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-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: Updated with Launchpad translations.

2009-09-17  Kristof Bal <kristof@localhost.(none)>

  * avogadro/src/avogadro.desktop: Fixed icon name in desktop file  The correct
  icon (the one we install) is called avogadro-icon.png. The desktop file
  points to avogadro_icon, so fix the name here.

2009-09-17  Casper Steinmann <casper.steinmann@gmail.com>

  * libavogadro/src/extensions/gamesshighlighter.cpp: Added all GAMESS keywords
  to the highlighter.

2009-09-10  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/surfaceextension.cpp: Only display the MO meshes
  if both are ready.

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

  * avogadro/src/mainwindow.cpp, libavogadro/src/molecule.cpp: Fixed some
  issues with file modification and saving.  Issue 2854213 should now be fixed,
  modification of the molecule is more accurately reflected now. Specifically
  when closing a molecule the empty window will not be marked as modified, when
  saving a molecule the window will be reset to reflect it was not modified
  since save and unsaved new files will prompt for a file name.

  * CMakeLists.txt, Doxyfile: Bumped version number to 0.9.8 in preparation for
  new release.

  * libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonmeshgenerator.cpp,
  libavogadro/src/engines/cartoonmeshgenerator.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/glpainter_p.cpp, libavogadro/src/glpainter_p.h,
  libavogadro/src/mesh.cpp, libavogadro/src/mesh.h,
  libavogadro/src/python/mesh.cpp: Use Color3f to store colors in Mesh, port
  other classes.  The Mesh class now uses Color3f to store color information
  for colored meshes. Other classes were ported to work with this new class.

  * libavogadro/src/color.h: Small fix to incorrect use of inline keyword.

  * libavogadro/src/CMakeLists.txt, libavogadro/src/color3f.h: Added simple
  color class that uses 3 floats to store color.  This is a very simple color
  class that uses 3 floats to store the red, green and blue components of
  color. It is designed to be used with OpenGL calls (OpenGL stores colors as
  floats normally), but can also be used with other display types. It allows
  vectors of color objects to be passed directly to OpenGL functions as GLfloat
  pointers.

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Added
  some locking back into the draw tool.

  * libavogadro/src/extensions/forcefieldextension.cpp: Extra logic for locking
  the molecule and updating geometry.  I have added some extra logic to attempt
  to acquire a write lock on the molecule, and then update the geometry. This
  seems to improve the situation significantly when optimizing the geometry.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Removed the
  function level locks in the Molecule class.  The locks have been causing
  performance issues due to multiple locks/unlocks in tight loops, along with
  some deadlocks. Migrating code to use tryLock* gets rid of deadlocks and has
  improved performance in some of the tight loops.  The Python bindings could
  do with some extra logic to take care of locking, or the documentation should
  make it clear that scripts need to take care of this.

2009-09-08  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 translations from Launchpad.

2009-09-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/tests/moleculefiletest.cpp, libavogadro/tests/moleculetest.cpp,
  testfiles/fail1.drawlog, testfiles/fail1.drawlog.ignore,
  testfiles/fail2.drawlog, testfiles/fail2.drawlog.ignore: Fix setAllConformers
  to just replace all conformers (and make sure there is always at least one
  conformer). See doxygen comments for more info. There is also a unit test for
  this in moleculetest.cpp.

2009-09-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glpainter_p.cpp: std::vector::data() is not part of the STL
  - used &(v[0]) instead.

2009-09-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/color.cpp, libavogadro/src/color.h: Just use float, rather
  than GLFloat for colors.

2009-09-02  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glpainter_p.cpp: Use at least the OpenGL 1.1 calls to load
  geometry onto the card.

2009-08-25  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp: Improved handling of setting unit cell axes
  and related view properties.

2009-08-24  Marcus D. Hanwell <marcus@cryos.org>

  * .../src/extensions/molecularpropextension.cpp: Bring back the dipole moment
  to the molecular properties dialog.  If a dipole moment calculated by an
  external program was read in it is displayed, otherwise N/A is displayed.

  * libavogadro/src/molecule.cpp: Fixes to ensure the dipole moment is handled
  correctly.  A few small fixes to ensure that when a dipole moment is read in
  from a file, it is preserved until the molecule is changed.

  * libavogadro/src/molecule.cpp: Fixed the calculation of the estimated dipole
  moment.

2009-08-22  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: More clean ups for
  the recent file list.  Cleaned up the recent file list code to ensure it is
  called on first load. Also removed a duplicate function and replaced with a
  default parameter.

  * libavogadro/src/engines/dipoleengine.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h: Fixed bug 2823931 - memory corruption on molecule
  close.  This bug was caused by a dangling pointer, updateGeomInfo was
  deleting the dipole moment pointer every time, but not setting the pointer to
  zero. I have cleaned up the dipole moment code, but it is still not doing
  anything useful as far as I can tell right now.

  * avogadro/src/mainwindow.cpp: Clean up conditional Mac specific code to be
  totally inside #ifdef.

  * avogadro/src/mainwindow.cpp: Removed some debug output from the recent file
  list functions.

2009-08-21  Marcus D. Hanwell <marcus@cryos.org>

  * .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h: Hide the dipole moment for now,
  some clean ups and GLWidget signal fix.

  * avogadro/src/mainwindow.cpp: Improvements to recent file list handling -
  duplicates, cleaned.  Added several improvements to remove duplicate entries,
  empty entries and non-existant entries from the recent file list. This
  squashes an annoying bug where the currently opened file would be shown
  twice, along with retaining stale file entries silently (or empty entries).

  * libavogadro/src/extensions/molecularpropdialog.ui: Small fix to molecule
  properties dialog.

  * libavogadro/src/extensions/spectratype_nmr.cpp: Fixed compilation error for
  min/max variables, and function style.

2009-08-21  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectratype_ir.cpp: Fix segfault on exit.

  * libavogadro/src/extensions/spectratype_nmr.cpp,
  libavogadro/src/extensions/spectratype_nmr.h: Update NMR plots to reflect
  changes to spectratype.*

  * libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h: Added a function to generate a
  list of sampling points so that long flat stretches aren't sampled at high
  resolution.

2009-08-21  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/glwidget.cpp: Added an option to
  reset display types to default for a view.  This was a long standing bug that
  caused issues for many users. I had to add a new string to the view menu, but
  I think it is worth it to improve the user experience. In addition to
  previous improvements to saving/loading display type settings, the user can
  now reset the display types. We should probably add a more global option to
  reset Avogadro to defaults without requiring users to manually delete the
  configuration file.

2009-08-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp: Fixed the mislabelled display types that
  could occur in certain situations.

  * avogadro/src/main.cpp: Minor clean up of commented code, style.

  * libavogadro/src/glwidget.cpp: Corrected unit cell axes loading setting into
  wrong variable on load.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Changed the
  energy function to take a signed int, works as expected now.

2009-08-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp: Added some additional read locking, still not
  tracked down the cause of the crash.

  * libavogadro/src/molecule.cpp: No longer require access to the d-pointer in
  these functions.

  * libavogadro/src/extensions/surfaceextension.cpp: Temporary workaround to
  crashes caused by inadequate locking.

  * libavogadro/src/atom.cpp: Some code cleanup, do not call update in the
  setAtomPos function.

  * libavogadro/src/glwidget.cpp: Unit cell geometry calculations were being
  calculated even when no unit cell was present.

  * libavogadro/src/molecule.cpp: Only invalidate molecule geometry when atoms
  are updated.

  * libavogadro/src/tools/autorotatetool.cpp: Made the central point of the
  sliders easier to see.

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h, libavogadro/src/mesh.cpp,
  libavogadro/src/mesh.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h: Removed the lock from the base Primitive class,
  added to classes that need it.

  * libavogadro/src/extensions/basisset.cpp: Fixed an issue with incorrect
  debug output code - should correct some crashes.

2009-08-11  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h, libavogadro/src/molecule.cpp:
  Remove leaked DOS code from master branch...

2009-08-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/tests/CMakeLists.txt,
  libavogadro/tests/drawcommandtest.cpp, testfiles/basic1.drawlog,
  testfiles/basic2.drawlog, testfiles/basic3.drawlog, testfiles/basic4.drawlog,
  testfiles/basic5.drawlog, testfiles/basic6.drawlog, testfiles/fail1.drawlog,
  testfiles/fail2.drawlog: * Fix various draw tool bugs * Update draw command
  unit tests: If you uncomment the DEBUG_COMMANDS define in drawcommand.cpp,
  all information needed to replay the commands are output using qDebug().
  Capturing this output and placing moving it to testfiles/*.drawlog will make
  the drawcommandtest replay the commands. Each command is undone/redone before
  executing the next command. At the end, all commands in the stack are
  undone/redone 10 times. Various values are veryfied while doing all this.
  There are still some cases for which the replay fails but these don't cause a
  segfault. In short, the draw commands are in better shape than ever before.

2009-08-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/pluginmanager.cpp: Made Avogadro run from the build
  directory on a Mac - different relative paths.

2009-08-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/molecule.cpp: Set DOS object to nul during init.

2009-08-06  David Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h, libavogadro/src/molecule.cpp: DOS
  plotting

2009-08-05  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/unitcellextension.cpp: Try to fix PR#2798634.
  setMolecule() should now update the dialog parameters.

  * avogadro/src/CMakeLists.txt: Ensure proper Mac translation directories are
  created.

  * avogadro/src/main.cpp, 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 Launchpad translations.

2009-08-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/python/molecule.cpp: Fixed the Python bindings for
  Molecule.  The new setEnergy function caused a break in the Python bindings.
  Also fixed white space issues in the file.

2009-08-03  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp: Set autoscaled plot limits to be zoomed out
  just a tad so that all points are easily in view.

  * libavogadro/src/molecule.cpp: Copy energy in Molecule::setOBMol()

2009-08-02  Marcus D. Hanwell <marcus@cryos.org>

  * cmake/modules/FindOpenBabel2.cmake: Bumped our Open Babel dependency to
  2.2.2.

  * avogadro/src/mainwindow.cpp: Workaround for strange CML bug on Windows. We
  need to track down the real source of the crash.

  * libavogadro/src/neighborlist.cpp: Use qobject_cast, it is faster for
  QObjects, check for null pointers.

  * libavogadro/src/extensions/shaderextension.cpp: Locate shaders relative to
  the binary location.

2009-08-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Added turbomole IR as a
  loadable spectra type.

  * libavogadro/src/extensions/spectratype_ir.cpp: Remove old work around for
  QChem spectra.

2009-08-01  Marcus D. Hanwell <marcus@cryos.org>

  * .../src/extensions/networkfetchextension.cpp: Experimental use of the
  Chemical Identifier Resolver  Added support for the Chemical Identifier
  Resolver, found at http://cactus.nci.nih.gov/chemical/structure. The user can
  type in a structure name such as ethanol, and this service will be used to
  attempt to retrieve an SDF file. Seems to work well in my initial testing.
  Also switch to the Navigate tool when loading structures.  The reverse should
  also be possible, sending an inchi key and attempting to resolve that to a
  structure name. I will look into that soon.

2009-07-29  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/molecule.cpp: Remove noisy debug statement.

2009-07-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Update geometry
  also needs to be called in order to render the whole molecule.

2009-07-19  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added a function
  to change an arbitrary conformer's energy.

2009-07-18  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt: Bumped Qt version requirement to 4.5.0, should have been
  done for 0.9.7 release.

2009-07-18  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp: Fix typo in
  vibrationdialog.cpp -- again?

2009-07-18  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, Doxyfile, INSTALL: Bumping to version 0.9.7 in preparation
  for the release.

2009-07-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h: Improved handling of loaded cube
  files, default for loaded cubes.

2009-07-17  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-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-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: Translations updates
  before 0.9.7

2009-07-17  Sergey Smirnov <sasmir@gmail.com>

  * avogadro/src/application.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/pythonwhenidle.cpp, libavogadro/src/pythonwhenidle.h: Release
  the python's GIL when Avogadro is idle (waiting for new events).

2009-07-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/surfacedialog.cpp: Set default iso surface
  values based upon the type of cube.

2009-07-11  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-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-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: Launchpad export of
  current translations.

2009-07-10  Sergey Smirnov <sasmir@gmail.com>

  * libavogadro/src/python/sip.cpp: Fixed Avogadro failing to load python
  scripts when built with SIP 4.8.x

2009-07-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/surfacedialog.cpp: Only enable MOs and other
  combo items if there is at least one MO.

2009-07-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: The non const slot is the one that
  is generally used.

2009-07-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h: Change
  PlotObject::addPoint() to return a reference to the added PlotPoint.

  * libavogadro/src/plotpoint.cpp, libavogadro/src/plotpoint.h: Added a
  customData property to PlotPoint -- this can be used to store extra
  information to help identify the point.

2009-07-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/moleculefile.cpp: Stopped the zero length .new files from
  being created, improved logic. Tested on Linux and Windows for saving a new
  file, and replacing a file. Works well.

  * CMakeLists.txt: Removed the embed openbabel stuff - done better by a parent
  CMakeLists.txt.

  * libavogadro/src/extensions/surfacedialog.cpp: Disable the resolution combo
  for cubes loaded from files.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/surfaceextension.cpp: Removed the old orbital
  extension, now replaced by the surface extension.

  * libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/molecule.cpp: Added ability to use loaded cube files in the
  surface extension too.

2009-07-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/extensions/surfaceextension.h: Ported to use the enum in the
  Cube class to denote cube types.

2009-07-02  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/surfaceextension.cpp: Some fixes for slater type
  basis sets.

  * libavogadro/src/extensions/surfacedialog.cpp: Updated to use the surfaces
  engine (renamed from orbitals engine).

2009-07-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui,
  libavogadro/src/extensions/surfacedialog.cpp: Moved the orbital engine to the
  surface engine, made necessary changes for move.

2009-06-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui: Removed the surface engine
  - the orbital engine will take its place.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: A few minor cleanups to the orbitals
  engine - it is a general surface engine now.

  * libavogadro/src/engines/orbitalengine.cpp: Only include mesh.h as meshes
  are not generated in this engine any more.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Renamed function for drawing boxes,
  made it private and inline.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Cleaned up the mesh combo update
  code, made the color combo work correctly again.

2009-06-29  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/molecule.cpp: Remove debug

2009-06-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/cube.h, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/extensions/surfaceextension.cpp, libavogadro/src/mesh.h,
  libavogadro/src/primitive.h: Updates to the orbital engine, soon to be the
  surface engine...  Added a cubeType property to cubes, allows for easy
  enumeration of cubes/meshes. Made the surface mesh selection work again in
  the orbital engine. Still needs some more fix ups but it is looking a lot
  better.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/surfacedialog.cpp,
  libavogadro/src/extensions/surfacedialog.h,
  libavogadro/src/extensions/surfacedialog.ui,
  libavogadro/src/extensions/surfaceextension.cpp,
  libavogadro/src/extensions/surfaceextension.h: The new, improved surface
  extension/dialog - simpler and more intuitive.  This is the first working
  version of the new, improved surface dialog. Not everything is finished yet,
  and it is basically a rewrite of the orbital extension/dialog. I think that
  most of the logic is in there now, need to add a little more for color
  mapping cubes onto each other, showing progress dialogs for mesh calculations
  and fixing a few remaining crashers. It is much simpler and allows users to
  accomplish calculations using a single form.

  * libavogadro/src/engines/orbitalengine.cpp: Fixed a bug with assigning new
  meshes, this still needs some attention after the numerous changes to
  cubes/meshes.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h: Added a new signal, improved debug
  output. These classes need an overhaul - common base.

  * libavogadro/src/mesh.cpp: Default the other mesh to FALSE_ID - not 0 which
  is a valid mesh id.

  * libavogadro/src/engines/orbitalengine.cpp: A few small improvements, do not
  assume there are always two meshes.

2009-06-28  David C. Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp: Undo some krazy fixes -- allow for
  arbitrarily small plot limits.

  * libavogadro/src/plotwidget.cpp: setDefaultLimits() gives a more intuitive
  result here.

2009-06-26  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/moleculefile.cpp: Fixed problem reading multiple files from
  gzip. Now needs OB changes (for seekg).

2009-06-26  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Removed debugging for parentless windows.

  * avogadro/src/mac/MacOSXBundleInfo.plist.in: Add ChemDraw CDX and CDXML to
  acceptable file types.

2009-06-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gamessinputdata.cpp: Fix for PR#2811323. Only
  use METHOD=NUMERIC for AM1, PM3, etc.

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Display unit cell axes by default if present. Add
  a signal/slot for updating the unit cell axes menu item when changed in
  glwidget.

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Make sure to
  remove deleted primitives from the selected list.

2009-06-25  Geoff Hutchison <babel@geoffhutchison.net>

  * .../src/extensions/molecularpropextension.cpp: Try to debug Vista crashing
  on molecule properties.

  * avogadro/src/mainwindow.cpp: Only show YesToAll and NoToAll buttons if we
  have a molecule file with multiple molecules.

  * .../src/extensions/insertfragmentextension.cpp: Perform a quick cleanup
  with UFF before inserting a SMILES fragment.

2009-06-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mac/MacOSXBundleInfo.plist.in: Updated Mac Info.plist. Should
  no longer "steal" file types from Mercury or GaussView (or anything else).

2009-06-23  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h: Add virtual to
  indicate if certain actions use the network. Currently unused.

2009-06-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/icons/AvoDocument.png, avogadro/src/icons/avogadro.png,
  avogadro/src/icons/avogadro.svg, avogadro/src/mac/AvogadroDocument.icns,
  avogadro/src/mac/avogadro.icns: Fix Avogadro icon slightly -- layering of one
  "orbit" was off. (Sorry, I'm obsessive compulsive about these things.)

2009-06-21  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/textrenderer_p.cpp: Make sure to handle lighting as well.
  Seems to fix "color leak" from label engine.

  * libavogadro/src/textrenderer_p.cpp: Bug fix suggested by Benoit. Solves
  part of CIF/RES corruption with Label engine. Still seems to be some sort of
  "color leak" -- probably similar issue.

2009-06-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povrayextension.cpp: Fixes for better file
  permission checking when rendering with POV-Ray.

  * libavogadro/src/python/eigen.cpp: Last few spots that needed x86_64 fixes
  in the Eigen Python bindings.

2009-06-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/eigen.cpp: Python eigen.cpp fix for x86_64

2009-06-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/eigen.cpp: python/eigen.cpp: replace old
  PyArray_[INT/FLOAT/DOUBLE] with new NPY_[INT/FLOAT/DOUBLE].

2009-06-20  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/clickmeasuretool.cpp: Fix bug found by Burkhard Luck.

2009-06-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/cartoonengine.cpp: CartoonEngine: Set reasonable
  (not black!) initial colors.

  * libavogadro/src/bond.h, libavogadro/src/camera.h, libavogadro/src/color.h,
  libavogadro/src/glwidget.h, libavogadro/src/molecule.h,
  libavogadro/src/moleculefile.h, libavogadro/src/painter.h,
  libavogadro/src/plugin.h, libavogadro/src/pluginmanager.h,
  libavogadro/src/primitive.h, libavogadro/src/primitivelist.h,
  libavogadro/src/surfacemeshgenerator.h, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.h: Some header documentation changes resulting from
  updating python bindings.

