * libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h: Bug #3043641, fix auto-bonding
  in saved animation.  Have makeVideo also use the Animation class, and respect
  the autobonding option exposed in the animation dialog. 

2011-04-07  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gamessinputdialog.cpp: For 1.0.2, hide GAMESS
  Compute button -- doesn't work yet.

  * libavogadro/src/tools/drawcommand.cpp: Fix for crash bug PR#3102431. Draw
  tool to change atom to H.

2011-04-07  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * CMakeLists.txt: Address bug #3174124 - lib directory and cache.  This
  works, but the cache can end up in an inconsistent state. By using FORCE we
  ensure that the lib and plugin directories remain consistent with the
  selected lib suffix. 

  * libavogadro/src/extensions/mopacinputdialog.cpp: Fix bug #2977797, use
  LARGE keyword.  This restores MOPAC's previous behavior of printing all MOs,
  I also have a local patch to read the modified output and will target that at
  master, as more changes are required to deal with partial sets of MOs. 

2011-04-06  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp: Fix for crash-after-delete bug.
  Previously, after right-click with draw tool, future drawing would crash. We
  needed to reset all the private variables for new drawing properly.

2011-03-22  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt: Made Linguist optional for build time.  This
  is already the case in master. Some installations of Qt do not come with
  lconvert, this should not block compilation.

2011-03-17  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/molecule.cpp: Prevented possible crash in
  Molecule::setAtomPos if m_atomPos == 0 

  * libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/inputfileextension.cpp,
  .../src/extensions/insertfragmentdialog.cpp,
  .../src/extensions/insertpeptideextension.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/moleculefile.cpp: Finally fixed OB file operations with
  non-Latin characters in file paths  QFile::encodeName() and
  QString::toLocal8Bit() do not allow correct opening of fstream objects on
  localized Windows if Avogadro is compiled with MSVC. This patch should fix
  all related issues. 

2011-03-13  David C. Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp: Fix bug in extension menu searching.  Now
  extensions can place items more than two levels deep in the menu structure. 

2011-03-02  Jens Thomas <linucks42@gmail.com>

  * libavogadro/src/extensions/nwcheminputdialog.cpp: Fix bug 3174370 with
  NWChem input generator  This fixes bug 3174370. Changed so that the dedicated
  mp2 and ccsd modules are used, rather then the tce engine. mp2 and ccsd jobs
  now run with frozen core to emulate default behaviour of Gaussian.  Run with
  spherical basis sets when using Dunning correlation-consistent basis sets. 
  Default behaviour is now to echo the input in the output.  Thanks to
  Konstantin Tokarev <annulen@yandex.ru> for backporting fix. 

2011-01-30  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h: Address bug #3019539 - add wireframe
  pick method.  The pick method actually renders balls and sticks so that the
  bonds do not clobber the atoms. This could probably be streamlined, but
  provides one possible solution to this issue. 

2011-03-01  Konstantin Tokarev <annulen@yandex.ru>

  * scripts/installer/installer_languages/russian.nsh,
  scripts/installer/setup.nsi: Cherry-picked Russian translation of NSIS from
  master 

2011-02-28  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/engine.cpp: Prevent possible segfaults in Engine if
  m_molecule==0 

2011-02-24  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/animation.cpp: Prevent segfaults in Animation::start() and
  stop() if m_molecule == 0 

2011-02-14  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/engines/python/wireframe.py,
  libavogadro/src/pythonengine_p.cpp: Fixed readSettings and writeSettings in
  PythonEngine  To illustrate bugfix, saving of width was added to Python
  wireframe engine 

2011-02-11  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/molecule.cpp: Prevent crash in setDipoleMoment and related
  memory leak in setOBMol 

2011-02-10  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/residue.cpp: Prevent segfault in Residue::addAtom and
  removeAtom if m_molecule == 0 

2011-02-08  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/glwidget.cpp: Prevent crash in renameNamedSelection if
  index is out of range 

  * libavogadro/src/animation.cpp: Animation::setFrame - protection from
  m_molecule == 0 

2011-01-31  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/tools/drawcommand.cpp: Fixes exception in drawcommand test.
   This fixes the exception seen in the draw command test, and looking at bug
  #3091185 and #3102431 still doesn't crash when following the recipes
  provided. 

2011-01-30  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/cube.cpp: Ensure consistent bounds are calculated for
  cubes.  This setLimits method is used for all surface calculations in
  Avogadro right now. It was creating a cube with an incorrect maximum point,
  due to the constraints placed. Ensure we always calculate the max point after
  all other parameters are set. Tested with several symmetric small molecules
  successfully. 

2011-02-03  Geoff Hutchison <geoff.hutchison@gmail.com>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-da.po,
  i18n/avogadro-de.po, i18n/avogadro-el.po, i18n/avogadro-en_AU.po,
  i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po, i18n/avogadro-es.po,
  i18n/avogadro-eu.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-he.po, i18n/avogadro-hr.po, i18n/avogadro-hu.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-kn.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-oc.po, i18n/avogadro-pl.po,
  i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po,
  i18n/avogadro-sk.po, i18n/avogadro-sv.po, i18n/avogadro-th.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-vi.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-da.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_AU.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-eu.po,
  i18n/libavogadro-fi.po, i18n/libavogadro-fr.po, i18n/libavogadro-he.po,
  i18n/libavogadro-hi.po, i18n/libavogadro-hu.po, i18n/libavogadro-id.po,
  i18n/libavogadro-it.po, i18n/libavogadro-ja.po, i18n/libavogadro-kn.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-oc.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-vi.po, i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po,
  i18n/libavogadro.pot: Updated with latest Launchpad translations for 1.0
  branch. 

2011-01-31  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/python/sip.cpp: Fixed SIP major API version - should have
  been 4.  The SIP_API_MAJOR_NR and MINOR are always defined, so stopped being
  overly defensive (if they are not then we have more problems than that). I
  got the initial mapping from version number to API version wrong - most of
  them should have referred to 4. 

2011-01-29  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/extensions/gamessinputdialog.cpp: Fix bug #3139144 - NGAUSS
  incorrect for 6-311++G. 

  * libavogadro/src/extensions/gamessinputdialog.ui: Fix bug #3108280, add
  missing Binning/Curtis entry.  The Binning/Curtis DZ entry was missing from
  the drop down. Verified all subsequent entries now match up as expected. 

2011-01-28  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/PythonDeps.cmake, libavogadro/src/python/sip.cpp: Clean up
  the SIP support, import suggested fixes.  This will also apply cleanly to the
  1.0 branch. I have tested with both master and 1.0 using SIP 4.12. Get rid of
  the symbol definitions - use the ones provided by SIP instead. This means we
  no longer need to run the sip binary to get the SIP version. Thanks to all
  the distro guys for putting patches up pointing me in the right direction. 

2011-01-25  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/atom.cpp: Fixed memory leak of the atom d_ptr. 

2011-01-21  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/PythonDeps.cmake: Backported fixes to PythonDeps.cmake from
  master. 

  * cmake/modules/FindPythonLibs.cmake: Sync FindPythonLibs with what will be
  in CMake 2.8.4.  When we bump our CMake requirement to CMake 2.8.4 we should
  finally be able to stop maintaining our own FindPythonLibs module... 

2011-01-14  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * Doxyfile: Updated the version number in Doxyfile.

  * cmake/modules/FindAvogadro.cmake: Remove the FindAvogadro module - this is
  not used.  Avogadro is found using the AvogadroConfig.cmake installed by us.

  * cmake/modules/FindPackageHandleStandardArgs.cmake: Remove
  FindPackageHandleStandardArgs - in CMake 2.6.0.

2010-11-23  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/python/CMakeLists.txt: Fixed installation path of Python
  module (PR #3116423) 

2010-11-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-da.po,
  i18n/avogadro-de.po, i18n/avogadro-el.po, i18n/avogadro-en_AU.po,
  i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po, i18n/avogadro-es.po,
  i18n/avogadro-eu.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-he.po, i18n/avogadro-hr.po, i18n/avogadro-hu.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-kn.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-oc.po, i18n/avogadro-pl.po,
  i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po,
  i18n/avogadro-sk.po, i18n/avogadro-sv.po, i18n/avogadro-tr.po,
  i18n/avogadro-uk.po, i18n/avogadro-vi.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-da.po, i18n/libavogadro-de.po, i18n/libavogadro-el.po,
  i18n/libavogadro-en_AU.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-eu.po,
  i18n/libavogadro-fi.po, i18n/libavogadro-fr.po, i18n/libavogadro-he.po,
  i18n/libavogadro-hi.po, i18n/libavogadro-hu.po, i18n/libavogadro-id.po,
  i18n/libavogadro-it.po, i18n/libavogadro-ja.po, i18n/libavogadro-kn.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-oc.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-vi.po, i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po,
  i18n/libavogadro.pot: Merged launchpad translation improvements. 

2010-11-11  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/pluginmanager.cpp: Cross-platform library filtering for
  plugin loading

2010-11-09  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/forcefieldextension.cpp: Fix forcefieldextension
  to work again.  There needs to be an OBConversion object instantiated before
  OBForceField::FindForceField will work correctly. 

2010-11-08  Konstantin Tokarev <annulen@yandex.ru>

  * avogadro/src/main.cpp: Don't try to open non-existent file. 

  * avogadro/src/mainwindow.cpp: Fixed crash when file is opened as command
  line argument

2010-11-11  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/extensions/pythonterminal.cpp: Import Avogadro module
  automatically in Python terminal

  * cmake/modules/FindNumpy.cmake: Check for presence of required Numpy header 
  On Mandriva there are python-numpy and python-numpy-devel packages. When the
  former is present, but second is missing, compilation is impossible, but
  cmake enables Python if other requirements are met

2010-11-09  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/pluginmanager.h: Fixed typo in documentation

2010-11-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/color.h, libavogadro/src/engine.h,
  libavogadro/src/extension.h, libavogadro/src/tool.h: Fix 3104853: allow
  plugin macros to be used outside of the Avogadro namespace. 