  * libavogadro/src/animation.cpp, libavogadro/src/bond.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/python/Avogadro.py,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/TODO,
  libavogadro/src/python/animation.cpp, libavogadro/src/python/atom.cpp,
  libavogadro/src/python/bond.cpp, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/color.cpp, libavogadro/src/python/cube.cpp,
  libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/elementtranslator.cpp,
  libavogadro/src/python/engine.cpp, libavogadro/src/python/extension.cpp,
  libavogadro/src/python/fragment.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/mesh.cpp, libavogadro/src/python/meshgenerator.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/molecule.h,
  libavogadro/src/python/moleculefile.cpp,
  libavogadro/src/python/moleculelist.cpp, libavogadro/src/python/navigate.cpp,
  libavogadro/src/python/neighborlist.cpp, libavogadro/src/python/painter.cpp,
  libavogadro/src/python/painterdevice.cpp, libavogadro/src/python/plugin.cpp,
  libavogadro/src/python/pluginmanager.cpp,
  libavogadro/src/python/primitive.cpp,
  libavogadro/src/python/primitivelist.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/residue.cpp, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/std_vector.cpp, libavogadro/src/python/tool.cpp,
  libavogadro/src/python/toolgroup.cpp,
  libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/camera.py,
  libavogadro/src/python/unittest/color.py,
  libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/extension.py,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/mesh.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/python/unittest/tool.py,
  libavogadro/src/python/unittest/toolgroup.py,
  libavogadro/src/python/unittest/util.py: Update python, cleanup & added
  docstrings (copied from doxygen docs). Also checked function overloading &
  default arguments.  Minor code changes in cpp files: Animation: implement
  dynamicBonds() Bond: initialize m_aromaticity to false in ctor.
  Molecule::calculateAromaticity(): prevent crash (use OBMol::NumBonds()
  instead of numBonds() when accessing bonds from an OBMol.)

2009-06-19  Jordan Mantha <jordan.mantha@gmail.com>

  * scripts/extract-doc-messages.sh: add docbook->pot script

2009-06-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/cartoonmeshgenerator.cpp: CartoonMeshGenerator: Fix
  typo in normal rotation, this made the cartoon mesh less smooth.

2009-06-17  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-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-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: Updated launchpad
  translations.

2009-06-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/python/wireframe.py: Fix python wireframe engine
  example (Color::set -> Color::setFromPrimitive)

2009-06-17  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/moleculefile.cpp: Fix typo

2009-06-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/moleculefile.cpp,
  libavogadro/src/moleculefile.h: Handle VASP files as a special case in
  MoleculeFile

  * libavogadro/src/python/sip.cpp: More sip 4.8 changes...

2009-06-17  David Lonie <loniedavid@gmail.com>

  * testfiles/VASP-8LiH/INCAR, testfiles/VASP-8LiH/KPOINTS,
  testfiles/VASP-8LiH/POSCAR, testfiles/VASP-8LiH/POTCAR,
  testfiles/VASP-8LiH/readme: Added VASP input set to testfiles.

2009-06-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/sip.cpp: Some more sip 4.8 changes (python)

2009-06-16  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/python/example.py: Switch menuPath to "Scripts"
  which will make more sense for most people IMHO.

2009-06-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/PythonDeps.cmake: PythonDeps.cmake: Change SIPVERSION MATCHES
  "4.8.0" to "4.8" (will match 4.8, 4.8.0, 4.8.1, ...)

  * cmake/modules/PythonDeps.cmake, libavogadro/src/python/sip.cpp: Add support
  for sip 4.8.0

2009-06-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/protein.cpp: Protein: don't include non amino acid residues
  in the chains. This used to result in ligands being added to the end of the
  chain. MeshGenerator uses these chains to create the cartoon mesh and there
  were ugly tails because the ligands can be at a distance from the last amino
  acid residue in the chain.

  * libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/tests/moleculefiletest.cpp:
  CartoonEngine: remove debug output MoleculeFile: bug fix, make sure streampos
  contains the correct number of positions (was causing an endless loop in
  replaceMolecule)

2009-06-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/directorytreemodel.cpp,
  libavogadro/src/extensions/directorytreemodel.h,
  .../src/extensions/insertfragmentdialog.cpp,
  libavogadro/src/extensions/insertfragmentdialog.ui,
  libavogadro/src/filetreeitem.cpp, libavogadro/src/filetreeitem.h: Fix
  PR#2663883 -- switch fragment window to QFileSystemModel. The downside is
  that we only can have the default set of fragments, not a list of
  directories, but this should be fine for 1.0. Evidently the best way to
  handle multiple root directories is with a proxy model.

2009-06-14  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp: MainWindow: delete the d->moleculeFile in
  saveAs since we need to save to a new file.

  * avogadro/src/savedialog.cpp: SaveDialog: Call updateDefaultSuffix after
  setting the default filter. On linux, the "All files (*.*)" filter used to
  result in attempts to save out.* (instead of out.pdb, after opening a pdb
  file and "Save As...")

  * libavogadro/src/moleculefile.cpp: MoleculeFile: check format pointers
  before calling OBConversion::Set[In/Out]Format. When there is only one
  molecule, clear the conformers and set m_conformerFile to false.

2009-06-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindLinguist.cmake: Add lconvert-qt4. Thanks to Tim for the
  heads-up.

2009-06-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/tests/moleculefiletest.cpp: Update MoleculeFile unit test after
  merge with OpenbabelWrapper

2009-06-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/FindLinguist.cmake: Fix copy error (I think) in
  FindLinguist.cmake (lrelease --> lconvert)

2009-06-12  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/h2methylextension.cpp: Fix disappearing molecule
  & crash bug. Solves PR#2632541.

  * i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.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,
  libavogadro/src/extensions/gamessinputdialog.ui: Updated typo in GAMESS input
  builder.

  * libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/molecule.cpp: Add back feature to add hydrogens by pH. Fixes
  PR#2799259.

2009-06-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-ar.po, i18n/avogadro-bg.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/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.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,
  libavogadro/src/extensions/surfacedialog.ui: One more -- disambiguation of
  "In Display Type:"

  * avogadro/src/mainwindow.cpp, libavogadro/src/extensions/linmorphdialog.ui,
  libavogadro/src/extensions/spectratabnmr.ui: Translation corrections from
  Louis Ricard.

  * i18n/avogadro-ar.po, i18n/avogadro-bg.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/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.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,
  libavogadro/src/elementtranslator.cpp,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/linmorphdialog.ui,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/tools/aligntool.h: Spelling corrections on translatable
  strings.

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

  * i18n/avogadro-ar.po, i18n/avogadro-bg.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/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.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,
  scripts/create-translations.sh: Latest translations from Launchpad plus
  updated POT files.

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: Fix prop model to handle numeric
  sorting. Solves PR#2803874

  * avogadro/src/mainwindow.cpp: More debugging code for parentless widgets.

  * libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/numbertableitem.cpp, libavogadro/src/numbertableitem.h: Qt
  doesn't have a numeric QTableWidgetItem because it you can't subclass it
  correctly.

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  cmake/modules/FindLinguist.cmake, libavogadro/src/CMakeLists.txt: Switch PO
  translations to a new QT_WRAP_PO macro in FindLinguist. Works much, much
  better -- only updates when needed.

  * libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/numbertableitem.h, libavogadro/src/undosequence.h: Update
  documentation for NumberTableItem

  * libavogadro/src/numbertableitem.cpp, libavogadro/src/numbertableitem.h:
  Small class to handle numeric sorting -- surprused Qt doesn't have one.

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autorotatetool.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/zmatrixtool.cpp: Added some work and debugging messages
  to find parentless widgets. There's a bug on Mac where the program won't quit
  correctly.

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

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, scripts/create-translations.sh: Improve
  translation creation & updating. The replacing of "-" with "_" caused some
  problems here since my build directory contains a "-" character.

2009-06-10  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/animation.cpp,
  libavogadro/src/extensions/vibrationextension.cpp: Fix bugs with "animate
  speed based on frequency" now works smoothly. Thanks to Jan Jensen for the
  suggestion.

  * libavogadro/src/python/moleculefile.cpp,
  libavogadro/src/python/openbabelwrapper.cpp, libavogadro/src/python/sip.cpp:
  Finish merge of OpenbabelWrapper -- didn't get Python code.

2009-06-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp, libavogadro/src/openbabelwrapper.h:
  Merge OBwrapper & MOleculeFile. Now one class.

2009-06-09  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp: Fixed typo in vibration
  dialog.

2009-06-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/primitivelist.cpp: Fix a strange crash: draw, select all,
  clear, draw again -- bang! Check primitives for valid types before append()

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/overlaysettingswidget.ui: Remove overlay settings
  widget -- confusing carbon copy of label engine.

  * i18n/avogadro-ar.po, i18n/avogadro-bg.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/avogadro.pot,
  i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.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,
  libavogadro/src/extensions/surfacedialog.ui: Added some translation context,
  particularly for surfacedialog.ui

  * libavogadro/src/tools/zmatrixdialog.cpp: Make sure z-matrix table stretches
  properly.

  * i18n/libavogadro-ar.po, i18n/libavogadro-bg.po, i18n/libavogadro-ca.po,
  i18n/libavogadro-cs.po, i18n/libavogadro-de.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.

  * avogadro/src/mainwindow.cpp: Fix bugs with tab close button appearing even
  on default launch (i.e., no loading files)

  * avogadro/src/avogadro.qrc, avogadro/src/icons/configure.png,
  avogadro/src/icons/document-open-recent.png,
  avogadro/src/icons/document-open-remote.png,
  libavogadro/src/tools/autoopttool.png, libavogadro/src/tools/measure.png:
  More icon updates. Now with an auto-opt icon (E with arrow)

  * avogadro/src/mainwindow.cpp: One last setTabsClosable() call.

  * libavogadro/src/extensions/forcefieldextension.cpp: Add shortcut key to
  "Optimize Geometry"

2009-06-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.ui: Marked some numbers as
  non-translatable.

  * libavogadro/src/extensions/surfacedialog.ui: Added prototype of the new
  surface dialog - much more streamlined interface.

2009-06-08  Geoff Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, scripts/create-translations.sh: Probably the
  last PO translation update. Seems to work smoothly now. I *HATE*
  add_custom_target -- it re-runs all the time. If someone knows Cmake magic,
  let's fix this.

  * CMakeLists.txt: Fix lupdate call to prevent it from modifying PO files.

2009-06-08  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/glgraphicsview.h: Removed A_EXPORT - not part of our public
  API anymore.

2009-06-08  Geoff Hutchison <geoff@geoffhutchison.net>

  * : Launchpad PO files -- something modifies them in CMake scripts? I'll
  check.

  * i18n/libavogadro-zh_TW.po: Add PO files from Launchpad.

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, scripts/create-translations.sh: Switch to use
  PO files and lconvert for building translations. (Ideally,
  avogadro/src/CMakeLists.txt and libavogadro/src/CMakeLists.txt won't wrap TS
  files until translations are built.) CMake help here would be appreciated.
  Right now, it's a race condition.

2009-06-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/CMakeLists.txt: Fix icon filename in
  avogadro/src/CMakeLists.txt

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/main.cpp:
  Ommit python module wrapper for now (wasn't working)

2009-06-08  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: Added feature for faster
  vibration animations for high-frequency modes. Currently crashes for unknown
  reason.

  * libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/qcheminputdialog.ui: Add "Compute..." buttons for
  local calculations.

2009-06-08  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/engineitemmodel.cpp: Only the first column should be editable
  or checkable.

  * avogadro/src/mainwindow.cpp: Added an extra check - never close the last
  view in the central tab widget.

  * avogadro/src/mainwindow.cpp: Ensure views in the central tab can only be
  closed if there is more than one view.

2009-06-08  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/engineviewwidget.cpp: Fix layout on engine view.

2009-06-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/hbondengine.cpp: Hydrogen bond engine: prevent
  crash when there are no atoms. (Fixes #2803050)

2009-06-08  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/avogadro.qrc, avogadro/src/engineitemmodel.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/autoopttool.png,
  libavogadro/src/tools/measure.png, libavogadro/src/tools/zmatrixtool.cpp,
  libavogadro/src/tools/zmatrixtool.qrc: Updated icons.

  * avogadro/src/avogadro.qrc, avogadro/src/engineitemdelegate.cpp,
  avogadro/src/engineitemmodel.cpp, avogadro/src/engineprimitiveswidget.ui,
  avogadro/src/icons/application-exit.png, avogadro/src/icons/arrow-down.png,
  avogadro/src/icons/arrow-left.png, avogadro/src/icons/arrow-right.png,
  avogadro/src/icons/arrow-up.png, avogadro/src/icons/avogadro-icon.png,
  avogadro/src/icons/avogadro_icon.png, avogadro/src/icons/back.png,
  avogadro/src/icons/colorize.png, avogadro/src/icons/configure.png,
  avogadro/src/icons/copy.png, avogadro/src/icons/cut.png,
  avogadro/src/icons/document-close.png,
  avogadro/src/icons/document-export.png,
  avogadro/src/icons/document-import.png, avogadro/src/icons/document-new.png,
  avogadro/src/icons/document-open.png, avogadro/src/icons/document-print.png,
  avogadro/src/icons/document-revert.png,
  avogadro/src/icons/document-save-as.png,
  avogadro/src/icons/document-save.png, avogadro/src/icons/down.png,
  avogadro/src/icons/edit-add-child.png, avogadro/src/icons/edit-add.png,
  avogadro/src/icons/edit-clear.png, avogadro/src/icons/edit-copy.png,
  avogadro/src/icons/edit-cut.png, avogadro/src/icons/edit-paste.png,
  avogadro/src/icons/edit-redo.png, avogadro/src/icons/edit-remove.png,
  avogadro/src/icons/edit-select-all.png, avogadro/src/icons/edit-undo.png,
  avogadro/src/icons/edit_add.png, avogadro/src/icons/edit_remove.png,
  avogadro/src/icons/exit.png, avogadro/src/icons/fileclose.png,
  avogadro/src/icons/fileexport.png, avogadro/src/icons/filenew.png,
  avogadro/src/icons/fileopen.png, avogadro/src/icons/filesave.png,
  avogadro/src/icons/filesaveas.png, avogadro/src/icons/fill-color.png,
  avogadro/src/icons/forward.png, avogadro/src/icons/minus.png,
  avogadro/src/icons/paste.png, avogadro/src/icons/plus.png,
  avogadro/src/icons/preferences-plugin.png, avogadro/src/icons/rebuild.png,
  avogadro/src/icons/redo.png, avogadro/src/icons/revert.png,
  avogadro/src/icons/tab-close.png, avogadro/src/icons/tab-detach.png,
  avogadro/src/icons/tab-duplicate.png, avogadro/src/icons/tab-new.png,
  avogadro/src/icons/tab_new.png, avogadro/src/icons/tab_remove.png,
  avogadro/src/icons/tools-report-bug.png, avogadro/src/icons/undo.png,
  avogadro/src/icons/up.png, avogadro/src/icons/view-fullscreen.png,
  avogadro/src/icons/view-list-tree.png, avogadro/src/icons/view-restore.png,
  avogadro/src/icons/window_fullscreen.png,
  avogadro/src/icons/window_nofullscreen.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.ui, avogadro/src/projecttreeeditor.qrc,
  avogadro/src/projecttreeeditor.ui, avogadro/src/settingsdialog.ui,
  libavogadro/src/tools/autoopttool.png, libavogadro/src/tools/autorotate.png,
  libavogadro/src/tools/manipulate.png, libavogadro/src/tools/measure.png,
  libavogadro/src/tools/zmatrix.png: Icon update, including new icons from KDE
  Oxygen theme.

2009-06-07  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, libavogadro/src/openbabelwrapper.cpp: Ported
  the bug fixes to file saving from MainWindow.  I ported the changes I made in
  MainWindow to fix the file saving bugs. I also added back in some error
  checking for normal saves of single molecules. Actual file saving seems to be
  working OK, but Avogadro does not register the changes have been saved and so
  prompts the user when closing - this needs fixing. We also need to do a lot
  of testing on these functions on all three platforms to ensure we have not
  had any regressions, such as the zero length file bug.

  * libavogadro/src/openbabelwrapper.cpp: This caused a crash, check whether we
  have a format pointer. Possibly an OB bug.

2009-06-07  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: fix compile error with includes.

2009-06-07  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp: New Qt 4.5 function - fixes rendering issues
  on Linux with GLWidget in tabs.

  * avogadro/src/mainwindow.cpp: Make sure detach view is disabled if there is
  only one view.

  * avogadro/src/detachedview.cpp: Removed that slot now as it did not work as
  intended.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added in some extra
  logic to figure out which widget is active.

  * avogadro/src/detachedview.cpp, avogadro/src/detachedview.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Bring back the
  detached view functionality I have been missing so much!  This is me bringing
  back a detached GLWidget view. This is now mostly working, with the main
  remaining issue being how to set the active display to change the settings of
  the GLWidget. I have a few ideas, please take a look and see if you can see
  any more issues with it.

2009-06-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.h, libavogadro/src/python/glgraphicsview.cpp,
  libavogadro/src/python/main.cpp: Merge + remove GLGraphicsView python binding

2009-06-07  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/glgraphicsview.cpp, avogadro/src/glgraphicsview.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/glgraphicsview.cpp,
  libavogadro/src/glgraphicsview.h: Moved the GLGraphicsView classes into
  avogadro and out of our API.

  * avogadro/src/engineitemdelegate.cpp: Trying it with no icon when the engine
  does not have a settings widget.

  * avogadro/src/engineitemdelegate.cpp, avogadro/src/engineitemmodel.cpp:
  Improvements to the model and delegate - background comes out right now too.

  * libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/hbondengine.h, libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h: Implemented hasSettings virtual to
  speed up engine tree view display.

  * avogadro/src/engineitemdelegate.cpp: Now with an added icon - not sure it
  is the best one but it shows how it works better.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Removed settings
  button, added new engine view. Need icon for settings!  I removed the
  settings button, the grey boxes can now be used to get the settings dialog. I
  need a picture, but it works very nicely here. I would appreciate feedback
  and testing. I will look for an image to put in there too, but am open to
  suggestions.

  * avogadro/src/engineitemdelegate.cpp, avogadro/src/engineitemdelegate.h,
  avogadro/src/engineviewwidget.cpp, avogadro/src/engineviewwidget.h: New
  engine tree view with inline settings buttons.  First pass at a mew engine
  tree view with inline settings buttons. We could extend this to have inline
  duplicate and remove buttons in the future. I really need some images for
  settings (tools?). Remove and duplicate images would be useful too. They can
  be drawn by the item delegate if I can find/draw some icons.

  * avogadro/src/engineitemmodel.cpp, avogadro/src/engineitemmodel.h: Additions
  and improvements to the engine item model, facilitates inline settings now.

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h: Added a new signal
  for engines to indicate whether they have a settings dialog.

2009-06-07  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/savedialog.cpp: Allow "always
  build" 3D coordinates for multi-molecule file. Prevent saving to gzip files.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Switch to table
  widget for selecting molecules. Looks great.

2009-06-06  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix bug with selection mode in multi-molecule
  browser.

  * avogadro/src/mainwindow.cpp: Add a working progress dialog to let the user
  know something is happening!

  * libavogadro/src/extensions/constraintsdialog.cpp: Make sure constraints
  table is properly stretched.

  * avogadro/src/mainwindow.cpp: Finish off "all molecules" list view. Fast!