2010-11-05  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/tools/navigatetool.h: Fixed dangling pointer in
  navigatetool (fixes PR 3103523)

2010-11-04  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/tools/drawcommand.cpp: Added missing braces in
  DeleteAtomDrawCommand  Fixes PR 3091179

2010-11-03  Konstantin Tokarev <annulen@yandex.ru>

  * libavogadro/src/tools/drawcommand.cpp: Don't create pre- and postcommands
  for H atoms  This patch fixes PR 3102431 and partially PR 3091185 (in the
  latter case crash occurs after Undo, but not immediately as without this
  patch)

2010-10-26  Konstantin Tokarev <annulen@yandex.ru>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Added Del as
  alternative shortcut for actionClear 

2010-07-19  Konstantin Tokarev <annulen@yandex.ru>

  * avogadro/src/mainwindow.cpp: Fixed opening of file with default name  If
  file was saved with default name (e.g., untitled.cml), it was not opened.
  Also this change prevents possible loss of unsavd data if such file is opened

2010-06-28  Geoff Hutchison <geoff.hutchison@gmail.com>

  * avogadro/src/main.cpp: Make sure to use the right path for Mac OB data. 

2010-05-23  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, cmake/modules/FindOpenBabel2.cmake: Fixed up the logic in
  the superbuild.  Fixed up the logic in the superbuild, use the actual target
  instead of files for the openbabel library. Also, setting one additional
  variable in the superbuild simplifies the find logic in the openbabel module.

2010-05-07  annulen <annulen@yandex.ru>

  * libavogadro/src/extensions/gamessinputdialog.ui: Made Gamess dialog more
  i18n-friendly (no new strings introduced)

2010-05-07  Konstantin Annulen Tokarev <kostya@localhost.localdomain>

  * CMakeLists.txt, avogadro.prf.in, avopkg.in,
  cmake/modules/FindOpenBabel2.cmake: Ported build system changes from trunk

2010-05-02  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/elementtranslator.cpp: Updated element name now it has
  changed.

2010-03-30  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/tools/navigatetool.cpp: Added WASD keyboard navigation (for
  left hand)

2010-04-01  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * libavogadro/src/extensions/gaussianinputdialog.ui,
  libavogadro/src/extensions/molproinputdialog.ui,
  libavogadro/src/extensions/mopacinputdialog.ui,
  libavogadro/src/extensions/nwcheminputdialog.ui,
  libavogadro/src/extensions/qcheminputdialog.ui: Killed translation of some
  basis set combos

  * libavogadro/src/extensions/gamessinputdialog.ui: Gamess - no translate
  basis sets

2010-04-03  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * avogadro/src/projecttreeeditor.cpp: Fixed segfault in projecttreeeditor

2010-04-28  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-es.po, i18n/libavogadro-ru.po: Update translations for 1.0.1.

  * avogadro/src/mainwindow.cpp: Strip "&" when comparing menu paths -- solves
  problems with duplicate menus due to incorrect paths in extensions or
  scripts.

  * libavogadro/src/extensions/python/example.py: Fix example script to use
  "&S" for menu. Eliminates duplicate script menus.

2010-04-27  Marcus D. Hanwell <marcus@cryos.org>

  * .../src/extensions/networkfetchextension.cpp: Use the 3D structures -
  roughly sync with master.

2010-03-30  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/tools/autoopttool.cpp: Fixed crash on exit if FFs were not
  loaded

2010-04-26  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-da.po,
  i18n/avogadro-de.po, i18n/avogadro-el.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-he.po, i18n/avogadro-hr.po,
  i18n/avogadro-hu.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-kn.po, i18n/avogadro-ko.po,
  i18n/avogadro-nb.po, i18n/avogadro-nl.po, i18n/avogadro-oc.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-da.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-he.po, i18n/libavogadro-hi.po,
  i18n/libavogadro-hu.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-kn.po, i18n/libavogadro-ko.po,
  i18n/libavogadro-nb.po, i18n/libavogadro-nl.po, i18n/libavogadro-oc.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Updated translations from Launchpad for 1.0.1
  release.

2010-04-25  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/drawtool.cpp: Set and store the bond order - fixes a
  Kalzium bug.

2010-03-29  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix -- check for default filename on Mac
  before deciding to load in new window.

2010-03-19  Konstantin Tokarev <annulen@users.sourceforge.net>

  * avopkg.in: Avopkg: fixed bug with manifest, moved pack/extract commands to
  variables

2010-03-18  Geoff Hutchison <babel@geoffhutchison.net>

  * README, doc/CMakeLists.txt, doc/avogadro.1, doc/avopkg.1: Manual
  cherry-pick from annulen's "master" repo.

2010-03-18  Konstantin Tokarev <annulen@users.sourceforge.net>

  * avopkg.in: Avopkg: support for Python and Mac

2010-03-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindOpenBabel2.cmake: Initial pass at finding embedded Open
  Babel -- pull includes for superpackage.

2010-03-12  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * CMakeLists.txt: Check if QT_MKSPECS_DIR exists before installing prf file,
  show warning otherwise

2010-03-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/sip.cpp: Make sure Avogdro.toPyQt works with
  MeshGenerator

2010-03-07  Konstantin Tokarev <annulen@users.sourceforge.net>

  * avopkg.in: Deleted unnecessary comments in avopkg

  * CMakeLists.txt, avogadro.prf.in: Added avogadro.prf generation and
  installation

2010-03-06  Konstantin Tokarev <annulen@users.sourceforge.net>

  * CMakeLists.txt, avopkg.in: Added avopkg tool

2010-03-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/FindNumpy.cmake, cmake/modules/PythonDeps.cmake: Another
  update to cmake files for numpy (wasn't working before)

2010-03-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-da.po,
  i18n/avogadro-de.po, i18n/avogadro-el.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-he.po, i18n/avogadro-hr.po,
  i18n/avogadro-hu.po, i18n/avogadro-id.po, i18n/avogadro-it.po,
  i18n/avogadro-ja.po, i18n/avogadro-kn.po, i18n/avogadro-ko.po,
  i18n/avogadro-nb.po, i18n/avogadro-nl.po, i18n/avogadro-pl.po,
  i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po,
  i18n/avogadro-sk.po, i18n/avogadro-sv.po, i18n/avogadro-tr.po,
  i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-da.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-he.po, i18n/libavogadro-hi.po, i18n/libavogadro-hu.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-kn.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po: Import of translations
  for 1.0.1 release.