  * libavogadro/src/engine.cpp: Prevent infinite loop in my testing.

2009-06-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Keep the spectra plot widget the
  same size on toggleCustomize(). Fixes PR#2801471

2009-06-06  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/primitiveitemmodel.cpp: Changes and improvements to work with
  less caching of the primitives.  Still might need a little more work, but
  these changes allow the model to work with the GLWidget class without all the
  caching. Some improved logic and improved display of Atom and Bond
  information. Also using 1 based indexes as we have in the rest of the user
  interface.

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Finally got rid
  of the two argument moleculeChanged signal.

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h: Some changes and
  improvements to the Engine base class.  The default implementation only pays
  attention to Atom and Bond objects. If your engine handles other types the
  virtual functions can be reimplemented.

  * libavogadro/src/plugin.h: Bumped the plugin version - remember to do a make
  clean.

2009-06-06  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Added "view all molecules" -- need to debug, but
  heading out for errands.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Use MoleculeFile.
  Ready to use a QListWidget for selecting slices.

  * libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp: Update to use titlesRef and
  streamposRef()

  * libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h: Add
  filename parameters (currently unused) for replaceMolecule methods.

2009-06-02  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/engineprimitiveswidget.cpp,
  avogadro/src/engineprimitiveswidget.h, avogadro/src/mainwindow.cpp,
  avogadro/src/primitiveitemmodel.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/molecule.cpp,
  libavogadro/src/python/engine.cpp, libavogadro/src/python/glwidget.cpp:
  Getting rid of all the primitive caching in GLWidget.  This is the first part
  of my attempt to get rid of all the primitive caching in GLWidget. This works
  and compiles, but the PrimitiveItemModel is totally broken. Should be able to
  fix that up with a little work.

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

  * libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp: Add QStringList& MoleculeFile::titles()
  again as titles_p()

2009-06-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/plugin.cpp, libavogadro/src/plugin.h: Added a license
  virtual function to plugin, so that plugins can declare their license.

  * CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt: Find and link to
  zlib, qiocompressor implicitly links to zlib anyway.

2009-06-06  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/importdialog.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/moleculefile.cpp,
  libavogadro/src/moleculefile.h, libavogadro/src/openbabelwrapper.cpp,
  libavogadro/src/python/openbabelwrapper.cpp: First pass at migrating
  MainWindow to OpenbabelWrapper & MoleculeFile. NOT ready for "prime-time"

2009-06-05  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/tools/autoopttool.cpp: Add
  energy of the molecule when doing forcefield or autoopt interactions. Fixes
  PR#1976211.

  * scripts/find-po-email.py, scripts/find-translators.sh: Add scripts to pull
  e-mail addresses (or names) from Launchpad PO files.

2009-06-05  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/CMakeLists.txt: Fixed endif that did not match opening if
  statement.

  * CMakeLists.txt, Doxyfile, cmake/modules/AvoCPack.cmake: Bumped version
  number to 0.9.6 in preparation for release.

  * cmake/modules/AvoCPack.cmake: Make sure the license is pulled in by CPack
  for NSIS.

2009-06-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h: Fix bug in vibration dialog
  sorting. Closes PR#2801711

2009-06-05  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Track the current
  conformer (e.g., for setting current energy). Track whether we're using an
  estimated dipole moment -- if so, delete the cache when the geometry changes.

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/glpainter_p.h, libavogadro/src/painter.h: Add ellipsoid
  placeholder for ORTEP diagrams.

  * libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Minor warning fix.

2009-06-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp: Switch bond orders when typing 1, 2, 3,
  or 4.

2009-06-04  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt: GNU/kFreeBSD build fix from Michael Banck --
  PR#2801267.

  * builder/amino/l-ala.zmat, .../src/extensions/insertpeptideextension.cpp:
  Fix some peptide builder bugs. Now ensures all amino acids will have bonds.

  * libavogadro/src/extensions/gamessinputdata.cpp: Fix bug with GAMESS point
  groups with axes (PR#2712161).

2009-06-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/orbitalextension.cpp: Added support for reading
  .fchk.gz Gaussian output.

2009-06-03  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp: Fixes for bug 2800647, 2789533 for file saving
  bugs.  Adding some more cautious logic, also popup warning messages when
  files fail to read or save. This seems to work here on Linux and Windows. We
  should double check all is still well on the Mac too. I think the messgae
  boxes are better than status messages.

  * avogadro/src/main.cpp: A few small fixes for the Windows package logic.

2009-06-03  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h: Finish addition of local
  Gaussian runs. Now works cleanly and will try to run formchk.

  * libavogadro/qtiocompressor/qtiocompressor.cpp,
  libavogadro/qtiocompressor/qtiocompressor.h: Added LGPL QtIOCompressor for
  reading compressed streams.

  * fragments/cyclic sugars/alpha-D-allopyranose.cml, .../cyclic
  sugars/alpha-D-arabinopyranose.cml, fragments/cyclic
  sugars/alpha-D-fucopyranose.cml, .../cyclic
  sugars/alpha-D-galactopyranose.cml, .../cyclic
  sugars/alpha-D-galacturonopyranose.cml, fragments/cyclic
  sugars/alpha-D-glucopyranose.cml, .../cyclic
  sugars/alpha-D-glucuronopyranose.cml, fragments/cyclic
  sugars/alpha-D-gulopyranose.cml, fragments/cyclic
  sugars/alpha-D-idopyranose.cml, fragments/cyclic
  sugars/alpha-D-lyxopyranose.cml, fragments/cyclic
  sugars/alpha-D-mannopyranose.cml, fragments/cyclic
  sugars/alpha-D-psicopyranose.cml, fragments/cyclic
  sugars/alpha-D-rhamnopyranose.cml, fragments/cyclic
  sugars/alpha-D-ribopyranose.cml, fragments/cyclic
  sugars/alpha-D-tagatopyranose.cml, fragments/cyclic
  sugars/alpha-D-talopyranose.cml, fragments/cyclic
  sugars/alpha-D-xylopyranose.cml, .../cyclic
  sugars/alpha-L-arabinopyranose.cml, fragments/cyclic
  sugars/alpha-L-fucopyranose.cml, .../cyclic
  sugars/alpha-L-galactopyranose.cml, fragments/cyclic
  sugars/alpha-L-lyxopyranose.cml, fragments/cyclic
  sugars/alpha-L-rhamnopyranose.cml, fragments/cyclic
  sugars/alpha-L-ribopyranose.cml, fragments/cyclic
  sugars/alpha-L-sorbopyranose.cml, fragments/cyclic
  sugars/alpha-L-xylopyranose.cml, fragments/cyclic
  sugars/beta-D-allopyranose.cml, fragments/cyclic
  sugars/beta-D-arabinopyranose.cml, fragments/cyclic
  sugars/beta-D-fructopyranose.cml, fragments/cyclic
  sugars/beta-D-fucopyranose.cml, fragments/cyclic
  sugars/beta-D-galactopyranose.cml, fragments/cyclic
  sugars/beta-D-glucopyranose.cml, fragments/cyclic
  sugars/beta-D-gulopyranose.cml, fragments/cyclic
  sugars/beta-D-idopyranose.cml, fragments/cyclic
  sugars/beta-D-lyxopyranose.cml, fragments/cyclic
  sugars/beta-D-mannopyranose.cml, fragments/cyclic
  sugars/beta-D-rhamnopyranose.cml, fragments/cyclic
  sugars/beta-D-ribopyranose.cml, fragments/cyclic
  sugars/beta-D-tagatopyranose.cml, fragments/cyclic
  sugars/beta-D-talopyranose.cml, fragments/cyclic
  sugars/beta-D-xylopyranose.cml, fragments/cyclic
  sugars/beta-L-arabinopyranose.cml, fragments/cyclic
  sugars/beta-L-lyxopyranose.cml, fragments/cyclic
  sugars/beta-L-ribopyranose.cml, fragments/cyclic
  sugars/beta-L-xylopyranose.cml,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h: Added cyclic sugars from
  Klotho repository, suggested by Magnus Lundborg

2009-06-02  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt: Make sure to create en and en_US language
  folders for Mac bundle. Fixes bug with other languages showing up in the
  interface.

2009-06-02  Marcus D. Hanwell <marcus@cryos.org>

  * Doxyfile, INSTALL, cmake/modules/AvoCPack.cmake,
  libavogadro/src/glwidget.h: Bumped version number in Doxyfile, few small
  updates to build files and docs.

  * avogadro/src/projecttreeeditor.cpp: Fix for bug 2798919 - segfault on
  settings dialog with languages loaded.  Not sure if this is the ideal fix,
  just added some checks for null before writing settings. This does allow
  users of other languages to use the settings dialog, it seems to still change
  settings and save them.

2009-06-02  Geoff Hutchison <babel@geoffhutchison.net>

  * CMakeLists.txt: Bump for 0.9.5 release.

  * i18n/avogadro.pot, i18n/libavogadro.pot: POT files for 0.9.5.

  * i18n/avogadro_ar.ts, i18n/avogadro_bg.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_CA.ts,
  i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts, i18n/avogadro_fi.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sk.ts, i18n/avogadro_sv.ts,
  i18n/avogadro_tr.ts, i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts,
  i18n/avogadro_zh_TW.ts, i18n/libavogadro_ar.ts, i18n/libavogadro_bg.ts,
  i18n/libavogadro_ca.ts, i18n/libavogadro_cs.ts, i18n/libavogadro_de.ts,
  i18n/libavogadro_en_CA.ts, i18n/libavogadro_en_GB.ts, i18n/libavogadro_es.ts,
  i18n/libavogadro_fi.ts, i18n/libavogadro_fr.ts, i18n/libavogadro_it.ts,
  i18n/libavogadro_ja.ts, i18n/libavogadro_ko.ts, i18n/libavogadro_nb.ts,
  i18n/libavogadro_nl.ts, i18n/libavogadro_pl.ts, i18n/libavogadro_pt.ts,
  i18n/libavogadro_pt_BR.ts, i18n/libavogadro_ru.ts, i18n/libavogadro_sk.ts,
  i18n/libavogadro_sv.ts, i18n/libavogadro_tr.ts, i18n/libavogadro_uk.ts,
  i18n/libavogadro_zh_CN.ts, i18n/libavogadro_zh_TW.ts: Last pile of up-to-date
  translations.

2009-06-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/AvoCPack.cmake: include Avogadro.py in CPack

2009-06-02  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp: Added engine.h include that was snuck in
  before using primitiveitemmodel.h.

  * avogadro/src/engineprimitiveswidget.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/primitivetreeview.cpp: Fixed primitiveitemmodel.h includes for
  new location.

  * avogadro/src/primitiveitemmodel.cpp, avogadro/src/primitiveitemmodel.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/primitiveitemmodel.h: Moved primitiveitemmodel - only used by
  the engine widget.

2009-06-01  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/molecularpropdialog.ui,
  .../src/extensions/molecularpropextension.cpp,
  .../src/extensions/molecularpropextension.h,
  libavogadro/src/extensions/propextension.cpp: New molecular property window
  with formula, number of atoms, etc.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Add parameter to
  test if dipole moments are estimated or known accurately.

  * avogadro/src/mainwindow.cpp: Ignore debug comments on close events.

2009-06-01  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt: Only enable extra GCC warnings for non-release builds.
  Suppress debug output for release builds.

  * libavogadro/tests/moleculefiletest.cpp: Rename function - assumed the last
  function should have been appendMolecule().

  * libavogadro/src/tools/navigatetool.cpp: Removed debug statement from eye
  candy setting in navigate tool.

2009-06-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/tests/moleculefiletest.cpp: MoleculeFileTest: replace unsigned
  int/unsigned long with std::vector<...>::size_type

  * avogadro/src/mainwindow.cpp: MainWindow: close ofstream before attempting
  to rename the file

2009-06-01  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Use a double-rename procedure for saving
  (i.e., create ".old" and ".new")

2009-06-01  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp: Fix bug 2799186 - background color set to
  black on cancel.  Added a check to see if the QColor returned is valid, so if
  the user cancels the background color change it is not changed to black.

2009-06-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/CMakeLists.txt: Add an option to not install python
  module (INSTALL_PYTHON_MODULE)

2009-06-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povrayextension.cpp: Fix for bug 2786154 - check
  if output files can be written.  Added checks for whether the pov and png
  files can be written, pops up a warning if not. Fixes bug 2786154.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added a default
  file name for new molecules.  Added a default file name for new molecules,
  this should make handling of molecules without a name easier for plugins.
  Fixes part of bug 2786154 for example.

  * libavogadro/tests/moleculefiletest.cpp: This is an unsigned long here,
  would not compile. A better fix may to to use the vector site type.

  * CMakeLists.txt: Made the extra GCC warnings optional - EXTRA_WARNINGS.  On
  Linux with GCC 4.3.3 and Qt 4.5.1 these extra GCC flags were generating
  thousands of warnings. Introduced an option to turn them on if needed,
  otherwise the debug builds were less useful as there were too many warnings
  generated from included library headers.

  * avogadro/src/updatecheck.cpp: Removed unnecessary return from void
  function.

2009-06-01  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/periodictablescene_p.cpp,
  libavogadro/src/primitiveitemmodel.cpp: Add more krazy ignore comments

2009-06-01  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/settingsdialog.ui, i18n/avogadro.pot, i18n/libavogadro.pot,
  scripts/extract-application-messages.sh, scripts/extract-library-messages.sh:
  Update POT to give contexts to messages.

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_bg.ts,
  i18n/avogadro_ca.ts, i18n/avogadro_cs.ts, i18n/avogadro_de.ts,
  i18n/avogadro_en_CA.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fi.ts, i18n/avogadro_fr.ts, i18n/avogadro_id.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sk.ts, i18n/avogadro_sv.ts, i18n/avogadro_tr.ts,
  i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts,
  i18n/libavogadro.pot, i18n/libavogadro_ar.ts, i18n/libavogadro_bg.ts,
  i18n/libavogadro_ca.ts, i18n/libavogadro_cs.ts, i18n/libavogadro_de.ts,
  i18n/libavogadro_en_CA.ts, i18n/libavogadro_en_GB.ts, i18n/libavogadro_es.ts,
  i18n/libavogadro_fi.ts, i18n/libavogadro_fr.ts, i18n/libavogadro_id.ts,
  i18n/libavogadro_it.ts, i18n/libavogadro_ja.ts, i18n/libavogadro_ko.ts,
  i18n/libavogadro_nb.ts, i18n/libavogadro_nl.ts, i18n/libavogadro_pl.ts,
  i18n/libavogadro_pt.ts, i18n/libavogadro_pt_BR.ts, i18n/libavogadro_ru.ts,
  i18n/libavogadro_sk.ts, i18n/libavogadro_sv.ts, i18n/libavogadro_tr.ts,
  i18n/libavogadro_uk.ts, i18n/libavogadro_zh_CN.ts, i18n/libavogadro_zh_TW.ts,
  scripts/extract-application-messages.sh, scripts/extract-library-messages.sh:
  Updated translations for 0.9.5 from Launchpad.

  * libavogadro/src/openbabelwrapper.cpp: Fix strings for translation.

2009-05-31  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationextension.cpp: Fix bug PR#2781989 --
  changing the scale while the animation occurs works now.

2009-06-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp, libavogadro/tests/CMakeLists.txt,
  libavogadro/tests/moleculefiletest.cpp: Update OpenbabelWrapper &
  MoleculeFile + unit tests

2009-05-31  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/animation.cpp: Fixed "hiccup" with vibrations -- default
  timeline in Qt is nonlinear. (Bad for chemical animations!)

  * avogadro/src/mainwindow.cpp, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/colors/customcolor.cpp,
  libavogadro/src/colors/customcolor.h,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/simplewireengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/povpainter.cpp, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/python/color.cpp, libavogadro/src/tools/eyecandy.cpp: Revised
  syntax for Color class. No shadowed methods anymore.

  * avogadro/src/aboutdialog.cpp, avogadro/src/application.cpp,
  avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/updatecheck.cpp, .../src/extensions/insertfragmentdialog.cpp,
  .../src/extensions/insertpeptideextension.cpp,
  libavogadro/src/extensions/pythonterminal.cpp, libavogadro/src/global.cpp,
  libavogadro/src/global.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/primitiveitemmodel.cpp: Krazy fixes (and comments for krazy
  ignore).

2009-05-30  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/updatedialog.cpp: Few small clean
  ups, added the option to disable the update checker at compile time.

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/updatecheck.cpp,
  avogadro/src/updatecheck.h, avogadro/src/updatedialog.cpp,
  avogadro/src/updatedialog.h: Added a class to check for an updated Avogadro
  version.  This is the first pass at a tool to check for an updated version of
  Avogadro. Feedback would be appreciated. It checks a file on the web server,
  parses it and displays the release notes if the version is greater than that
  installed. It will only prompt once for any given version update, and should
  provide a link to our updates page.

2009-05-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/src/moleculefile.h,
  libavogadro/src/openbabelwrapper.cpp, libavogadro/src/openbabelwrapper.h,
  libavogadro/src/python/fileio.cpp,
  libavogadro/src/python/openbabelwrapper.cpp: Add support for error messages
  to OpenbabelWrapper and MoleculeFile

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/tools/autoopttool.cpp: Extract forces from OBMol to set
  Atom::forceVector() (AutoOptTool & ForceFieldExtension)

2009-05-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/python/template.py, python/extensiontemplate.py,
  python/proteinextension.py, python/standalone.py, python/tooltemplate.py:
  Move the python tool template to an example folder. (Fixes #2795303, bug
  about "('paint(', <Avogadro.GLWidget object at 0x10adf30>, ')')")

  * libavogadro/src/protein.cpp, libavogadro/src/protein.h: Update
  documentation & remove some obsolete methods (were used by old cartoon
  engine)

  * libavogadro/src/residue.cpp: Trim the (PDB) atom ID returned by
  Residue::atomId(unsigned long) (trimmed in set function)

  * libavogadro/src/python/Avogadro.py, libavogadro/src/python/CMakeLists.txt,
  libavogadro/src/python/main.cpp: Rename Avogadro.[so/pyd] to
  _Avogadro.[so/pyd] and create Avogadro.py to ensure standalone scripts can
  load OB formats.

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/neighborlist.cpp, libavogadro/src/neighborlist.h,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h,
  libavogadro/src/python/neighborlist.cpp,
  libavogadro/tests/neighborlisttest.cpp: NeighborList: Add constructor taking
  QList<Atom*> HBondEngine: respect engine's primitives (draw H-bonds only to
  atoms in the engine's primitive list) Protein: Add some documentation
  OrbitalExtension: update for NeighborList changes

2009-05-29  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/pluginmanager.cpp: Don't sort extensions yet.

2009-05-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/boxcontrol.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/line.cpp, libavogadro/src/line.h,
  libavogadro/src/point.cpp, libavogadro/src/point.h,
  libavogadro/src/python/glwidget.cpp: Remove BoxControl, Point & Line classes

2009-05-28  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/colors/customcolor.cpp: Save
  and read settings for colors.

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/pluginmanager.cpp: Add usefulness for extensions. Sort tools,
  extensions and colors before returning.

2009-05-28  Marcus D. Hanwell <marcus@cryos.org>

  * .../src/extensions/insertpeptideextension.cpp: Changed from AddAtom to
  InsertAtom - seems to fix weird Windows name mangling bug with the peptide
  builder.

  * .../src/extensions/insertpeptideextension.cpp: Ensure that the peptide
  builder fails gracefully when it cannot locate files.

2009-05-28  Geoff Hutchison <babel@geoffhutchison.net>

  * .../src/extensions/insertpeptideextension.cpp: Argh. Mac case-insensitive
  file system saved me from typo. "L" and "D" designations must be lower case!

  * .../src/extensions/insertpeptideextension.cpp: More defensive tests.

  * .../src/extensions/insertpeptideextension.cpp: Add some defensive tests to
  track down Linux segfaults.

  * libavogadro/src/molecule.cpp: When creating new OBMol, copy residues.

  * .../src/extensions/insertpeptideextension.cpp: Cleanup AddTerminus -- use a
  safety check and add a new bond.

2009-05-28  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt: Improvements to the build system on Windows - better
  compiler flags.  We should not globally set /MD as this prevents debug builds
  being made. We were also throwing away the default flags for release and
  debug builds. Adding /MP globally on MSVC as this speeds up builds.

2009-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/elementdetail_p.cpp, libavogadro/src/elementitem_p.cpp:
  Fixed include, got rid of etab instantiations.

2009-05-27  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/chargecolor.h, libavogadro/src/colors/customcolor.cpp,
  libavogadro/src/colors/customcolor.h, libavogadro/src/colors/distancecolor.h,
  libavogadro/src/colors/elementcolor.h, libavogadro/src/colors/indexcolor.h,
  libavogadro/src/colors/residuecolor.h: Added custom color plugin. This should
  be statically linked.

2009-05-27  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added
  scaleLimits(PlotObject*) slot to plot widget. Automatically sets the limits
  of the plot based on the extremes of the passed PlotObject reference. The
  PlotObject can be omitted to look at all PlotObjects added to the widget.

2009-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/highlighter.h,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h,
  libavogadro/src/extensions/pythonterminalwidget.ui: Improve python terminal,
  now a single widget like a real terminal...

2009-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/trajvideomaker.h: Few minor clean ups, looking for
  the source of Windows linking issues.

2009-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/cartoonmeshgenerator.cpp,
  libavogadro/src/cartoonmeshgenerator.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonmeshgenerator.cpp,
  libavogadro/src/engines/cartoonmeshgenerator.h: Move CartoonMeshGenerator
  ouside libavogadro's API

2009-05-27  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/insertpeptidedialog.ui,
  .../src/extensions/insertpeptideextension.cpp,
  .../src/extensions/insertpeptideextension.h: Add chain numbering, plus
  terminal modifications.

  * builder/amino/l-arg.zmat, builder/amino/l-ser.zmat: Fix bonding in ARG and
  SER residues.

2009-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/cartoonmeshbench.cpp:
  Remove CartoonMeshBench (obsolete)

2009-05-27  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Added element symbol + atom
  number for PR#2781947.

  * avogadro/src/mainwindow.cpp: Add shortcuts to Tool Settings and Display
  Settings buttons.

2009-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt: Added the /MP to parallelise the build at the object file
  level. Only use /MD for RELEASE - should make debug builds possible.

  * libavogadro/src/elementdetail_p.cpp, libavogadro/src/elementdetail_p.h,
  libavogadro/src/elementitem_p.cpp, libavogadro/src/elementitem_p.h,
  libavogadro/src/periodictablescene_p.cpp,
  libavogadro/src/periodictablescene_p.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h:
  Separated private PeriodicTableView classes out into their own files.  Only
  the periodic table view class is exported, and so the rest did not belong in
  a public header. There are some issues with the global etab that should be
  looked at, but they are in private classes.

2009-05-27  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/insertpeptidedialog.ui: New layout for peptide
  builder

2009-05-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter_p.cpp,
  libavogadro/src/glpainter_p.h, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h, libavogadro/src/python/painter.cpp: First pass at
  cleaning up the Painter API ready for 1.0.  I think most of the changes made
  are quite conservative. Made the API a little more consistent, removed the
  QObject as I do not see any need for this to be a QObject. Added a couple of
  placeholder functions.

2009-05-26  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt: Fix the Mac installation -- create lproj
  translation directories based on .ts files.

2009-05-26  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/animation.h: Updated documentation.

  * .../src/extensions/insertfragmentextension.cpp: Fix "Insert SMILES..."
  command name

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/src/openbabelwrapper.cpp: Track
  down all remainin filenames needing QFile::encodeName.

  * avogadro/src/mainwindow.cpp, libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_nmr.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/periodictableview.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp: More localized numbers. This
  should be all of them.

2009-05-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/propmodel.cpp: Minor fix - scoping inside cases
  for local variable.

2009-05-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/tools/bondcentrictool.cpp: Better localizations of numbers.

2009-05-25  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectratabir.ui,
  libavogadro/src/extensions/spectratabnmr.ui,
  libavogadro/src/extensions/spectratype.cpp,
  libavogadro/src/extensions/spectratype.h,
  libavogadro/src/extensions/spectratype_ir.cpp,
  libavogadro/src/extensions/spectratype_ir.h,
  libavogadro/src/extensions/spectratype_nmr.cpp,
  libavogadro/src/extensions/spectratype_nmr.h: Separated out the different
  spectra types to make it easier to add more and reduce clutter.

2009-05-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/clickmeasuretool.cpp: Fix PR#2781959. Use 3 decimal
  accuracy for distance display.

  * libavogadro/src/extensions/vibrationdialog.cpp: Fix PR# 2781590 and related
  bugs for good.

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationextension.cpp: Fix PR#2728372. Sync force
  engine and display force vector in dialog.

  * libavogadro/src/extensions/vibrationdialog.ui: Fix bug PR#2728368. Replace
  cancel/ok buttons with "close"

  * libavogadro/src/extensions/vibrationdialog.cpp: Fix bug PR#2734399. Sort
  vibrations by frequencies.

  * libavogadro/src/extensions/propextension.cpp: Add sorting to the property
  tables via QSortFilterProxyModel

  * .../src/extensions/insertpeptideextension.cpp: Minor cleanups.

  * libavogadro/src/molecule.cpp: Add support for copying residue information.

  * CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/insertpeptidedialog.ui,
  .../src/extensions/insertpeptideextension.cpp,
  .../src/extensions/insertpeptideextension.h: Peptide builder, including
  fragments. Still needs end-group modification.

  * .../src/extensions/insertfragmentdialog.cpp: Fix install directory for
  fragments on Mac.

  * libavogadro/src/extensions/directorytreemodel.cpp: Add table header to
  translatable strings.

2009-05-24  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Moved spectra tabs to separate
  ui files.

  * libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added
  PlotWidget::setPointFollowMouse(bool), which places a small blue dot on the
  point nearest the cursor.

  * libavogadro/src/plotwidget.h: Pass a const ref for the QList.

  * libavogadro/src/plotobject.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Added some slots for selecting points  The
  following slots will draw or clear (or both!) yellow circles at indicated
  points:  selectPoint(PlotPoint*) Draw circle at indicated PlotPoint
  selectPoints(QList<PlotPoint*>) Draw a circle at each PlotPoint in the list 
  clearAndSelectPoints(PlotPoint*) Same as selectPoint(PlotPoint*), but clears
  the selection first. clearAndSelectPoint(QList<PlotPoint*>) Same as
  selectPoints(QList<PlotPoint*>), but clears the selection first. 
  clearSelection() Clears all selected points.

2009-05-24  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/cartoonengine.cpp: Don;t generate meshes unless
  residues are present.

2009-05-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Fix some compiler warnings.

  * libavogadro/src/plotwidget.h: Added a useful tidbit about mouseovers and
  mousetracking to API

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added a
  mouseover signal with the x, y coords in data units.

2009-05-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/cartoonmeshgenerator.cpp,
  libavogadro/src/cartoonmeshgenerator.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/cartoonsettingswidget.ui, libavogadro/src/mesh.h,
  libavogadro/tests/CMakeLists.txt, libavogadro/tests/cartoonmeshbench.cpp:
  CartoonMeshGenerator: put the mesh generating code in a thread, clean it up
  and fix a some performance problems. For some reason I was calling
  Mesh::setVertices (and setNormals/setColors) after generating mesh parts for
  each residue inside one of the inner loop functions. The mesh is now
  generated in a few msec.  CartoonEngine: Add settings dialog with shape &
  color settings.  Mesh: Add numVertices() & numNormals(), calling
  mesh->vertices.size() always copies the whole list right?  CartoonMeshBench:
  Add benchmark for generating protein meshes. (not really needed anymore
  though)

2009-05-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added three
  new signals to PlotWidget to retrieve points from a left click. 
  pointClicked(double x, double y)	x and y coordinates of click in data units.
  pointClicked(QList<PlotPoint*> pl)	List of PlotPoints within 4 pixels of
  click. pointClicked(PlotPoint*)		PlotPoint nearest click. NULL if no points
  nearby.

2009-05-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/directorytreemodel.cpp,
  libavogadro/src/extensions/directorytreemodel.h,
  libavogadro/src/extensions/insertcommand.cpp,
  libavogadro/src/extensions/insertcommand.h,
  .../src/extensions/insertfragmentdialog.cpp,
  libavogadro/src/extensions/insertfragmentdialog.h,
  libavogadro/src/extensions/insertfragmentdialog.ui,
  .../src/extensions/insertfragmentextension.cpp,
  .../src/extensions/insertfragmentextension.h,
  libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/insertfragmentdialog.ui: Move insert fragment into an
  extension (out of the draw tool).

2009-05-23  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mac/CompleteBundle.cmake.in: Add handling for Qt plugins
  including linking to the embedded Qt.  I am not sure we really want to
  include all the plugins, as this means that we basically include the whole of
  the Qt framework too. This makes the install size large for parts of Qt we
  are not using. For now I added handling for all plugins - I think we only use
  the image plugins right now. We can just more selectively install the plugins
  and this script will continue to work as plugins are removed from the bundle.

2009-05-22  David Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp: Whitespace/indentation cleanup

  * avogadro/src/mainwindow.cpp: Proposed fix to keep multi-molecule checks --
  untested, I have no multi-molecule files here.

2009-05-22  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/propextension.cpp: Add selection for atoms and
  torsions. Fixes PR#2781961.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/extension.h: Add new signal for extensions with "delayed"
  undo commands (e.g., show a window) Should work well for property extension
  and others.

  * libavogadro/src/engines/cartoonengine.cpp: Don't create meshes for empty
  molecules. (Actually, we need a way to create a trial mesh, e.g. for a
  non-protein)

2009-05-22  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Small clean up of
  old classes no longer used/included.

2009-05-22  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/projecttreeeditor.qrc: Update QRC for project tree editor.

  * avogadro/src/back.png, avogadro/src/down.png, avogadro/src/forward.png,
  avogadro/src/icons/back.png, avogadro/src/icons/down.png,
  avogadro/src/icons/forward.png, avogadro/src/icons/minus.png,
  avogadro/src/icons/plus.png, avogadro/src/icons/up.png,
  avogadro/src/minus.png, avogadro/src/plus.png, avogadro/src/up.png: Moved
  icons for project tree editor to be internally consistent.

  * avogadro/src/flowlayout.cpp, avogadro/src/flowlayout.h,
  avogadro/src/icontabwidget.cpp, avogadro/src/icontabwidget.h,
  avogadro/src/mainwindow.cpp: Removed flow layout in icon widget.

  * CMakeLists.txt, avogadro/src/mac/CompleteBundle.cmake.in,
  avogadro/src/mac/CreateBundle.sh.in: Attemping to get Qt plugins working for
  the Mac relocatable package.

  * CMakeLists.txt: Make sure to install plugins in correct directory.

  * i18n/avogadro.pot, i18n/libavogadro.pot: Current PO templates for
  Launchpad.

  * libavogadro/src/engines/cartoonengine.cpp: Minor Eigen porting for zero
  vectors.

2009-05-22  David Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp: Use OBConversion::ReadFile instead of Read(). 
  Certain formats such as VASP use multiple output files. OB needs to be able
  to know the absolute path to the files in order to read them all, and streams
  just don't cut it.

2009-05-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/CMakeLists.txt: Fixed header installation directory.

2009-05-20  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/extension.h,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  .../src/extensions/networkfetchextension.cpp: Added a new parameter to the
  Extension moleculeChanged signal.  This is still experimental, especially the
  naming of the enums. This allows the extension to specify how the new and old
  Molecule objects should be treated. So you can request a new window if the
  old molecule has been modified, prevent the old molecule from being deleted
  etc.

  * libavogadro/src/CMakeLists.txt, libavogadro/src/glhit.cpp,
  libavogadro/src/glhit.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Moved GLHit to its own header/implementation.

2009-05-20  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/engines/cartoonengine.cpp: A few more minor Eigen fixes.

  * CMakeLists.txt: Copy Qt plugins and translations -- at least on Mac.

  * builder/amino/d-ala.zmat, builder/amino/d-arg.zmat,
  builder/amino/d-asn.zmat, builder/amino/d-asp.zmat, builder/amino/d-cys.zmat,
  builder/amino/d-gln.zmat, builder/amino/d-glu.zmat, builder/amino/d-his.zmat,
  builder/amino/d-ile.zmat, builder/amino/d-leu.zmat, builder/amino/d-lys.zmat,
  builder/amino/d-met.zmat, builder/amino/d-phe.zmat, builder/amino/d-pro.zmat,
  builder/amino/d-ser.zmat, builder/amino/d-thr.zmat, builder/amino/d-trp.zmat,
  builder/amino/d-tyr.zmat, builder/amino/d-val.zmat, builder/amino/gly.zmat,
  builder/amino/l-ala.zmat, builder/amino/l-arg.zmat, builder/amino/l-asn.zmat,
  builder/amino/l-asp.zmat, builder/amino/l-cys.zmat, builder/amino/l-gln.zmat,
  builder/amino/l-glu.zmat, builder/amino/l-his.zmat, builder/amino/l-ile.zmat,
  builder/amino/l-leu.zmat, builder/amino/l-lys.zmat, builder/amino/l-met.zmat,
  builder/amino/l-phe.zmat, builder/amino/l-pro.zmat, builder/amino/l-pyl.zmat,
  builder/amino/l-sec.zmat, builder/amino/l-ser.zmat, builder/amino/l-thr.zmat,
  builder/amino/l-trp.zmat, builder/amino/l-tyr.zmat, builder/amino/l-val.zmat:
  Rename builder files to lowercase.

  * builder/amino/D-Ala.zmat, builder/amino/D-Arg.zmat,
  builder/amino/D-Asn.zmat, builder/amino/D-Asp.zmat, builder/amino/D-Cys.zmat,
  builder/amino/D-Gln.zmat, builder/amino/D-Glu.zmat, builder/amino/D-His.zmat,
  builder/amino/D-Ile.zmat, builder/amino/D-Leu.zmat, builder/amino/D-Lys.zmat,
  builder/amino/D-Met.zmat, builder/amino/D-Phe.zmat, builder/amino/D-Pro.zmat,
  builder/amino/D-Ser.zmat, builder/amino/D-Thr.zmat, builder/amino/D-Trp.zmat,
  builder/amino/D-Tyr.zmat, builder/amino/D-Val.zmat, builder/amino/Gly.zmat,
  builder/amino/L-Ala.zmat, builder/amino/L-Arg.zmat, builder/amino/L-Asn.zmat,
  builder/amino/L-Asp.zmat, builder/amino/L-Cys.zmat, builder/amino/L-Gln.zmat,
  builder/amino/L-Glu.zmat, builder/amino/L-His.zmat, builder/amino/L-Ile.zmat,
  builder/amino/L-Leu.zmat, builder/amino/L-Lys.zmat, builder/amino/L-Met.zmat,
  builder/amino/L-Phe.zmat, builder/amino/L-Pro.zmat, builder/amino/L-Pyl.zmat,
  builder/amino/L-Sec.zmat, builder/amino/L-Ser.zmat, builder/amino/L-Thr.zmat,
  builder/amino/L-Trp.zmat, builder/amino/L-Tyr.zmat, builder/amino/L-Val.zmat:
  Renaming builder files to lowercase.

2009-05-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/navigatetool.cpp: Removed debug statement that is not
  needed.

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/navigatesettingswidget.ui,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  New navigate settings widget - first phase - make Noel happier ;-)  Added a
  new settings widget to allow control of whether the eye candy (visual cues)
  are displayed. This is a long requested feature from a few users and closes
  feature request 2349900.

  * libavogadro/src/engines/bsdyengine.cpp: Tidied up the signal/slot
  connections.

2009-05-20  David Lonie <loniedavid@gmail.com>

  * avogadro/src/mainwindow.cpp: Don't show recent files that aren't on the
  filesystem anymore.

2009-05-20  Geoff Hutchison <geoff@geoffhutchison.net>

  * builder/amino/D-Ala.zmat, builder/amino/D-Arg.zmat,
  builder/amino/D-Asn.zmat, builder/amino/D-Asp.zmat, builder/amino/D-Cys.zmat,
  builder/amino/D-Gln.zmat, builder/amino/D-Glu.zmat, builder/amino/D-His.zmat,
  builder/amino/D-Ile.zmat, builder/amino/D-Leu.zmat, builder/amino/D-Lys.zmat,
  builder/amino/D-Met.zmat, builder/amino/D-Phe.zmat, builder/amino/D-Pro.zmat,
  builder/amino/D-Ser.zmat, builder/amino/D-Thr.zmat, builder/amino/D-Trp.zmat,
  builder/amino/D-Tyr.zmat, builder/amino/D-Val.zmat, builder/amino/Gly.zmat,
  builder/amino/L-Ala.zmat, builder/amino/L-Arg.zmat, builder/amino/L-Asn.zmat,
  builder/amino/L-Asp.zmat, builder/amino/L-Cys.zmat, builder/amino/L-Gln.zmat,
  builder/amino/L-Glu.zmat, builder/amino/L-His.zmat, builder/amino/L-Ile.zmat,
  builder/amino/L-Leu.zmat, builder/amino/L-Lys.zmat, builder/amino/L-Met.zmat,
  builder/amino/L-Phe.zmat, builder/amino/L-Pro.zmat, builder/amino/L-Pyl.zmat,
  builder/amino/L-Sec.zmat, builder/amino/L-Ser.zmat, builder/amino/L-Thr.zmat,
  builder/amino/L-Trp.zmat, builder/amino/L-Tyr.zmat, builder/amino/L-Val.zmat:
  Amino acid builder files.

2009-05-19  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/cartoonengine.cpp: Change renderQuick() to just
  render the mesh. Solves crash on common MacBooks. (I hate driver issues.)

  * libavogadro/src/engines/cartoonengine.cpp: Small fixes and some porting to
  Eigen.

2009-05-19  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/meshgenerator.cpp: Fixed bug introduced by krazy fixing -
  broken isosurfaces.  Commit 4678b8d53bab0e5104515276da0332fdb619dc74
  introduced a bug where isosurfaces were broken. Minor fix to bracket the
  difference between val1 and val2. We need more unit tests to catch problems
  like this - I will make it a priority!

2009-05-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/cartoonengine.cpp: CartoonEngine: Smooth color
  transitions

2009-05-19  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/zmatrixtool.h: Fix
  some compile warnings.

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/modeltest.cpp,
  libavogadro/tests/modeltest.h, libavogadro/tests/primitivemodeltest.cpp: Add
  test for QAbstractItemModels. Currently doesn't link.