2010-03-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/FindNumpy.cmake, cmake/modules/PythonDeps.cmake: Fix bug
  where cmake incorrectly detects numpy when it is not there. (Fixes: #2886558)

2009-12-03  Marcus D. Hanwell <marcus@cryos.org>

  * CTestConfig.cmake: Updated the  submission URL for CDash.

2010-01-30  Konstantin Tokarev <kostya@tdlab1.chem.msu.su>

  * libavogadro/src/extensions/propmodel.cpp: Display translatable "Yes"/"No"
  for bond's 'rotable' property instead of bool value

2010-01-31  Konstantin Tokarev <annulen@users.sourceforge.net>

  * avogadro/src/mainwindow.cpp: Added some output extensions to Computation
  Chemistry filter

2010-02-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/PythonDeps.cmake: Make sure python support compiles with sip
  4.10.

2010-02-23  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * libavogadro/src/elementdetail_p.h: Silence warning about qobject_cast.

2010-03-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fixed compile error.

2010-02-24  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/propextension.cpp: Fixed highlights when sorting
  is used in propextension

2010-02-20  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/moleculefile.cpp:
  s/QFile::encodeName(m_fileName)/m_fileName.toLocal8Bit()

2010-02-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pluginmanager.h: Add documentation for
  PluginManager::instance()

2010-02-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/color.h: Remove "virtual" attribute from signal.

2010-02-24  Konstantin Tokarev <annulen@users.sourceforge.net>

  * AUTHORS: Added myself to contributors

2010-02-28  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/moleculefile.cpp: Use local8Bit everywhere in file names
  (probably will fix Russian Windows compatibility)

  * libavogadro/src/pluginmanager.cpp: Don't try to load libavogadro.so and
  Avogadro.so as plugins

2010-03-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/moleculefile.cpp: MoleculeFile::writeMolecule: Parse chains
  before writing. (Fixes #2960889)

2010-03-01  Geoff Hutchison <babel@geoffhutchison.net>

  * CMakeLists.txt: Disable -fvisibility support on Mac. GCC42 from Apple seems
  to have a bug in this feature.

2010-03-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Always load files into new windows on Mac
  PR#2945916.

  * avogadro/gl2ps/README.txt, avogadro/gl2ps/TODO, avogadro/gl2ps/TODO.txt,
  avogadro/gl2ps/gl2ps.c, avogadro/gl2ps/gl2ps.h, avogadro/gl2ps/gl2ps.pdf,
  avogadro/gl2ps/gl2psTest.c, avogadro/gl2ps/gl2psTestSimple.c: Import of gl2ps
  1.3.5

2010-02-20  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-da.po,
  i18n/avogadro-de.po, i18n/avogadro-el.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-he.po, i18n/avogadro-hu.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-kn.po, i18n/avogadro-ko.po, i18n/avogadro-nb.po,
  i18n/avogadro-nl.po, i18n/avogadro-pl.po, i18n/avogadro-pt.po,
  i18n/avogadro-pt_BR.po, i18n/avogadro-ru.po, i18n/avogadro-sk.po,
  i18n/avogadro-sv.po, i18n/avogadro-tr.po, i18n/avogadro-uk.po,
  i18n/avogadro-zh_CN.po, i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-da.po, i18n/libavogadro-de.po, i18n/libavogadro-el.po,
  i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po,
  i18n/libavogadro-fi.po, i18n/libavogadro-fr.po, i18n/libavogadro-he.po,
  i18n/libavogadro-hi.po, i18n/libavogadro-hu.po, i18n/libavogadro-id.po,
  i18n/libavogadro-it.po, i18n/libavogadro-ja.po, i18n/libavogadro-kn.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Updated Launchpad Translations.

2010-02-17  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * cmake/modules/FindPythonLibs.cmake: Updated to version from CMake CVS.

2010-01-19  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-da.po,
  i18n/avogadro-de.po, i18n/avogadro-el.po, i18n/avogadro-en_CA.po,
  i18n/avogadro-en_GB.po, i18n/avogadro-es.po, i18n/avogadro-fi.po,
  i18n/avogadro-fr.po, i18n/avogadro-he.po, i18n/avogadro-hu.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-da.po, i18n/libavogadro-de.po, i18n/libavogadro-el.po,
  i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po,
  i18n/libavogadro-fi.po, i18n/libavogadro-fr.po, i18n/libavogadro-he.po,
  i18n/libavogadro-hi.po, i18n/libavogadro-hu.po, i18n/libavogadro-id.po,
  i18n/libavogadro-it.po, i18n/libavogadro-ja.po, i18n/libavogadro-ko.po,
  i18n/libavogadro-nb.po, i18n/libavogadro-nl.po, i18n/libavogadro-pl.po,
  i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po,
  i18n/libavogadro-sk.po, i18n/libavogadro-sv.po, i18n/libavogadro-tr.po,
  i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po,
  i18n/libavogadro.pot: Update with latest Launchpad translations.