2009-05-19  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/zmatrixtool.h: Added comma to the tool macro -
  compiles correctly now.

  * libavogadro/src/engines/cartoonengine.cpp: Set the transparency of the
  ribbon correctly. Used by the POV-Painter.

2009-05-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonengine.h, libavogadro/src/protein.cpp,
  libavogadro/src/protein.h: Improve protein rendering (ported cartoon-like
  mesh generation from Zodiac www.zeden.org).

2009-05-19  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, i18n/avogadro.pot, i18n/libavogadro.pot,
  libavogadro/src/CMakeLists.txt, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/global.cpp, libavogadro/src/openbabelwrapper.cpp,
  scripts/create-translations.sh, scripts/extract-application-messages.sh,
  scripts/extract-library-messages.sh: More translation fixes.

  * libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/propmodel.cpp: Krazy fixes.

  * i18n/avogadro_ar.ts, i18n/avogadro_bg.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_CA.ts,
  i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts, i18n/avogadro_fi.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sk.ts, i18n/avogadro_sv.ts,
  i18n/avogadro_tr.ts, i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts,
  i18n/avogadro_zh_TW.ts, i18n/libavogadro.pot, i18n/libavogadro_ar.ts,
  i18n/libavogadro_bg.ts, i18n/libavogadro_ca.ts, i18n/libavogadro_cs.ts,
  i18n/libavogadro_de.ts, i18n/libavogadro_en_CA.ts, i18n/libavogadro_en_GB.ts,
  i18n/libavogadro_es.ts, i18n/libavogadro_fi.ts, i18n/libavogadro_fr.ts,
  i18n/libavogadro_it.ts, i18n/libavogadro_ja.ts, i18n/libavogadro_ko.ts,
  i18n/libavogadro_nb.ts, i18n/libavogadro_nl.ts, i18n/libavogadro_pl.ts,
  i18n/libavogadro_pt.ts, i18n/libavogadro_pt_BR.ts, i18n/libavogadro_ru.ts,
  i18n/libavogadro_sk.ts, i18n/libavogadro_sv.ts, i18n/libavogadro_tr.ts,
  i18n/libavogadro_uk.ts, i18n/libavogadro_zh_CN.ts, i18n/libavogadro_zh_TW.ts,
  scripts/extract-application-messages.sh, scripts/extract-library-messages.sh,
  scripts/extract-messages.sh: Split translations into libavogadro and avogadro
  templates.

  * libavogadro/src/animation.h, libavogadro/src/atom.h,
  libavogadro/src/bond.h, libavogadro/src/boxcontrol.h,
  libavogadro/src/camera.h, libavogadro/src/color.h,
  libavogadro/src/colorbutton.h, libavogadro/src/cube.h,
  libavogadro/src/global.h: Update some copyright lines based on automated
  copyright.py script from Carsten.

2009-05-19  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/savedialog.cpp: Added the QPointer includewq.

2009-05-19  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  .../src/extensions/networkfetchextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/pythontool_p.cpp, libavogadro/src/pythontool_p.h,
  libavogadro/src/tool.h, libavogadro/src/tools/aligntool.h,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h,
  libavogadro/src/tools/zmatrixtool.h: Translation fixes. Use QString::arg()
  more often, and add new Tool::settingsTitle() to improve context.

  * avogadro/src/main.cpp: Remove some debugging messages.

  * avogadro/src/main.cpp: When making an App bundle, make sure to reset the
  plugin search path

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/molpro.cpp,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/wiitrackextension.cpp: Fix additional
  QString/QChar krazy warnings.

  * libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Add support for running
  local g03 jobs.

2009-05-19  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/plotobject.cpp, libavogadro/src/plotwidget.cpp,
  libavogadro/src/tools/zmatrixtool.cpp: More krazy & compile warnings fixes.

2009-05-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/gl2ps/TODO, avogadro/gl2ps/gl2ps.c, avogadro/gl2ps/gl2ps.h,
  avogadro/gl2ps/gl2ps.pdf, avogadro/gl2ps/gl2psTest.c,
  avogadro/gl2ps/gl2psTestSimple.c: Import of GL2PS 1.3.3 -- latest stable
  release.

  * avogadro/src/aboutdialog.cpp, avogadro/src/addenginedialog.cpp,
  avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/pluginsettings.h, avogadro/src/projectdelegates/labeldelegate.h,
  avogadro/src/projectdelegates/selectiondelegate.h,
  avogadro/src/projecttreeitem.h, avogadro/src/savedialog.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/moleculefile.cpp, libavogadro/src/openbabelwrapper.cpp,
  libavogadro/src/plotwidget.cpp, libavogadro/src/protein.cpp,
  libavogadro/src/pythonengine_p.h, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonextension_p.h, libavogadro/src/pythontool_p.h,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/zmatrixdialog.h: A
  whole pile of Krazy fixes. Still a bunch of GCC warnings to clean up too.

2009-05-18  Marcus D. Hanwell <marcus@cryos.org>

  * scripts/runkrazy.rb: Change to text export as html export supoprt has been
  removed.

  * libavogadro/src/molecule.cpp: Fixed benchmark failure - double frees from
  clearConformers() when only one conformer.

  * libavogadro/src/extensions/propmodel.cpp: Fixes for Windows build - use the
  more portable numeric_limits functions to test for infinity.

  * libavogadro/src/tools/skeletontree.cpp,
  libavogadro/src/tools/skeletontree.h: Use const reference function arguments,
  rather than passing by value.

  * libavogadro/src/global.h: Fix the Windows build - the avogadro library
  target name changed.

2009-05-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * AUTHORS: Sort in alphabetical order, add Michael.

2009-05-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Rename output option -- I prefer Michael's
  suggestion.

  * avogadro/src/mainwindow.cpp: Fix PR#2781992. Add *.out and *.log to
  File->Open dialog options.

  * AUTHORS: Added David's e-mail to AUTHORS list.

2009-05-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/pluginsettings.cpp: PluginSettings: remove the restart
  warning. All plugin types are now reloaded without restart. The dockwidgets
  do tend to change places, probably need to read more QSettings?

  * avogadro/src/engineitemmodel.cpp, avogadro/src/engineitemmodel.h,
  avogadro/src/enginelistview.cpp, avogadro/src/enginelistview.h,
  avogadro/src/mainwindow.cpp: Avogadro: connect the
  PluginManager::reloadPlugins() signal to the new GLWidget::reloadEngines()
  method and properly repopulate the EngineListView (EngineItemModel)

  * libavogadro/src/glwidget.h: forgot glwidget.h

  * libavogadro/src/glwidget.cpp: Add GLWidget::reloadEngines()

2009-05-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Check visibility
  of toolbars before fullscreen/normal mode. Added shortcut of escape key to
  Full Screen / normal mode.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Make sure tool
  settings and engine settings buttons are synced with visibility of the docks.

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.h: Move most "properties" to the "View"
  menu -- hopefully it will be more intuitive to find them there.

  * libavogadro/src/glwidget.cpp: Fix compiler warning.

2009-05-17  Carsten Niehaus <cniehaus@kde.org>

  * AUTHORS: I prefere this address for OSS work

2009-05-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: More GUI changes. New toolbar adds QPushButtons
  to hide/show tool and display settings.

2009-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp: Added guards around the Python code - only
  include and use if Python supoprt enabled.

2009-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/fileio.cpp: forgot python/fileio.cpp (is
  openbabelwrapper now though)

  * libavogadro/src/python/pluginmanager.cpp: Add default method arguments for
  PluginManager's python wrapper.

  * libavogadro/src/toolgroup.cpp: Set the active tool in
  ToolGroup::append(Tool *tool).

  * libavogadro/src/glwidget.cpp, libavogadro/src/pythonengine_p.cpp,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythonthread_p.h,
  libavogadro/src/pythontool_p.cpp: Fix python Global Interpreter Lock (GIL)
  usage. (note: when running standalone python scripts, the Qt event loop seems
  to run in another thread which means we have to obtain the GIL. The
  pythonthread_p.h header contains a simple class which calls
  PyGILState_Ensure() in the constructor and PyStateGIL_Release in the
  destructor.

  * libavogadro/src/glwidget.cpp: GLWidget: remove some unneeded checks for
  d->molecule

2009-05-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.ui: Move the toolbar to the side and make it 16x16
  icons by default.

  * libavogadro/src/tools/drawtool.cpp: Fix bug with typing two-character
  elements.

2009-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pythonengine_p.cpp, libavogadro/src/pythonengine_p.h,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythonextension_p.h,
  libavogadro/src/pythontool_p.cpp, libavogadro/src/pythontool_p.h: Remove d
  pointer from private classes (PythonTool, PythonExtension, PythonEngine).

2009-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/CMakeLists.txt: Use set rather than unset - maintain
  compatibility with CMake 2.6.2.

2009-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/std_vector.cpp, libavogadro/src/pythonengine_p.cpp,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythoninterpreter.cpp,
  libavogadro/src/pythontool_p.cpp: Some changes to the way python is
  initialized.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Add
  Molecule::conformers() & fix for Molecule::clearConformers (set m_atomPos to
  m_atomConformers[0] after deleting all other conformers)

2009-05-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, avogadro/src/settingsdialog.cpp,
  avogadro/src/settingsdialog.ui, libavogadro/src/toolgroup.cpp: Move tools
  into a standard QToolBar with extra shortcuts (Ctrl+1, Ctrl+2, etc.) Still
  need to add buttons for toggling the toolSettings and displaySettings to the
  toolbar.

2009-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/glwidget.cpp: GLWidget: Add some checking before using
  d->molecule pointer. We don't want to segfault when a standalone python
  script calls show() on a glwidget before setting the molecule.

  * libavogadro/src/CMakeLists.txt, libavogadro/src/moleculefile.cpp,
  libavogadro/src/moleculefile.h, libavogadro/src/openbabelwrapper.cpp,
  libavogadro/src/openbabelwrapper.h: Add support for reading multiple
  molecules to OpenbabelWrapper. A file is read in a separate thread. By
  default, OpenbabelWrapper::readFile(...) waits for the thread to finish. It
  is also possible to connect to the returned object and a signal will be
  emitted when the file is read. (For reading large files +10000 molecules).
  Conformers are automatically detected which allows us to use any OBFormat
  with support for multiple molecules as conformer files.

  * libavogadro/src/animation.cpp, libavogadro/src/animation.h,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationdialog.h,
  libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/python/animation.cpp: Some improvements to the Animation
  class. Remove duplicated code from the animation extension and use Animation
  class. Also added optional "dynamic bonds" for animating QM reactions. TODO:
  add a plot widget to display the energy

2009-05-15  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gaussianinputdialog.ui,
  libavogadro/src/extensions/orbitaldialog.ui: Fix warnings from duplicate
  horizontal spacer names. Addresses PR#2786502.

  * libavogadro/src/extensions/propextension.cpp: Fix compile warning.

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/tools/bondcentrictool.cpp: Fix bugs with editing angle and
  torsion values. Now you can set them as you wish.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/quaternion.cpp, libavogadro/src/tools/quaternion.h,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/tools/skeletontree.h:
  Remove home-grown Quaternions from BondCentric tool and port to
  Eigen/Geometry classes. Much cleaner and appears to give a nice speed boost
  too.

  * libavogadro/src/animation.cpp, libavogadro/src/animation.h: Start on
  animation class documentation.

  * libavogadro/src/colorbutton.cpp,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/engines/surfacesettingswidget.ui: Switch ColorButton to the
  Avogadro namespace.

2009-05-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/engines/surfacesettingswidget.ui: Fixed to bring all the way
  into Avogadro namespace. Ported UI files.

2009-05-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colorbutton.h, libavogadro/src/glwidget.h,
  libavogadro/src/line.h, libavogadro/src/neighborlist.h,
  libavogadro/src/plotaxis.h, libavogadro/src/plotobject.h,
  libavogadro/src/plotpoint.h, libavogadro/src/plotwidget.h,
  libavogadro/src/point.h, libavogadro/src/protein.h,
  libavogadro/src/pythoninterpreter.h, libavogadro/src/zmatrix.h: Documentation
  fixes.

  * CMakeLists.txt, avogadro/src/mac/CompleteBundle.cmake.in,
  avogadro/src/mac/CreateBundle.sh.in, libavogadro/src/CMakeLists.txt: Fixes
  for Cmake builds with Mac .app package.

2009-05-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/openbabelwrapper.cpp, libavogadro/src/openbabelwrapper.h:
  Openbabel wrapper class to open and save files.  This class takes care of
  opening and saving files using Openbabel. It could use some finer grained
  error control possibly, it does take care of preserving UTF8 file names and
  allows for simple calls that can read and write molecule data files.

2009-05-14  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/projecttreemodel.cpp: Add real column headers.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.ui: Remove
  "smooth animations option." Always use smooth animations, unless the system
  is large (> 1000 atoms). We can debate the "large" threshold, but why
  wouldn't we want some eyecandy?

  * avogadro/src/mainwindow.cpp: So much for Mac sheets -- QMessageBox has a
  bug which will close the window entirely.

2009-05-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/CMakeLists.txt, libavogadro/src/colors/chargecolor.cpp,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/indexcolor.cpp,
  libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/simplewireengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/basisset.cpp,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  .../src/extensions/gamessefpmatchdialog.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/liganddialog.cpp,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  .../src/extensions/networkfetchextension.cpp,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/pocketdialog.cpp,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectraextension.cpp,
  libavogadro/src/extensions/supercelldialog.cpp,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/skeletontree.cpp,
  libavogadro/src/tools/zmatrixdialog.cpp,
  libavogadro/src/tools/zmatrixmodel.cpp,
  libavogadro/src/tools/zmatrixtool.cpp: Migrated plugins to use qt4_wrap_cpp
  to generate MOC files.  All plugins, apart from the few static ones, now use
  qt4_wrap_cpp macro to generate moc files, these are then built and linked to
  the plugin rather than directly included. Some extra logic has been
  introduced into the avogadro_plugin function to deal with grc and ui files
  more gracefully too.

2009-05-14  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Add a "slop" to make it easier to pick
  atoms.

2009-05-13  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/molpro.cpp, libavogadro/src/extensions/molpro.h:
  Patch from Michael Banck (PR#2786157) Update for the molpro molecular orbital
  code. Now can parse and display cc-pVDZ basis set based MOs. Cartesian basis
  sets still not implemented (but they are not default in MOLPRO anyway).

  * libavogadro/src/extensions/basisset.cpp: Patch from Michael Bank
  (PR#2786166). The attached patch tries to compensate for F-type orbitals -
  they are still not taken into account when calculating the electron density
  etc., but it tries to properly ignore them now.

  * avogadro/src/mainwindow.cpp: Add fine-grained control of the maybeSave()
  message box.

2009-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt: Only turn on all of the extra warnings for Debug builds. On
  Linux with GCC 4.3.3 this generates thousands of warnings, most of which are
  in library headers.

  * CMakeLists.txt, cmake/modules/AvogadroConfigVersion.cmake.in: Added
  versioning to the AvogadroConfig logic.  Now added versioning to the
  AvogadroConfig logic, see the documentation to find_package for more details.
  In CMakeLists.txt files simply add a line such as find_package(Avogadro 0.9.4
  REQUIRED) to only accept Avogadro versions greater than or equal to 0.9.4. As
  a side effect this will also stop Mac installed AvogadroConfig.cmake files
  from being used, if the config file has no accompanying version file is will
  be rejected when a version is requested.

2009-05-13  Marcus Hanwell <mhanwell@cobalt.chem.pitt.edu>

  * CMakeLists.txt: Install the AvogadroConfig.cmake file into the correct
  location in the bundle.

  * CMakeLists.txt, libavogadro/src/pluginmanager.cpp: Mac changes, default to
  installing in /Applications/Avogadro.app, load plugins relative to location
  only.

  * CMakeLists.txt, avogadro/src/CMakeLists.txt: Added a new option to make
  packages, initially just affects the make install for Mac.

2009-05-13  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/propmodel.cpp: Edit angles and torsions. My math
  is still off, but it does work.

2009-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp: Fixed bug 2791188 - the display lists should
  be invalidated when the molecule changes.

  * avogadro/src/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/tests/CMakeLists.txt: Improved the handling of library
  dependencies for Avogadro.  Renamed the avogadro-lib target to avogadro, this
  allows CMake to automatically assemble the library dependencies for the
  Avogadro library. This fixes link issues seen on the Mac.

  * libavogadro/src/pluginmanager.cpp: Fixed unintended leakage of Mac plugin
  searching on other platforms.

2009-05-13  Marcus Hanwell <mhanwell@cobalt.chem.pitt.edu>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/mac/CompleteBundle.cmake.in,
  avogadro/src/mac/CreateBundle.sh.in, avogadro/src/main.cpp,
  cmake/modules/AvoCPack.cmake, cmake/modules/AvoCPackOptions.cmake.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/pluginmanager.cpp:
  Relocatable Apple Mac package as part of a super project.  This is the first
  merge of work I have been doing to make a relocatable Mac application bundle
  with all libraries included. Currently this works if you run make install, I
  have been using Avogadro0.9.app as that can be installed in parallel to the
  default Avogadro.app directory. Initial testing looks pretty good, but some
  more work is needed to automate the actual building of a package.

2009-05-13  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp: General appearance and code cleanup
  of properties tables.

2009-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/CMakeLists.txt: Fixed for new private class names of python
  classes, simplified logic a little.

2009-05-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h: First pass at editing bond, angle,
  and dihedral properties. Changing bond length now works.

2009-05-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/animation.cpp, libavogadro/src/python/atom.cpp,
  libavogadro/src/python/bond.cpp, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/color.cpp, libavogadro/src/python/cube.cpp,
  libavogadro/src/python/elementtranslator.cpp,
  libavogadro/src/python/engine.cpp, libavogadro/src/python/extension.cpp,
  libavogadro/src/python/fragment.cpp,
  libavogadro/src/python/glgraphicsview.cpp,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/python/main.cpp,
  libavogadro/src/python/mesh.cpp, libavogadro/src/python/meshgenerator.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/navigate.cpp,
  libavogadro/src/python/neighborlist.cpp,
  libavogadro/src/python/periodictableview.cpp,
  libavogadro/src/python/plugin.cpp, libavogadro/src/python/pluginmanager.cpp,
  libavogadro/src/python/primitive.cpp,
  libavogadro/src/python/primitivelist.cpp, libavogadro/src/python/residue.cpp,
  libavogadro/src/python/std_vector.cpp, libavogadro/src/python/tool.cpp,
  libavogadro/src/python/toolgroup.cpp,
  libavogadro/src/python/unittest/mesh.py: Update python bindings for recent
  changes

  * libavogadro/src/molecule.cpp: libavogadro/src/molecule.cpp: Implement
  addCube(id), addMesh(id), addRing(id), addResidue(id)

2009-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/drawcommand.cpp: Missed one of the -1 calls - now
  FALSE_ID.

2009-05-12  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/cube.cpp, libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h, libavogadro/src/meshgenerator.cpp,
  libavogadro/src/navigate.cpp, libavogadro/src/neighborlist.cpp,
  libavogadro/src/neighborlist.h: Fix a variety of minor compiler errors.

  * libavogadro/src/extensions/supercellextension.cpp: Fix fillUnitCell based
  on sync with Open Babel 2.2.x.