2009-11-19  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/glwidget.cpp: Fix broken signals in GLWidget

2009-11-16  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Added annulen's
  default heuristics for pasting coordinates.

2009-11-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * testfiles/ferrocene.cml: Added ferrocene test file (with dummy atoms).

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/tools/autoopttool.cpp: Ignore dummy atoms for force field
  calcs. (Includes some debugging info.)

  * CMakeLists.txt: Bump to 1.0.1 for testing.

2009-11-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_nmr.cpp: Move connections to
  constructors for spectra tabs.

2009-11-06  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot, scripts/extract-application-messages.sh: Updated
  template -- main.cpp messages were not properly processed by
  extract-application-messages.sh.

2009-11-05  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/libavogadro.pot: Updated after removing new Cartesian editor.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h,
  .../src/extensions/icons/document-revert.png,
  libavogadro/src/extensions/icons/edit-clear.png,
  libavogadro/src/extensions/icons/edit-copy.png,
  libavogadro/src/extensions/icons/edit-cut.png,
  libavogadro/src/extensions/icons/edit-paste.png: Backout new Cartesian editor
  extension from 1.0 branch.

2009-11-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h,
  libavogadro/src/extensions/edit.qrc,
  libavogadro/src/extensions/icons/amarok_back.png,
  libavogadro/src/extensions/icons/amarok_next.png,
  libavogadro/src/extensions/icons/amarok_pause.png,
  libavogadro/src/extensions/icons/amarok_play.png,
  libavogadro/src/extensions/icons/amarok_stop.png,
  .../src/extensions/icons/document-revert.png,
  libavogadro/src/extensions/icons/edit-clear.png,
  libavogadro/src/extensions/icons/edit-copy.png,
  libavogadro/src/extensions/icons/edit-cut.png,
  libavogadro/src/extensions/icons/edit-paste.png: Re-merge annulen's cartesian
  editor.

2009-11-03  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated POT and PO files (with fewer messages)

  * avogadro/src/macchempasteboard.cpp.disabled,
  avogadro/src/macchempasteboard.h.disabled,
  libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/daltoninputdialog.cpp.disabled,
  .../src/extensions/daltoninputdialog.h.disabled,
  .../src/extensions/daltoninputdialog.ui.disabled,
  libavogadro/src/extensions/liganddialog.cpp,
  libavogadro/src/extensions/liganddialog.h,
  libavogadro/src/extensions/liganddialog.ui,
  libavogadro/src/extensions/linmorph.qrc,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphdialog.h,
  libavogadro/src/extensions/linmorphdialog.ui,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/pocketdialog.cpp,
  libavogadro/src/extensions/pocketdialog.h,
  libavogadro/src/extensions/pocketdialog.ui,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/extensions/wiitrackextension.h: Remove unused source files --
  these are still used for translations!

2009-11-02  Marcus D. Hanwell <marcus@cryos.org>

  * Doxyfile: Missed this version...

2009-10-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonterminal.cpp: PythonTerminal: Handle
  Key_Home as a special case

2009-10-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonterminal.cpp: Remove debug output

  * libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h: PythonTerminal extension: Allow
  selections in the python terminal widget without allowing to edit (i.e.
  delete) already processed commands

  * libavogadro/src/python/molecule.cpp: Fix python bindings for
  Molecule::numConformers

2009-10-30  Konstantin Tokarev <annulen@users.sourceforge.net>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h: Blocked old cartesian editor in
  propextension

  * libavogadro/src/extensions/CMakeLists.txt: Added Cartesian Editor to
  CMakeLists.txt

  * libavogadro/src/extensions/edit.qrc: Resource file for Cartesian Editor

  * .../src/extensions/icons/document-revert.png,
  libavogadro/src/extensions/icons/edit-clear.png,
  libavogadro/src/extensions/icons/edit-copy.png,
  libavogadro/src/extensions/icons/edit-cut.png,
  libavogadro/src/extensions/icons/edit-paste.png: Added icons for Cartesian
  Editor - copied form avogadro/src/icons

  * libavogadro/src/extensions/cartesianeditor.ui,
  libavogadro/src/extensions/cartesianextension.cpp,
  libavogadro/src/extensions/cartesianextension.h: Added extension "Cartesian
  Editor"

2009-10-29  Geoff Hutchison <babel@geoffhutchison.net>

  * INSTALL: Updated source requirements.

2009-10-28  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/main.cpp: Update Mac language detection code -- now tested and
  confirmed for Qt-4.6.

2009-10-28  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated POTs and translations.

  * scripts/extractrc.sh: Updated script from KDE -- fixes some problems with
  newer UI files.

  * avogadro/src/aboutdialog.cpp: Added Open Babel and Qt version numbers.
  Allow Git revision to be translated.

  * libavogadro/src/extensions/gamessinputdialog.ui: Add back "Compute..."
  button for GAMESS.

  * avogadro/src/main.cpp: Add support for Qt-4.6 Mac language preferences.

  * avogadro/src/mainwindow.ui: Set explicit MenuRole settings for appropriate
  actions. Should help translations on Mac.

  * scripts/find-translators.sh: Update scripts -- used to grab contributors
  for Avo 1.0.

  * i18n/avogadro-ar.po, i18n/avogadro-ca.po, i18n/avogadro-cs.po,
  i18n/avogadro-de.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po, scripts/clean-po.sh: Stripped PO files -- fixes
  bugs noted by Benoit and Annulen about untranslated messages (i.e., lupdate
  gets confused by obsolete translations).

2009-10-26  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  scripts/extract-application-messages.sh: Updated with translation suggestions
  from annulen

2009-10-25  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/updatecheck.cpp, .../src/extensions/networkfetchextension.cpp:
  Changed all deletes on the network reply to deleteLater() calls.

  * avogadro/src/updatecheck.cpp, .../src/extensions/networkfetchextension.cpp:
  Changed all deletes on the network reply to deleteLater() calls.

2009-10-24  Marcus D. Hanwell <marcus@cryos.org>

  * .../src/extensions/networkfetchextension.cpp: Fixed crash with Qt 4.5.3 -
  use deleteLater().

  * .../src/extensions/networkfetchextension.cpp: Fixed crash with Qt 4.5.3 -
  use deleteLater().

  * CMakeLists.txt, Doxyfile: Bumped build files in master to 1.1.0 -
  development versions.

2009-10-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/atom.cpp: Add python wrapper for
  Atom::formalCharge/Atom::setFormalCharge

  * libavogadro/src/python/pluginmanager.cpp: Fix python wrapper for
  PluginManager

2009-10-23  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/gaussianinputdialog.cpp: Some changes for
  finding Gaussian. Works if your profile is set correctly. (Not sure how to do
  this from the Mac GUI. Command-line works.)

  * libavogadro/src/extensions/gamessinputdialog.cpp: Whoops, just removed
  computeButton.

  * libavogadro/src/extensions/gamessinputdialog.ui: Temporarily remove the
  "Compute..." button for 1.0 release.

  * libavogadro/src/extensions/gamessinputdialog.cpp: Hide "Compute" button --
  currently non-functional.

  * libavogadro/src/extensions/gaussianinputdialog.cpp: Add support to find the
  g09 binary, if available.

  * libavogadro/src/pluginmanager.cpp: Fix Mac compilation.

2009-10-23  Marcus D. Hanwell <marcus.hanwell@kitware.com>

  * CMakeLists.txt: Install the USE file into the versioned directory too -
  more flexible.

  * libavogadro/src/CMakeLists.txt: Bumped SO version to 1 for the release.

2009-10-23  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile: Bumped the version number in preparation for the
  1.0.0 release.

2009-10-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Final import of translations before 1.0.

2009-10-22  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, avogadro/src/enginecolorswidget.cpp,
  avogadro/src/enginecolorswidget.h, libavogadro/src/config.h.in,
  libavogadro/src/glwidget.cpp, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h: Added versioned plugin directories - fixes
  bug 2882816.  I added versioned plugin directories on all architectures. This
  can be disabled, but it should not do any harm being left on. This
  necessitated soem changes to the plugin manager class. I removed the static
  and const methods and ported affected classes to get an instance of the
  singleton.

  * libavogadro/src/python/pluginmanager.cpp: Disabled wrapping of
  loadFactories method for now - Tim please look at it ;-)

2009-10-20  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix bug with isDefaultFileName -- check for
  empty strings.

  * libavogadro/src/extensions/inputfileextension.cpp: Fix PR#2881658 - Show
  Molpro window.

2009-10-20  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/molecule.cpp, libavogadro/src/residue.cpp,
  libavogadro/src/residue.h: When element changes with Atom::setAtomicNumber,
  issue an updated() signal from the atom. Residues will now listen for this
  signal and invalidate atom IDs accordingly. When saving residue information
  with molecules, check for invalid atom ids. Addresses PR#2855789.

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Latest Launchpad Translations.

  * avogadro/src/mainwindow.cpp: Switch out a missing "untitled" string.

2009-10-19  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/avogadro.pot, i18n/libavogadro-ar.po,
  i18n/libavogadro-bg.po, i18n/libavogadro-ca.po, i18n/libavogadro-cs.po,
  i18n/libavogadro-de.po, i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po,
  i18n/libavogadro-en_GB.po, i18n/libavogadro-es.po, i18n/libavogadro-fi.po,
  i18n/libavogadro-fr.po, i18n/libavogadro-id.po, i18n/libavogadro-it.po,
  i18n/libavogadro-ja.po, i18n/libavogadro-ko.po, i18n/libavogadro-nb.po,
  i18n/libavogadro-nl.po, i18n/libavogadro-pl.po, i18n/libavogadro-pt.po,
  i18n/libavogadro-pt_BR.po, i18n/libavogadro-ru.po, i18n/libavogadro-sk.po,
  i18n/libavogadro-sv.po, i18n/libavogadro-tr.po, i18n/libavogadro-uk.po,
  i18n/libavogadro-zh_CN.po, i18n/libavogadro-zh_TW.po, i18n/libavogadro.pot:
  Updated POTs. Will merge Launchpad shortly.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltoninputdialog.cpp,
  .../src/extensions/daltoninputdialog.cpp.disabled,
  libavogadro/src/extensions/daltoninputdialog.h,
  .../src/extensions/daltoninputdialog.h.disabled,
  libavogadro/src/extensions/daltoninputdialog.ui,
  .../src/extensions/daltoninputdialog.ui.disabled,
  libavogadro/src/extensions/inputfileextension.cpp,
  libavogadro/src/extensions/inputfileextension.h: Disable Dalton generation --
  not enough time for translations.