2009-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * cmake/modules/AvogadroConfig.cmake.in: The plugin directory already has the
  install prefix - fixed properly now.

  * libavogadro/src/atom.cpp, libavogadro/src/primitive.h,
  libavogadro/src/residue.cpp, libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/drawcommand.cpp: Use templated C++ function to find max
  unsigned long value.

  * libavogadro/src/tools/zmatrixmodel.cpp: Some fixes for z-matrix logic.

2009-05-12  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Also handle centering on selections without
  smooth translations.

  * libavogadro/src/bond.cpp: Fix initialization warnings for bond id.

2009-05-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/propmodel.cpp: Notes to allow editing bond
  lengths, atoms, and dihedrals by editing the table.

  * libavogadro/src/extensions/propextension.cpp: Add window titles to all
  property windows.

  * avogadro/src/mainwindow.cpp: Add back Control-Backspace as shortcut for
  clear()

  * avogadro/src/mainwindow.cpp: centerView() will now center based on a
  selection

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Added
  a timer-based key handler. Now accepts multi-character element symbols.

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h:
  Handle one-character elements. You can now type "c" or "o" to switch to
  carbon and oxygen.

  * avogadro/src/mainwindow.ui: Switch to only using backspace/delete for
  Clear. On Mac, 2 shortcuts doesn't seem to work and presents a strange menu
  item "Clear (****)"

  * libavogadro/src/glwidget.cpp: Fix typo in comment.

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

  * libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h:
  Add simple QWidget::event handlers for future expansion, as suggested by Qt
  coding conventions: http://qt.gitorious.org/qt/pages/CodingConventions

  * avogadro/src/engineitemmodel.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/pluginsettings.cpp, avogadro/src/settingsdialog.cpp,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/indexcolor.cpp, libavogadro/src/toolgroup.cpp: Don't
  use dynamic casts unless necessary. Even on Mac, qobject_cast works great.

  * libavogadro/src/atom.cpp, libavogadro/src/primitive.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/drawcommand.cpp: Fix use of -1 with unsigned int/long.
  Instead use UINT_MAX or ULONG_MAX.

  * CMakeLists.txt: Add a few warnings suggested by Qt coding conventions:
  http://qt.gitorious.org/qt/pages/CodingConventions

2009-05-10  marcus <marcus@eeepc.(none)>

  * libavogadro/src/molecule.h: Corrected a typo in the doxygen comments.

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/cylinder_p.cpp, libavogadro/src/cylinder_p.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glpainter_p.cpp, libavogadro/src/glpainter_p.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pythonengine.cpp, libavogadro/src/pythonengine.h,
  libavogadro/src/pythonengine_p.cpp, libavogadro/src/pythonengine_p.h,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythonextension.h,
  libavogadro/src/pythonextension_p.cpp, libavogadro/src/pythonextension_p.h,
  libavogadro/src/pythontool.cpp, libavogadro/src/pythontool.h,
  libavogadro/src/pythontool_p.cpp, libavogadro/src/pythontool_p.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/sphere_p.cpp, libavogadro/src/sphere_p.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h,
  libavogadro/src/textrenderer_p.cpp, libavogadro/src/textrenderer_p.h: Moved
  private headers to classname_p.h header flies.  All private headers should be
  placed in a classname_p.h style file name in order to make it clear that
  these are private classes not exposed in our API. Private classes do not need
  d-pointers etc as their symbols are not exported and no external programs
  should be referencing them.

  * libavogadro/src/CMakeLists.txt: Removed duplicate addition of pythonerror.h
  to the header list.

2009-05-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/pluginsettings.cpp, libavogadro/src/pythonengine.cpp,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythonscript.cpp,
  libavogadro/src/pythonscript.h, libavogadro/src/pythontool.cpp:
  libavogadro/src/pythonscript.*: Add identifier method. Use the Sha1 of
  script's content as identifier. (Fixes: 
  libavogadro/src/python[tool,engine,extension].cpp: Use the new
  PythonScript::identifier() method.

2009-05-08  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.ui: Openbabel uses km/mol for
  intensities, not a.u. -- thanks azeem.

2009-05-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/navigatetool.cpp: Added vi style hjkl keyboard
  navigation in addition to the arrow keys - thanks to Michael Banck for the
  suggestion.

2009-05-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/swig.cpp: libavogadro/src/python/swig.cpp: Fix
  delete void pointer warning.

2009-05-07  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/tools/navigatetool.cpp: Fix arrow key navigation on Mac
  without modifiers. (Qt thinks these are part of the keypad!?)

  * i18n/avogadro.pot: Update POT for latest changes. Will hopefully let me
  finally sync GB translation on Launchpad.

2009-05-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/gamesshighlighter.h: Added some more logic to the
  syntax highlighting, experimenting with the rules.

  * .../src/extensions/networkfetchextension.cpp,
  libavogadro/src/extensions/networkfetchextension.h: Added function to fetch a
  file from any URL.

2009-05-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Fixed segfault

2009-05-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Minor cleanups

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Added support for loading
  calculated spectra that may not be included in molecule, e.g. PWSCF output. 
  PWSCF output does not contain geometries, and a user requested the ability to
  load the IR data that it outputs.

  * libavogadro/src/extensions/spectradialog.cpp: Code cleanup

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Peak labeling for NMR

  * libavogadro/src/extensions/gaussianextension.h: Fix compiler warning.

2009-05-06  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/elementtranslator.cpp: Finish QOBJECT macro/moc changes.

2009-05-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Added gaussian widths to NMR
  spectra.

2009-05-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/tests/CMakeLists.txt: Fix test building now the header layout
  has changed.

2009-05-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Cleaned up whitespace.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Cleaned up signals and added a
  reference offset to NMR plots.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp: Allow inspection of
  vibrational frequencies when there are no intensities.  Spectra extension
  uses an arbitrary intensity and warns the user, vibration extension uses "-"
  in place of the intensity on the table.

2009-05-04  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Added inital support for
  visualizing NMR data stored as "NMR Isotropic Shift" per OBAtom.

2009-05-04  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot, libavogadro/src/elementtranslator.h: Update
  translations.

  * cmake/modules/PythonDeps.cmake: Update for Boost 1.39 release.

2009-05-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/glwidget.cpp: Fixed the engine list view when plugins are
  removed.  This fixes the case where an engine plugin is removed and the names
  got messed up. It still does not handle the case where new engine plugins are
  added but not added automatically.

  * cmake/modules/AvogadroConfig.cmake.in: Fixed paths after variable name
  change, fixes bug 2786607.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gamesshighlighter.cpp,
  libavogadro/src/extensions/gamesshighlighter.h,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h: Initial support for syntax
  highlighting in GAMESS input generator.  This is still quite early stage, and
  needs many more rules. It already demonstrates the basic concepts after
  talking to Albert DeFusco about GAMESS syntax highlighting and some of the
  work he has done with vim.

2009-05-03  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/nwcheminputdialog.cpp: NWChem input dialog now
  reads from OB data for multipliciticy.

2009-05-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonterminal.h, scripts/cmake-msvc2008.bat:
  libavogadro/src/extensions/pythonterminal.h: fix header issue.

2009-05-02  Marcus D. Hanwell <marcus@cryos.org>

  * cmake/modules/AvoCPack.cmake: Forgot to update this version number...

  * CMakeLists.txt, Doxyfile, avogadro/CMakeLists.txt,
  avogadro/src/config.h.in, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/config.h.in: Bumped the
  version number to 0.9.4 in preparation for tagging.  Centralised the version
  numbering - only needs changing in TWO places now!

  * CMakeLists.txt, avogadro/src/CMakeLists.txt: Added an option to use RPath
  at install tiem. Can cause issues on some distros if installed in /usr.

2009-05-02  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp: Fixed compile error introduced in previous
  merge

2009-05-02  Marcus D. Hanwell <marcus@cryos.org>

  * .../src/extensions/networkfetchextension.cpp: Few small fixes to the new
  PDB download extension.

2009-05-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotaxis.cpp, libavogadro/src/plotaxis.h,
  libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h,
  libavogadro/src/plotpoint.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Cleaned up whitespace with QtCreator.

2009-05-01  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot: Updated after merging changes from Tim and Cryos.

  * i18n/avogadro.pot: Updated translations for 0.9.4.

  * avogadro/src/mainwindow.ui: Added "delete" as an additional shortcut for
  clear.

2009-05-01  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp: Attempt to fix bug 2783747, unable to test
  adequately here as my filesystem is not currently UTF8 aware. It certainly
  still loads all other files and the Qt docs suggest this is the correct way
  to load UTF filenames using STL functions.

2009-05-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/pythonengine.cpp,
  libavogadro/src/pythonengine.h, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythonextension.h, libavogadro/src/pythonscript.cpp,
  libavogadro/src/pythonscript.h, libavogadro/src/pythontool.cpp,
  libavogadro/src/pythontool.h: Some changes to python includes to compile with
  cryos' recent changes

  * libavogadro/src/python/engine.cpp, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/pluginmanager.cpp, libavogadro/src/python/tool.cpp,
  libavogadro/src/python/toolgroup.cpp,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/toolgroup.py: Some updates to the python
  bindings and python unit tests. All tests should pass again.

  * scripts/cmake-msvc2008.bat, scripts/cmake-vs2005.bat: Rename
  scripts/cmake-vs2005.bat to scripts/cmake-msvc2008.bat

  * cmake/modules/AvoCPack.cmake, cmake/modules/FindNumpy.cmake,
  libavogadro/src/python/CMakeLists.txt, scripts/cmake-vs2005.bat:
  cmake/modules/AvoCPack.cmake: Changes to correctly include all python stuff 
  cmake/modules/FindNumpy.cmake: Small bug fix, wasen't working here 
  libavogadro/src/python/CMakeLists.txt: Set library SUFFIX property to ".pyd"
  on WIN32  scripts/cmake-vs2005.bat: update for python & GLSL support

2009-04-30  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt: Updated to get Mac icons back. Still needs to
  be updated to handle app packages.

2009-04-30  Michael Banck <michael.banck@ch.tum.de>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/molproinputdialog.cpp,
  libavogadro/src/extensions/molproinputdialog.h,
  libavogadro/src/extensions/molproinputdialog.ui: New Molpro input file
  generator.

2009-04-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/networkfetchextension.cpp,
  libavogadro/src/extensions/networkfetchextension.h: First network aware
  extension - direct PDB downloads.  This is the first network aware extension.
  I added QtNetwork to the Avogadro library as I think we will want to use the
  network more and more in the future. This extension is a very simple proof of
  concept - it attempts to download the named PDB from the PDB site.

  * libavogadro/src/extensions/molpro.cpp: Quick fix to Molpro parsing, as
  requested by Michael Banck.

  * libavogadro/src/CMakeLists.txt: On second thoughts, symlink on UNIX
  platforms and copy when not supported (Windows).

  * libavogadro/src/glwidget.h: Changed include order - Windows needs the
  NOMINMAX definition before any other includes.

  * avogadro/src/CMakeLists.txt, libavogadro/include/avogadro/animation.h,
  libavogadro/include/avogadro/atom.h, libavogadro/include/avogadro/bond.h,
  libavogadro/include/avogadro/boost.h,
  libavogadro/include/avogadro/boxcontrol.h,
  libavogadro/include/avogadro/camera.h, libavogadro/include/avogadro/color.h,
  libavogadro/include/avogadro/colorbutton.h,
  libavogadro/include/avogadro/cube.h, libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/elementtranslator.h,
  libavogadro/include/avogadro/engine.h,
  libavogadro/include/avogadro/extension.h,
  libavogadro/include/avogadro/filetreeitem.h,
  libavogadro/include/avogadro/fragment.h,
  libavogadro/include/avogadro/glgraphicsview.h,
  libavogadro/include/avogadro/global.h,
  libavogadro/include/avogadro/glpainter.h,
  libavogadro/include/avogadro/glwidget.h,
  libavogadro/include/avogadro/idlist.h, libavogadro/include/avogadro/line.h,
  libavogadro/include/avogadro/mesh.h,
  libavogadro/include/avogadro/meshgenerator.h,
  libavogadro/include/avogadro/molecule.h,
  libavogadro/include/avogadro/moleculetreeview.h,
  libavogadro/include/avogadro/navigate.h,
  libavogadro/include/avogadro/neighborlist.h,
  libavogadro/include/avogadro/painter.h,
  libavogadro/include/avogadro/painterdevice.h,
  libavogadro/include/avogadro/periodictableview.h,
  libavogadro/include/avogadro/plotaxis.h,
  libavogadro/include/avogadro/plotobject.h,
  libavogadro/include/avogadro/plotpoint.h,
  libavogadro/include/avogadro/plotwidget.h,
  libavogadro/include/avogadro/plugin.h,
  libavogadro/include/avogadro/pluginmanager.h,
  libavogadro/include/avogadro/point.h,
  libavogadro/include/avogadro/povpainter.h,
  libavogadro/include/avogadro/primitive.h,
  libavogadro/include/avogadro/primitiveitemmodel.h,
  libavogadro/include/avogadro/primitivelist.h,
  libavogadro/include/avogadro/protein.h,
  libavogadro/include/avogadro/pythonerror.h,
  libavogadro/include/avogadro/pythoninterpreter.h,
  libavogadro/include/avogadro/pythonscript.h,
  libavogadro/include/avogadro/residue.h,
  libavogadro/include/avogadro/sphere.h,
  libavogadro/include/avogadro/textrenderer.h,
  libavogadro/include/avogadro/tool.h,
  libavogadro/include/avogadro/toolgroup.h,
  libavogadro/include/avogadro/undosequence.h,
  libavogadro/include/avogadro/zmatrix.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glwidget.cpp, libavogadro/src/protein.cpp: Use CMake to
  generate the include directory at build time.  This is all part of my evil
  plan to have CMake do all the mundane tasks so that you have no excuse but to
  implement cool new features. The Avogadro headers are now copied at CMake
  time into the build directory, this is used to build against and those same
  headers are installed.

  * cmake/modules/CTestCustom.cmake.in: Removed first part of the path - should
  suppress eigen.cpp warnings now.

2009-04-28  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/plotwidget.cpp: Added an extra include that is needed for
  Open Babel 2.2.1.

  * avogadro/src/engineitemmodel.cpp, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/boxcontrol.h, libavogadro/src/color.h,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/glpainter.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/molecule.cpp,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/pythontool.cpp,
  libavogadro/src/pythontool.h, libavogadro/src/textrenderer.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/zmatrixdialog.cpp,
  libavogadro/src/tools/zmatrixdialog.h,
  libavogadro/src/tools/zmatrixdialog.ui,
  libavogadro/src/tools/zmatrixtool.cpp, libavogadro/src/tools/zmatrixtool.h:
  Removed several includes from glwidget.h, less global includes.

  * libavogadro/tests/moleculebench.cpp: Added a few more benchmarks examining
  the Molecule destructor behaviour.

  * CMakeLists.txt, cmake/modules/CTestCustom.cmake.in: GCC flags tweaked and
  CTestCustom.cmake added for CDash submission  I removed -Wundef from the GCC
  flags for now, too many warnings from the Boost headers are generated to be
  useful. I also added a CTestCustomConfig.cmake.in to ignore some warnings on
  Windows and for eigen.cpp which has a massive number of warnings (this should
  be looked at separately).

  * libavogadro/src/molecule.cpp: A few fixes to the molecule class after
  benchmarking and testing.

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/moleculebench.cpp:
  Added some initial Molecule benchmarking code.

  * libavogadro/tests/moleculetest.cpp: Added a few more tests for the Molecule
  class.

2009-04-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/zmatrixmodel.cpp: Fixed it up - less crashes. Still
  needs more work to get it ready.

  * libavogadro/src/molecule.cpp: Reduced number of loops in ComputeGeomInfo,
  tidied up the code a little.

2009-04-25  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp: Fixed bug in plotwidget.* where the widget
  redrew itself continuously.  Apparently the QLabels can't have the plotwidget
  as their parent.

2009-04-24  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Made file formats in image
  export a bit easier to read.

2009-04-24  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, cmake/modules/AvogadroConfig.cmake.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Modifications to build system to allow
  including in a super project.

2009-04-24  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Quite trivial.  Small typo in
  comment.

2009-04-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Major code changes to
  spectradialog.*  * Added many more comments * Organized functions a bit more
  logically * Separated out and identified all spectra-specific var, functions,
  etc * Rewrote import function to be much smaller.

2009-04-23  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h: Update
  to prevent Python breakage. Use an overloaded parameter for loadFactories().

2009-04-23  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, cmake/modules/AvogadroConfig.cmake.in,
  cmake/modules/AvogadroUse.cmake: Install an AvogadroConfig.cmake file and
  supporting files.  Changes to install an AvogadroConfig.cmake file, along
  with several supporting files. This negates the need for a FindAvogadro.cmake
  file and also introduces an AvogadroUse.cmake file which makes building
  against the installed Avogadro library much simpler. Supporting example
  project will be added to GitHub shortly.

  * libavogadro/src/extensions/basisset.cpp: Small changes to debug output.

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h: Tweaks
  to the plugin loading code  Addded the contrib directory to the list of
  default searched paths. Also added a new void
  PluginManager::loadFactories(const QString& dir) to load plugins from a
  supplied directory path.

  * avogadro/src/aboutdialog.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/savedialog.cpp,
  libavogadro/src/boxcontrol.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/color.cpp, libavogadro/src/colors/chargecolor.cpp,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/indexcolor.cpp,
  libavogadro/src/colors/residuecolor.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/simplewireengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/idlist.cpp, libavogadro/src/plugin.cpp,
  libavogadro/src/primitive.cpp, libavogadro/src/primitivelist.cpp,
  libavogadro/src/pythonengine.cpp, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythontool.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/undosequence.cpp: Fixing up config.h includes - many places
  where it was not needed.

2009-04-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/CMakeLists.txt: Removed the lib prefix from the plugins.

  * CMakeLists.txt, CTestConfig.cmake, cmake/modules/AvoCTestConfig.cmake: The
  CTestConfig.cmake was moved, some small changes to the build system.

2009-04-22  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.ui: Move scaling option to a more
  appropriate tab, fix stretching button.

  * libavogadro/src/extensions/spectradialog.cpp: Allow spectra schemes to be
  updated completely.

2009-04-21  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Don't load molecule if there
  isn't one to load.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h: Renamed member var and fixed
  segfault in Qt 4.4 work around.  schemes --> m_schemes QHashIterator in
  writeSettings() never advanced to allow data to be accessed, resulting in
  non-persistent schemes and assertion problems.

2009-04-21  Geoff Hutchison <geoff@geoffhutchison.net>

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

  * avogadro/src/mainwindow.cpp: Modified 2D cleanup -- now detects atoms with
  identical coordinates. Also uses conjugate gradients for better results.

2009-04-20  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h: Cleanup and put in frame work to
  begin thinking about other sorts of spectra.

2009-04-17  Marcus D. Hanwell <marcus@cryos.org>

  * testfiles/methane-gaussian.fchk: Added a methane formatted checkpoint as
  output from Gaussian 03.

  * libavogadro/src/extensions/gaussianfchk.cpp: Corrected issue with SP type
  orbitals. Still tracking down some remaining issues.

  * libavogadro/src/extensions/basisset.cpp: Added debug output to the Gaussian
  basis set code. Still tracking an issue with fchk parsing.