  * libavogadro/src/extensions/gamessextension.cpp: Comments for translators
  about QM selection and EFP selection.

  * libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/extensions/gamessinputdialog.ui: Update disambiguation of
  "loop" translations suggested by Konstantin Tokarev.

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui: Modified patch from Patch
  PR#2799140.

2009-10-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp: MainWindow: when opening a file, only create a
  new window if the current window is modified (isWindowModified).

2009-10-19  Jogvan Magnus Olsen <cyanat@hotmail.com>

  * libavogadro/src/extensions/daltoninputdialog.cpp: Minor correction to
  Dalton Input File plugin.

  * libavogadro/src/extensions/daltoninputdialog.cpp,
  libavogadro/src/extensions/daltoninputdialog.h: Added keyword "nosymm" when
  asking for excitation energies.

2009-10-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/CMakeLists.txt, libavogadro/src/CMakeLists.txt: WIN32: Don't
  attempt to create QM files on windows -- these should be copied from a linux
  build to avoid unicode problems with the translations [just place the QM
  files in avogadro/src and libavogadro/src] We could add the QM files to git
  but since there are only a handful of people building on windows, the
  downsides seem to outweigh the benefits. If not copied, Avogadro still build
  but will be untranslated.

2009-10-18  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, libavogadro/src/plugin.h: Bumped the plugin
  version number and config file versions - make clean required.

2009-10-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/PythonDeps.cmake: Check for Boost 1.40 now.

2009-10-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/PythonDeps.cmake: Recognise SIP 2.4.9

2009-10-17  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile: Bumped the version number to 0.9.9 in preparation
  for tagging.

2009-10-17  Kristof Bal <kristof.bal@gmail.com>

  * avogadro/src/engineitemdelegate.h,
  libavogadro/qtiocompressor/qtiocompressor.cpp,
  libavogadro/src/python/swig.cpp: Fix spelling errors (Krazy).  Spelling
  errors in comments and strings should be fixed as they may show up later in
  API documentation, handbooks, etc.

2009-10-16  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro-ca.po, i18n/libavogadro-cs.po, i18n/libavogadro-de.po,
  i18n/libavogadro-el.po, i18n/libavogadro-en_CA.po, i18n/libavogadro-en_GB.po,
  i18n/libavogadro-es.po, i18n/libavogadro-fi.po, i18n/libavogadro-fr.po,
  i18n/libavogadro-id.po, i18n/libavogadro-it.po, i18n/libavogadro-ja.po,
  i18n/libavogadro-ko.po, i18n/libavogadro-nb.po, i18n/libavogadro-nl.po,
  i18n/libavogadro-pl.po, i18n/libavogadro-pt.po, i18n/libavogadro-pt_BR.po,
  i18n/libavogadro-ru.po, i18n/libavogadro-sk.po, i18n/libavogadro-sv.po,
  i18n/libavogadro-tr.po, i18n/libavogadro-uk.po, i18n/libavogadro-zh_CN.po,
  i18n/libavogadro-zh_TW.po: Latest Launchpad Translations.

2009-10-16  Jogvan Magnus Olsen <cyanat@hotmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltonextension.cpp,
  libavogadro/src/extensions/daltonextension.h,
  libavogadro/src/extensions/daltoninputdialog.cpp,
  libavogadro/src/extensions/daltoninputdialog.h,
  libavogadro/src/extensions/daltoninputdialog.ui,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/inputfileextension.cpp,
  libavogadro/src/extensions/inputfileextension.h: Extended the Dalton input
  file plugin and renamed the gaussian extension to inputfile extension to make
  it more general.  All the input file generators, except GAMESS, were added to
  the Gaussian extension and therefore it makes sense to rename the extension
  to make it more general. Maybe also merge it with the GAMESS extension if
  possible.

2009-10-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Don't correct for pH when adding H atoms to
  2D->3D conversion. Made obvious by OpenBabel-devel mailing list message from
  James Jack.

2009-10-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gaussianinputdialog.cpp: Fix bug 2825731 -- make
  Gaussian z-matrix more like GaussView to help TURBOMOLE users.

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp: Fix more vibration bugs. Now
  arrow keys work correctly, and old vibrations don't reappear.x

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/tools/autoopttool.cpp: Convert all energies to kJ/mol for
  consistency.

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Fix vibration crash
  in recent versions -- don't always free conformer memory. We save it for
  vibrations.

  * avogadro/src/mainwindow.cpp: Fix bug on Mac with progress bar remaining
  visible after file opens.

  * .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h: Disable updating the properties
  window if it's not visible.

  * libavogadro/src/molecule.cpp: Fix "problem" with MMFF94 dipole moments. Now
  actually gets MMFF94 charges. PR#2875356.

  * avogadro/src/mainwindow.cpp: Fix Mac/Cocoa bug with enable/disable submenus
  when hiding and showing windows. Now works cleanly.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Fix bug with
  "extra" window when opening files. Now checks for default filename.

2009-10-13  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Tracking down a Mac/Cocoa bug with
  enable/disable submenus.

2009-10-11  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/updatecheck.cpp,
  avogadro/src/updatecheck.h: Made UpdateCheck a singleton, fixed segfault with
  Qt 4.5.3.  Fixed the segfault with Qt 4.5.3 - use reply->deleteLater()
  instead of deleting the object directly in the slot once finished. Also made
  this class into a singleton - there is no point in checking for an update
  more than once in any given instance of Avogadro!

  * libavogadro/src/engines/ribbonengine.cpp: Fixed the ribbon engine after
  changes to primitives.  Some changes to fix the ribbon engine to use the
  molecule object, as the primitive list no longer contains the residues. We
  should revisit what should and should not be kept in these lists, and use
  unique ids rather than pointers.

  * avogadro/src/CMakeLists.txt: Disabled the update checking code by default,
  causes segfaults with Qt 4.5.3.

2009-10-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationextension.cpp: More debugging looking for
  vibration crash.

2009-10-10  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.h: Removed unused m_pos variable.

2009-10-10  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationextension.cpp: First step for debugging
  vibration & animation. Attempt to lock Molecule more.

2009-10-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/propmodel.cpp:
  libavogadro/src/extensions/propmodel.cpp: Fix compile error

2009-10-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro.pot, i18n/libavogadro.pot: Updated with recent translatable
  strings, including formal charges.

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/extensions/propmodel.cpp: Add support for formal charges. You
  can set them using the Atom Properties, show them using atom labels, or draw
  appropriate bonding patterns to have them interpreted.

2009-10-09  Geoff Hutchison <babel@geoffhutchison.net>

  * builder/amino/l-arg.zmat: Fix PR#2839649 with L-Arg mistake.

  * .../src/extensions/molecularpropextension.cpp,
  libavogadro/src/molecule.cpp: Use MMFF94 to estimate dipole moment when
  available. On set of ~1000 molecules, correlation is R^2 = 0.769!

  * avogadro/src/mainwindow.cpp: Fix menu separators on Mac again.

2009-10-08  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix some Mac interface polish with Qt-Cocoa
  and Snow Leopard.

  * libavogadro/src/molecule.cpp: Fix for bug report PR#2803076 -- adding
  implicit hydrogens to Li, Be, etc. when drawing. (OpenBabel doesn't want to
  set these because formulas will be incorrect.)

2009-10-08  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt: If using Qt/Mac-Cocoa, make sure to install
  the "nib" directory.

  * libavogadro/src/tools/clickmeasuretool.cpp: Patch from Burkhard Lück to
  fix labels in click-measure tool using German.

2009-10-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/sip.cpp: Python: toPyQt(): convert GLWidget to
  QWdiget instead of QGLWidget (was not working here...)

2009-10-06  Casper Steinmann <casper.steinmann@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltonextension.cpp: Placed the Dalton extension
  in the appropriate menu by renaming the .so file generated

2009-10-01  Jogvan Magnus Olsen <cyanat@hotmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/daltonextension.cpp,
  libavogadro/src/extensions/daltonextension.h,
  libavogadro/src/extensions/daltoninputdialog.cpp,
  libavogadro/src/extensions/daltoninputdialog.h,
  libavogadro/src/extensions/daltoninputdialog.ui: First basic implementation
  of Dalton Input File generator extension

2009-09-30  Casper Steinmann <casper.steinmann@gmail.com>

  * libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gamessinputdialog.ui: Fixed bug "Error in GAMESS
  advanced setup menu - ID: 2836316"  Also: * Updated the input to use MWORDS
  instead of the old MEMORY keywork. * There are still minor issues with the
  input preview not updating when one selects a different unit of time, but no
  apparent fix was found.

2009-09-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp: Added locking for the surface
  engine.

2009-09-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/forcefieldextension.cpp: ForceField extension:
  show "busy" progress bar while doing weighted conformer search

  * libavogadro/src/molecule.cpp: Molecule::energies(): make sure the returned
  energies QList has an energy for each conformer (i.e. resize it if needed).
  Same for Molecule::energy(int).

2009-09-22  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro-af.po, i18n/avogadro-ar.po, i18n/avogadro-bg.po,
  i18n/avogadro-ca.po, i18n/avogadro-cs.po, i18n/avogadro-de.po,
  i18n/avogadro-el.po, i18n/avogadro-en_CA.po, i18n/avogadro-en_GB.po,
  i18n/avogadro-es.po, i18n/avogadro-fi.po, i18n/avogadro-fr.po,
  i18n/avogadro-id.po, i18n/avogadro-it.po, i18n/avogadro-ja.po,
  i18n/avogadro-ko.po, i18n/avogadro-nb.po, i18n/avogadro-nl.po,
  i18n/avogadro-pl.po, i18n/avogadro-pt.po, i18n/avogadro-pt_BR.po,
  i18n/avogadro-ru.po, i18n/avogadro-sk.po, i18n/avogadro-sv.po,
  i18n/avogadro-tr.po, i18n/avogadro-uk.po, i18n/avogadro-zh_CN.po,
  i18n/avogadro-zh_TW.po, i18n/libavogadro-ar.po, i18n/libavogadro-bg.po,
  i18n/libavogadro
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