2009-04-17  Michael Banck <michael.banck@ch.tum.de>

  * testfiles/methane.g03, testfiles/methane.inp, testfiles/methane.mp,
  testfiles/methane.mpo, testfiles/methane.nwo: Added some new test files for
  quantum output processing.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/molpro.cpp, libavogadro/src/extensions/molpro.h,
  libavogadro/src/extensions/orbitalextension.cpp: Added support for reading
  Molpro output files in.

2009-04-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp: Added back cube export, titles are not fed
  through correctly yet.

2009-04-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Make sure spectradialog.cpp
  compiles with Qt 4.4

2009-04-16  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Should fix the last of the Qt
  4.5 code issues.

2009-04-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added a new signal
  to the Molecule, used in the properties extensions. Still needs work.

  * libavogadro/src/extensions/supercellextension.cpp: Do not copy the unit
  cell on to itself - unwanted duplicate atoms.

2009-04-15  David Lonie <loniedavid@gmail.com>

  * avogadro/src/settingsdialog.cpp: Fixed display of fog level in main
  settings.

  * libavogadro/src/extensions/nwcheminputdialog.cpp: Fixed intial basis set in
  nwchem input

  * avogadro/src/mainwindow.cpp: Added NWChem to the common molecule formats

  * libavogadro/src/extensions/nwcheminputdialog.cpp: Corrected b3lyp directive
  for nwchem input

2009-04-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/include/avogadro/elementtranslator.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/elementtranslator.cpp,
  libavogadro/src/elementtranslator.h, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/simplewireengine.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/python/TODO,
  libavogadro/src/tools/drawtool.cpp: Moved the ElementTranslator class to be
  consistent with the class name.

2009-04-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/nwcheminputdialog.ui: Use a real basis set as
  the default.

2009-04-14  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Fixed bug in
  spectradialog.cpp concerning theme names.

  * libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.ui: Add multiplicity options
  back in to nwchem generator (only for DFT)

  * libavogadro/src/extensions/nwcheminputdialog.cpp: Fixed bug in nwchem
  extension.

2009-04-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/spectradialog.cpp: Small fix - be more explicit
  with function argument types.

2009-04-12  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.ui: Cleaned up nwchem input
  generator.

  * testfiles/methane.nwo: Added methane.nwo to testfiles

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/nwcheminputdialog.cpp,
  libavogadro/src/extensions/nwcheminputdialog.h,
  libavogadro/src/extensions/nwcheminputdialog.ui: Initial addition of NWChem
  input generator.

2009-04-09  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectraextension.cpp: Cleaned up whitespace with
  qt creator

2009-04-08  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp: Removed debugging output.

  * libavogadro/src/extensions/spectradialog.ui: GUI touch ups

  * libavogadro/src/extensions/spectradialog.cpp: Oops -- had some Qt 4.5 only
  code in there. Fixed.

2009-04-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/simplewireengine.cpp,
  libavogadro/src/engines/simplewireengine.h: Added a new engine - super simple
  wire frame engine. Mainly for testing purposes and as an example of a very
  simple engine.

2009-04-08  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Added a fun scheme to the
  spectra extension.

2009-04-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Handle cancelled dialog with
  a bit more forgiveness.

2009-04-07  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/main.cpp: Few small tweaks to version output, should help with
  debug output.

2009-04-07  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Added an option to optimize the font size of
  exported images to spectradialog.*, and the necessary code to plotwidget.*.

  * libavogadro/src/plotwidget.cpp: Rotate the left axis labels in the
  plotwidget.* drawAxes() to match the images and prevent clipping.

  * libavogadro/src/plotwidget.cpp: Rotated y-axis tick labels in image export
  of plotwidget.* to avoid clipping issues.

  * libavogadro/src/extensions/spectradialog.cpp: Fixed error with unit
  selection in spectra image export.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui, libavogadro/src/plotwidget.cpp:
  Fixed some font and spacing issues in image export.

  * libavogadro/src/extensions/spectradialog.ui: GUI changes

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui, libavogadro/src/plotobject.cpp,
  libavogadro/src/plotobject.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: * Fixed up image export with some new options.
  * Added file output to the plot widget

2009-04-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/CMakeLists.txt, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Added a new CMake function -
  avogadro_plugin. Migrated plugins to it.  The avogadro_plugin function allows
  developers to easily add new plugins, makes our build files more concise.
  Allows for global changes in the way plugins are built in the future.

2009-04-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Needed to clear out a combo
  box...

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Moved spectra image export to a
  tab.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Added a spectra tsv export
  feature.

  * libavogadro/src/extensions/spectradialog.cpp: Fixed segfault in spectra
  extension that occurred when switching molecules.

2009-04-06  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, avogadro/src/aboutdialog.cpp, avogadro/src/config.h.in,
  avogadro/src/main.cpp, libavogadro/src/config.h.in,
  libavogadro/src/global.cpp, libavogadro/src/global.h: Updates to the handling
  of builds from Git clones - now report the hash the build was made against.

2009-04-06  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Restructure GUI to use tabs in
  the spectra extension

2009-04-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectradialog.cpp: Fixed crash when loading
  incorrect spectra types.

  * libavogadro/src/plotwidget.cpp: Improvements to the plot widget's axis
  label placement.

  * libavogadro/src/extensions/spectradialog.cpp: Put a nice font on the
  publication scheme.

  * libavogadro/src/extensions/spectradialog.cpp: minor: typo

  * libavogadro/src/extensions/spectradialog.cpp: Added a third default color
  scheme.

  * libavogadro/src/extensions/spectradialog.cpp: Random punctuation is random.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui: Spectra now use persistent,
  customizable color schemes.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectraextension.cpp,
  libavogadro/src/extensions/spectraextension.h: * Added persistant settings to
  spectra extension * Cleaned up debugging output * Started framework for color
  schemes

2009-04-03  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/spectraextension.cpp: Fixed bug in launching
  spectradialog.*

  * testfiles/methanol.jdx, testfiles/methanol.nwo: Added two testfiles: an
  NWChem out with IR data, and a .jdx for JCAMP-DX spectrum tests.

  * libavogadro/src/extensions/spectradialog.cpp: Added support for .jdx
  spectra (i.e. from NIST) and cleaned up file handling in general.

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Better handling in spectra
  extension for files without valid data.

  * libavogadro/src/extensions/spectradialog.cpp: Removed debugging

  * libavogadro/src/extensions/spectradialog.ui: GUI cleanup

  * libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.ui: Fixed some bugs in the spectra
  extension

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/spectradialog.cpp,
  libavogadro/src/extensions/spectradialog.h,
  libavogadro/src/extensions/spectradialog.ui,
  libavogadro/src/extensions/spectraextension.cpp,
  libavogadro/src/extensions/spectraextension.h,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Moved spectra plotting to its
  own extension.

2009-04-02  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp: Changed vibrationplot.* to
  use superscript labels.

  * libavogadro/src/plotwidget.cpp: Rewrote the plotwidget.* text labels to be
  QLabel, and thus support rich text such as sub/superscript.

2009-04-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added a gaussian superposition
  of peaks to vibrationplot.*.

  * libavogadro/src/extensions/vibrationplot.cpp: Clear out old imported
  spectra before importing new.

2009-04-01  Marcus D. Hanwell <marcus@cryos.org>

  * Doxyfile: Bumped version for doxygen docs.

  * INSTALL: Updated the INSTALL file, changed dependency versions and removed
  the AVOGADRO_PLUGINS which is not required anymore - relative paths used
  instead.

2009-04-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp: Fixed bug: Axis label said %,
  but data was plotted in fraction.

2009-04-01  Geoff Hutchison <babel@geoffhutchison.net>

  * CMakeLists.txt: Fix typo in previous revision -- should read the CMake docs
  better.

  * CMakeLists.txt, scripts/create-translations.sh: Added custom command for
  "create-translations" -- use lconvert from PO -> TS

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Update translations from
  Launchpad.

  * libavogadro/src/tools/zmatrixmodel.cpp,
  libavogadro/src/tools/zmatrixmodel.h: Added Q_OBJECT macro and moc output.

2009-04-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Improvements to orbital
  engine handling of colored meshes.

  * CMakeLists.txt, avogadro/CMakeLists.txt, cmake/modules/AvoCPack.cmake,
  libavogadro/CMakeLists.txt: Version bump in preparation for tagging the 0.9.3
  release.

  * libavogadro/src/engines/orbitalengine.cpp: Added check for meshes - only
  try to display colored mesh if the mesh has colors.

2009-04-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Enable configuration of plot
  font in vibrationplot.*..

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Options to
  get font are nice too :)

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added code to
  change font in plot widget.

2009-04-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/zmatrixdialog.cpp,
  libavogadro/src/tools/zmatrixdialog.h,
  libavogadro/src/tools/zmatrixdialog.ui,
  libavogadro/src/tools/zmatrixmodel.cpp, libavogadro/src/tools/zmatrixmodel.h,
  libavogadro/src/tools/zmatrixtool.cpp, libavogadro/src/zmatrix.cpp,
  libavogadro/src/zmatrix.h: Lots of changes to the z matrix tool. It actually
  does stuff now, disabling by default. It is far from ready to be used yet.

  * libavogadro/src/global.h: Moved global Avogadro variables inside the
  Avogadro namespace.

2009-04-01  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp: Smoothed out some work from last night to
  use padding correctly.

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added support for absorbances in
  vibrationplot.*

  * libavogadro/src/extensions/vibrationplot.ui: Added tooltip to plotwidget.

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Replaced vibrationplot.* scaling
  slider/text edit with spin box

2009-03-31  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: plotwidgets
  can zoom with scroll wheel now.

  * libavogadro/src/extensions/vibrationplot.cpp: Update vibrationplot.* to use
  a default limit set.

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Allow a
  default limit to be set and reapplied by a doubleclick. Also change the
  click-and-drag to use the right mouse button for consistancy with the gl
  canvas.

2009-03-31  Marcus D. Hanwell <marcus@cryos.org>

  * cmake/modules/FindPythonLibs.cmake: Modified FindPythonLibs.cmake that does
  not use the path suffix. As far as I can tell this should work on all Linux
  distributions (not just Debian based ones as is now the case). Feedback would
  be appreciated.

  * libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h: Initial fixes for bug 2723686,
  create dialogs for the views. I am not sure that the logic is correct for the
  views created here.

2009-03-31  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/residue.cpp: Don't pass -1 for an unsigned value. Use
  ULONG_MAX instead.

2009-03-31  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Added simple
  click-and-drag plot movement.

2009-03-30  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.ui: Minor GUI changes.

  * libavogadro/src/extensions/vibrationplot.cpp: Fix a stupid typo :)

  * libavogadro/src/extensions/vibrationplot.ui: Cleaned up dialog (tab order,
  buddies, accelerators, etc.)

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added option to toggle off the
  calculated spectra, just for completeness sake.

2009-03-29  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.ui: Fixed some git-merging
  conflicts...

  * testfiles/sampleIRSpectra.tsv: Added a sample experimental IR spectra for
  testing the import feature in libavogadro/src/extensions/vibrationplot.*

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added options to vibrationplot.*
  for color, font size, etc...

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added options to vibrationplot.*
  for color, font size, etc...

2009-03-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/molecule.cpp: Do not do ring perception on load - terrible
  performance for big systems. Also blocked signals for performance reasons and
  updated the super cell extension a little.

2009-03-28  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp: Some translation friendly
  additions.

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Grouped customization options
  together.

2009-03-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/include/avogadro/zmatrix.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/zmatrixdialog.cpp,
  libavogadro/src/tools/zmatrixdialog.h,
  libavogadro/src/tools/zmatrixdialog.ui,
  libavogadro/src/tools/zmatrixmodel.cpp, libavogadro/src/tools/zmatrixmodel.h,
  libavogadro/src/tools/zmatrixtool.cpp, libavogadro/src/tools/zmatrixtool.h,
  libavogadro/src/zmatrix.cpp, libavogadro/src/zmatrix.h: Initial work on a new
  z matrix editor. Far from complete just yet. Questionable whether it belongs
  with the other tools, but does need mouse interaction.

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Some
  improvements to the drawing tool, lazy initialization, clean ups.

  * libavogadro/src/extensions/supercellextension.cpp: Various improvements to
  the unit cell code - speed improvements, interactivity. Should probably
  dispatch most work off to a separate thread.

2009-03-27  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp: Fixed bug in
  vibrationdialog.* caused by a GUI change.

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added simple image output to
  vibrationplot.*.

2009-03-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/aligntool.h:
  Reduced the number of includes massively.

  * libavogadro/src/tool.cpp: QObject parenting takes care of destroying the
  QAction.

2009-03-26  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.h: Removed unused function.

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added in an import function to
  vibrationplot.* that can overlay experimental spectra. General retooling of
  plotobject handling. GUI changes.

2009-03-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h: Small changes to indentation
  and variable names.

2009-03-26  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationextension.cpp: More GUI changes

2009-03-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/python/molecule.cpp: Inlined a few functions that are called
  a lot.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Moved the atom
  and bond storage into the class, should allow some inlining.

2009-03-25  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationplot.ui: GUI changes for vibrationplot.*

2009-03-25  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt: Second thoughts - relative
  RPATH is only needed for executables.

  * CMakeLists.txt: Added relative RPATH for Linux installations, symbol
  resolution on link for MODULE and EXE linking.

2009-03-25  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/plotwidget.cpp: Fix indentation issues.

2009-03-24  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/extensions/povpainter.cpp, libavogadro/src/glpainter.cpp: A
  few small adjustments to use the correct colour transparency when rendering
  using colorMesh.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Fixed up the orbital
  selection, previously had bugs when several meshes were present.

2009-03-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Added labels to the peaks and
  changed the font so that it would actually be legible. Removed debug output
  and unnecessary credits.

  * libavogadro/src/plotaxis.cpp, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Removed debug output and added the ability to
  change font size through PlotWidget::setFontSize(int pointSize).

2009-03-23  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h: Removed #warning - it is a GCC
  extension. Removed unimplemented slot - caused link issues on Windows.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h: Added the D5 type orbitals for
  electron density calculations.

  * libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/tools/navigatetool.cpp: Only do space group transformations
  when there is a space group. Otherwise duplicate the unit cell to make a
  supercell.

  * libavogadro/src/extensions/supercellextension.cpp: Check whether there is a
  valid spacegroup. Needs error messages and the option to make a supercell
  without a space group.

2009-03-23  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Cleaned up vibration plot a
  bit..

2009-03-22  David Lonie <loniedavid@gmail.com>

  * libavogadro/include/avogadro/plotaxis.h,
  libavogadro/include/avogadro/plotobject.h,
  libavogadro/include/avogadro/plotpoint.h,
  libavogadro/include/avogadro/plotwidget.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui, libavogadro/src/plotaxis.cpp,
  libavogadro/src/plotaxis.h, libavogadro/src/plotobject.cpp,
  libavogadro/src/plotobject.h, libavogadro/src/plotpoint.cpp,
  libavogadro/src/plotpoint.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Added plotting widget based off of KPlotWidget
  as <avogadro/plotwidget.h> and added a dialog to plot mock IR spectra to the
  vibrations extension..

2009-03-22  David Lonie <dl@david-laptop.(none)>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui: Initial working vibration
  plotting (Has hack to get around bug in qchem files).

  * libavogadro/src/plotaxis.cpp: Fixed axis ticks for plotting ranges where
  the axis runs from high -> low.

  * libavogadro/include/avogadro/plotaxis.h,
  libavogadro/include/avogadro/plotobject.h,
  libavogadro/include/avogadro/plotpoint.h, libavogadro/src/plotwidget.cpp,
  libavogadro/src/plotwidget.h: Fixed some issues in the plotwidget.

  * libavogadro/include/avogadro/plotwidget.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/kplotaxis.cpp, libavogadro/src/kplotaxis.h,
  libavogadro/src/kplotobject.cpp, libavogadro/src/kplotobject.h,
  libavogadro/src/kplotpoint.cpp, libavogadro/src/kplotpoint.h,
  libavogadro/src/kplotwidget.cpp, libavogadro/src/kplotwidget.h,
  libavogadro/src/plotaxis.cpp, libavogadro/src/plotaxis.h,
  libavogadro/src/plotobject.cpp, libavogadro/src/plotobject.h,
  libavogadro/src/plotpoint.cpp, libavogadro/src/plotpoint.h,
  libavogadro/src/plotwidget.cpp, libavogadro/src/plotwidget.h: Completed
  integrating kde's KPlotWidget to Avogadro::PlotWidget.

  * libavogadro/src/extensions/vibrationplot.cpp,
  libavogadro/src/extensions/vibrationplot.h,
  libavogadro/src/extensions/vibrationplot.ui, libavogadro/src/kplotaxis.cpp,
  libavogadro/src/kplotaxis.h, libavogadro/src/kplotobject.h,
  libavogadro/src/kplotpoint.cpp, libavogadro/src/kplotpoint.h,
  libavogadro/src/kplotwidget.cpp, libavogadro/src/kplotwidget.h: Initial
  attempt to create a plot of the vibrations.

2009-03-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/forceengine.cpp: Small improvement to the display
  of forces in the force engine, removed includes etc that were not needed.

  * avogadro/src/avogadro.desktop: Fixed issues with .desktop file pointed out
  in PR #2665637.

  * libavogadro/src/extensions/shaders/vmd.frag,
  libavogadro/src/extensions/shaders/vmd.vert, testfiles/icsd_83086.cif,
  testfiles/icsd_83086.res: Removed files, Daniel Leidert pointed out possible
  copyright issues.

2009-03-05  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui: Fixed segfault when starting
  vibration animation with no mode selected. 

  * avogadro/src/mainwindow.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/wiitrackextension.cpp: Fixed shortcut collision in
  menubar. 

2009-03-04  David Lonie <loniedavid@gmail.com>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui: Fixed segfault when starting
  vibration animation with no mode selected.

  * avogadro/src/mainwindow.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/wiitrackextension.cpp: Fixed shortcut collision in
  menubar.

2009-03-04  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationdialog.cpp: Make sure we don't run off
  the end of the vector for frequencies.

2009-03-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonterminal.cpp: PythonTerminal: Don't delete
  the widget in destructor. Prevents crashes on closing.

2009-03-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp: Changed from David Lonie
  for an "export" feature.

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

  * libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui: Updates to Q-Chem input
  builder. Now offers new DFT functionals and basis sets.

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

  * libavogadro/src/extensions/vibrationextension.cpp: Turn off warning for
  right now -- some GAMESS files have strange numbers of atoms.

  * libavogadro/src/extensions/propextension.cpp: Fix some parenting issues
  with the properties windows.

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

  * libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui: Update Q-Chem -- no AM1 or
  PM3, and we should always output a FCHK file.

  * avogadro/src/pluginsettings.ui: Update capitalization for "Display Types"

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Updated translations and POT
  template.

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

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp: Added support for colored
  MOs and electron density in the orbital engine.

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

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h, testfiles/methane.FChk,
  testfiles/methane.out: Added example files (methane.out for vibrations) and
  minor cleanups.

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

  * libavogadro/src/extensions/orbitalextension.cpp: Small changes to get the
  triangle winding right for electron densities - much more tweaking is needed.

  * avogadro/src/avogadro.desktop: Added a few more categories that seem
  appropriate. Education appears to be required for Gnome as it has no science
  category...

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

  * libavogadro/src/extensions/vibrationextension.cpp: Smoothed out many
  animation bugs.

2009-03-02  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: More fixes. Still has a
  double free, and a slight hitch in the frames.

  * libavogadro/src/engines/forceengine.cpp: Adopt code from label engine to
  "float" forces to always appear in front of atoms.

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationextension.cpp: Better vibrational
  implementation. Now smoother animation and you can use the arrow keys in the
  dialog.

  * libavogadro/src/animation.cpp, libavogadro/src/animation.h,
  libavogadro/src/extensions/vibrationextension.cpp: Set up continual loopback
  for vibration animations. Still needs testing.

  * libavogadro/include/avogadro/animation.h, libavogadro/src/animation.cpp,
  libavogadro/src/animation.h,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Initial effort at
  an animation framework, including animation for vibrations.

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: First pass at signals/slots
  for animations and other options.

2009-03-01  David Lonie <loniedavid@gmail.com>

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts,
  libavogadro/src/extensions/animationdialog.cpp: Fixed typo in the animation
  file dialog.

2009-03-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/supercelldialog.ui: Removed signals I am not
  using anymore.

  * libavogadro/src/extensions/supercellextension.cpp: Code clean up.

  * libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/neighborlist.h: Do a little of that optimization I mentioned
  on the supercell builder...

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/supercelldialog.cpp,
  libavogadro/src/extensions/supercelldialog.h,
  libavogadro/src/extensions/supercelldialog.ui,
  libavogadro/src/extensions/supercellextension.cpp,
  libavogadro/src/extensions/supercellextension.h: Added a new super cell
  builder extension. Still a little rough but can already build large zeolite
  super cells.

2009-03-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/vdwsurface.cpp: VdWSurface: when generating a
  vdw cube, check if the current GLWidget has any selections, if so use the
  selected atoms only.

2009-03-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.cpp, libavogadro/src/extensions/qcheminputdialog.cpp:
  Emit a signal when atom positions are modified, and also improve the update
  logic a little in the Q-Chem input dialog.

  * libavogadro/src/extensions/mopacaux.cpp: Reduced the debug output
  verbosity. Still needs more error checking logic.

2009-03-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/qlist.cpp: Add python wrapper for QList<Mesh*>

2009-03-01  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/main.cpp: Commented out the library translation loading, not
  currently used.

  * avogadro/src/main.cpp: Use the full path on the Mac still - different
  binary position.

2009-02-28  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt: Relaxes the required CMake versin back to 2.6.0 for now.
  Would be good to increase this soon.

  * avogadro/src/avogadro.desktop, avogadro/src/icons/avogadro_icon.png: Added
  a .desktop file and icon for Linux, improves the end user experience.

  * CMakeLists.txt, avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  cmake/modules/AvoCPack.cmake, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/config.h.in, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Build system improvements, handle
  installation locations more logically, some rpath logic and bumped our
  version number in preparation for release.

  * libavogadro/src/molecule.cpp: Disconnect all signals before destructing the
  molecule.

  * libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.cpp: Fixed some compiler warnings.

2009-02-28  Simon Ochsenreither <soc@desktop06.(none)>

  * i18n/avogadro_de_AT.ts, i18n/avogadro_de_CH.ts, i18n/avogadro_de_DE.ts:
  Symlinks aren't needed. Qt falls back to de if it doesn't find de_DE.

  * i18n/avogadro_de_AT.ts, i18n/avogadro_de_CH.ts, i18n/avogadro_de_DE.ts:
  Symlinked de_DE, de_AT and de_CH to de because we use a single translation
  file for all german-speaking countries at the moment.

2009-02-28  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp: Use QDir::homePath() as the
  default location if we have an untitled file.

2009-02-27  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp: Change "slop" factor a bit. For
  renderPick, add a bit of slop to bonds for the bond-centric tool. Also
  subtract a bit from hydrogens to make them harder to hit.

2009-02-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/molecule.cpp, libavogadro/src/python/qlist.cpp: Fix
  compile error in the python bindings (include glwidget.h sicne extension.h no
  longer includes it) + add some missing functions for Molecule

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/tests/drawcommandtest.cpp:
  DrawCommands: You can now drag (with C selected for example) from a hydrogen
  to an empty space (or another atom) which will result in a ChangeElement,
  AddBond and/or AddAtom command. This used to "steal" the hydrogen from the
  atom it was attached to. The new behaviour is much more intuitive and
  probably what most people would expect to happen.

2009-02-27  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Add suport for showing/hiding unit cell axes. By
  default, this will be disabled on PDB files -- matching most users'
  expectations.

  * libavogadro/src/python/qlist.cpp: Compile fix -- GLHit is in glwidget.h

2009-02-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp: Use simpler
  AdjustHydrogens[Pre/Post]Command constructors when only one atom should be
  adjusted

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/tests/drawcommandtest.cpp: DrawCommands: Replace the int
  adjustHydrogens with QFlags for more control

2009-02-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/plugin.h: Bumped our plugin version number. Lots of big
  changes to the plugin API, prevents old plugins from being loaded.

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/painter.h: Removed the triangle
  windings hack as it is not needed anymore. Fixed a bug in transparency in
  coloured meshes in POV-Ray output too.

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp: Reduced the verbosity of
  the debug output.

2009-02-27  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Use "Window" menu
  on all platforms, not just Mac.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Merge from Cryos.

2009-02-27  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/main.cpp: Added untranslated version information to the top of
  output.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Add configuration
  file versioning, reject unversioned configuration with the option to bump in
  the future. Should address issues with stale configuration files.

  * avogadro/src/mainwindow.cpp: Fixed UI issue where the quick render check
  box did not reflect the current setting when it was disabled in settings.

2009-02-26  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Bring back offset windows on Mac and Windows
  -- Linux should handle window management.

2009-02-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.cpp: Sorted out some of the
  parenting issues and updates on destruction - quantum codes only care about
  atoms!

  * libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h: Updates to the MOPAC dialog,
  respect cancel for job submission, plugged a small memory leak in the
  z-matrix code and save whether preview is shown or not.

  * libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaderextension.h: Fixed parenting issues in these
  extensions.

  * libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp: Small fixes to destruction
  of extensions and parenting of dialogs.

  * libavogadro/src/plugin.cpp, libavogadro/src/plugin.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h: Few small improvements to
  the plugin and tool classes.

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp: Removed the GLWidget
  include and replaced with some forward declarations. Added includes to
  extensions missing them.

  * avogadro/src/mainwindow.cpp: Fixed some parenting issues in the
  constructor.

  * libavogadro/src/extensions/qcheminputdialog.cpp: Plugged a small memory
  leak in the z-matrix code.

  * libavogadro/src/extensions/gaussianinputdialog.cpp: Plugged a small memory
  leak in the z-matrix code.

2009-02-26  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Make sure tools and extensions have parents.

2009-02-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Bring back framebuffer objects if supported.
  (More reliable for most users.)

  * libavogadro/src/engine.cpp: Also make sure to ignore descriptions unless
  set explicitly.

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Updated surface engine -- uses
  single color mesh for renderQuick. Solves PR# 2619826.

  * libavogadro/src/color.h: Fix bug with Surface color always being black --
  properly assign QColor using floats.

  * libavogadro/src/toolgroup.cpp: Fix localization issue with tool names and
  settings.

2009-02-25  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/main.cpp: Inject BABEL_DATADIR into the process environment on
  Windows to address a bug where OpenBabel cannot find its data files.

  * cmake/modules/AvoCPack.cmake, cmake/modules/AvoCPackOptions.cmake.in:
  Updates to the CPack build, more improvements on the way.

2009-02-25  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/engineprimitiveswidget.ui: Remove string mentioning "Engine"

  * libavogadro/src/engine.cpp: Don't save an alias unless the user set it.
  This allows changing language and properly updating engine names.

2009-02-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Don't update for renderPick()

  * libavogadro/src/glpainter.cpp: Remove stray color.apply()

2009-02-24  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/chargecolor.h,
  libavogadro/src/colors/distancecolor.cpp,
  libavogadro/src/colors/distancecolor.h: Add color by distance from atom 0
  (i.e., ignore atom index, just look at distances)

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/chargecolor.cpp, libavogadro/src/colors/chargecolor.h:
  Add color by charge: negative = red, positive = blue

2009-02-24  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.cpp: Fixed bug 2635034 - assigning primitives to an
  engine now works as expected again.

2009-02-24  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gamessinputdialog.ui: Remove time limit and memory
  limit from GAMESS input generator. Not necessary.

  * cmake/modules/PythonDeps.cmake: Use boost 1.38 over 1.37.

  * i18n/avogadro.pot, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: More translation updates from
  Launchpad.

  * libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessinputdialog.ui: String updates.

  * libavogadro/src/extensions/propmodel.cpp: Go back to proper string
  translation for units.

  * libavogadro/src/extensions/gaussianinputdialog.ui,
  libavogadro/src/extensions/qcheminputdialog.ui: UI consistency -- use "..."
  for showing a new dialog box.

  * libavogadro/src/engines/labelengine.cpp: Set default to label atom numbers,
  and not bonds.

  * avogadro/src/engineitemmodel.cpp: Make sure to *always* resort the entire
  engine list. Seems to fix order issues.

  * avogadro/src/engineitemmodel.cpp, avogadro/src/engineitemmodel.h: Make sure
  to update when an engine is updated (e.g., enabled by an extension).

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: Enable the force engine when
  displaying vibrations.

  * libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h: Update MOPAC dialog to show a
  progress dialog and allow cancelling jobs.

  * libavogadro/src/molecule.cpp: Don't use a default filename -- it should be
  set by other code. Otherwise, our recent files menu gets fouled up.

  * libavogadro/src/engine.cpp: Use empty strings for efficiency.

  * libavogadro/src/engines/labelengine.cpp: For now, be consistent with atom
  index -- display index starting at 1 to user.

  * libavogadro/src/extensions/pythonterminal.h: Missed python terminal when
  updating extension strings.

2009-02-24  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp: Update GLWidget to engine identifiers.

  * libavogadro/src/extensions/propmodel.cpp: Cleanups of strings (e.g.,
  Angstrom unit) and warnings.

  * libavogadro/src/extensions/orbitaldialog.cpp: Use identifiers to find
  Orbitals and Surface engines.

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h: Use
  identifiers to check plugins -- won't change with translations.

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h: Fix settings -- don't
  automatically save aliases and descriptions. Empty strings are handled
  correctly.

2009-02-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro.pot: Update POT file after string cleanup.

  * i18n/avogadro_ar.ts, i18n/avogadro_ca.ts, i18n/avogadro_cs.ts,
  i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fi.ts, i18n/avogadro_fr.ts, i18n/avogadro_it.ts,
  i18n/avogadro_nl.ts, i18n/avogadro_pl.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sv.ts, i18n/avogadro_zh_CN.ts,
  i18n/avogadro_zh_TW.ts: Update translations after recent string cleanup.

  * libavogadro/src/extension.h,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/fileimportextension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/povrayextension.h,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/shaderextension.h,
  libavogadro/src/extensions/templateextension.h,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/vibrationextension.h,
  libavogadro/src/extensions/wiitrackextension.h: String cleanup for
  extensions.

  * libavogadro/src/engine.h, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.h, libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h: Further cleanups of
  strings/names/descriptions with engines, being consistent with other plugins.

  * libavogadro/src/color.h, libavogadro/src/colors/elementcolor.h,
  libavogadro/src/colors/indexcolor.h, libavogadro/src/colors/residuecolor.h,
  libavogadro/src/colors/residuecolorsettings.ui: String update for color
  plugins.

  * libavogadro/src/engine.h, libavogadro/src/tool.h,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h: String cleanup for tools -- similar
  to engines.

2009-02-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawtool.cpp: Prevent a crash in the drawtool while
  dragging (left mousebutton pressed) and pressing the right mouse button.

2009-02-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engine.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h:
  Cleanup of engine translatable strings. Macros only define names,
  identifiers, and descriptions once.

2009-02-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/cartoonengine.cpp,
  libavogadro/src/engines/cartoonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Split RibbonEngine into its original
  ribbon only and the experimental new CartoonEngine.

  * libavogadro/src/protein.cpp: Protein::extractFromPDB(): extract more helix
  types and sheets.

  * libavogadro/src/molecule.cpp: Molecule::setOBMol(): use Residue::setChainID

  * libavogadro/src/residue.cpp, libavogadro/src/residue.h: Add
  Residue::chainID / Residue::setChainID (note: this is not always the same as
  the chainNumber. Chains often get ids like 'A', 'B', ... but also ' ')

  * libavogadro/src/protein.cpp, libavogadro/src/protein.h: Protein: Use HELIX
  records from pdb file when available

2009-02-23  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitalextension.cpp: Fixed possible crash if no
  orbital engine was loaded.

  * avogadro/src/CMakeLists.txt, libavogadro/src/extensions/basisset.h,
  libavogadro/src/painter.h, libavogadro/src/periodictableview.cpp,
  libavogadro/src/periodictableview.h, libavogadro/src/primitive.h: Some more
  fixes and small changes.

  * cmake/modules/AvoCPack.cmake, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Several
  small fixes to classes. Made Python packaging on Windows optional.

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/drawcommandtest.cpp,
  libavogadro/tests/hydrogenscommandtest.cpp,
  libavogadro/tests/moleculetest.cpp, libavogadro/tests/neighborlisttest.cpp:
  Small updates to some tests. Disabled hydrogens test for now - moc issues.

2009-02-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Improve helix rendering...

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: RibbonEngine: Improve helix
  rendering...

  * libavogadro/src/tools/drawcommand.cpp: DeleteAtomDrawCommand: don't copy
  the molecule, the command now holds all info needed to add the atom again
  (including it's bonds to heavy atom neighbors)

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: improve 4-turn helix rendering,
  currently the points are rendered as spheres. These points can be used to
  generator a nurbs or mesh...

  * avogadro/src/mainwindow.cpp: Make sure to select navigate tool when opening
  avogadro with a molecule

  * libavogadro/tests/drawcommandtest.cpp: More drawing command unit tests

2009-02-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/tests/drawcommandtest.cpp,
  libavogadro/tests/hydrogenscommandtest.cpp: update unit tests

  * libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/tests/hydrogenscommandtest.cpp: Fix HydrogensCommand (bug
  #2624046)

  * libavogadro/tests/CMakeLists.txt,
  libavogadro/tests/hydrogenscommandtest.cpp: Add unit test for
  HydrogensCommand

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: continue working on drawing commands

  * libavogadro/src/tools/drawcommand.cpp: DeleteAtomDrawCommand: Use
  Pre/PostCommand instead of copying the molecule every time

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: Continue working on DrawCommands...

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: AddBondDrawCommand &
  ChangeBondOrderDrawCommand: Use AdjustHydrogens[Pre/Post]Command + unit tests

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: More unit testing and improvements for
  DrawCommands

2009-02-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp,
  libavogadro/tests/drawcommandtest.cpp: Unit tests for AddAtomDrawCommand,
  ChangeElementDrawCommand and DeleteAtomDrawCommand. All three pass, but
  DeleteAtom only because it copies the molecules. AddAtom and ChangeElement
  already use the Pre/Post Commands.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Molecule: Also
  (optionally) reuse bond ids when adding hydrogens.

  * libavogadro/tests/CMakeLists.txt, libavogadro/tests/drawcommandtest.cpp:
  Add DrawCommandTest: unit testing for the Draw tool's QUndoCommands

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h:
  Add AdjustHydrogensPreCommand class, use this QUndoCommand before performing
  one of the real commands (ChangeElementDrawCommand, ...). Add
  AdjustHydrogensPostCommand class, use this QUndoCommand after performing one
  of the real commands (ChangeElementDrawCommand, ...).

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Molecule:
  (changes from DrawCommandTest) * bugfix in Molecule::operator=(...): call
  Atom::addBond * change addHydrogens(...) to optionally specify the hydrogen
  ids. This will be used by the AdjustHydrogens[Pre/Post]Command in the future.

  * libavogadro/src/python/atom.cpp, libavogadro/src/python/bond.cpp,
  libavogadro/src/python/main.cpp: Add some missing python
  functions/properties: * Atom::residue * Atom::residueId * Bond::beginAtom *
  Bond::endAtom Actualy export MoleculeList in main.cpp

  * libavogadro/src/pythonextension.cpp: PythonExtension: Fix a bug where the
  PythonExtension always assumes performAction() returns a QUndoCommand

  * libavogadro/src/bond.cpp, libavogadro/src/bond.h: Implement Bond::midPos().

2009-02-20  Simon Ochsenreither <soc@desktop06.(none)>

  * libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/tools/python/template.py: Python 3 fixes (automated)

2009-02-19  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Better window menu logic (check for this,
  rather than name).

  * libavogadro/src/pluginmanager.cpp: Remove inadvertant debugging message.

2009-02-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * cmake/modules/AvoCPack.cmake, libavogadro/src/python/swig.cpp: Changes from
  win32 build...

2009-02-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/pluginmanager.cpp: Change Mac search path to match current
  install location.

  * avogadro/src/mainwindow.cpp: Make sure to test that menus have items before
  we look for extra separators. Prevents a crash. (For example, if no plugins
  are loaded, we have empty menus!)

2009-02-18  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, libavogadro/src/pluginmanager.cpp: First pass at using the
  avogadro binary location to locate plugins. Allows for multiple build
  directories and no environment variables, relocatable installs and all that
  good stuff. Feedback appreciated, does mean our wiki pages need updating.
  Also need to do this for scripts etc.

2009-02-18  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h: Use the new
  Extension::moleculeChanged() signal to handle reading new files.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/extension.h: Add new signal for extensions opening a molecule
  underneath a MainWindow.

  * avogadro/src/enginelistview.cpp: Use alternating row colors -- looks
  better.

2009-02-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/mopacinputdialog.cpp: Modify to generate cleaner
  MOPAC input syntax. I'll need to verify tomorrow.

2009-02-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/gaussianfchk.cpp: Changes to the GaussianFchk
  class, now with much more error checking. This should make the formatted
  checkpoint parsing much more resilient. Need to spend some more time with our
  parsing classes to improve resilience and fault detection.

2009-02-17  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/mopacinputdialog.cpp,
  libavogadro/src/extensions/mopacinputdialog.h,
  libavogadro/src/extensions/mopacinputdialog.ui: Initial pass at a MOPAC
  generator, including local calculations.

  * libavogadro/src/camera.cpp: Don't attempt to find a fitting plane for one
  atom. Fixes problem with single atom files never being drawn.

  * libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h: Update density matrix import to
  handle columns (e.g, Q-Chem fchk files)

2009-02-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/gaussianfchk.cpp: Finally solved the GTO electron
  density bug! It was a single stray readline statement. The underlying
  mathematics was all correct. Spotted an issue with the S normalization which
  is now fixed too.

2009-02-17  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, i18n/avogadro_ar.ts, i18n/avogadro_ca.ts,
  i18n/avogadro_cs.ts, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fi.ts, i18n/avogadro_fr.ts,
  i18n/avogadro_it.ts, i18n/avogadro_ja.ts, i18n/avogadro_ko.ts,
  i18n/avogadro_nb.ts, i18n/avogadro_nl.ts, i18n/avogadro_pl.ts,
  i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts, i18n/avogadro_ru.ts,
  i18n/avogadro_sv.ts, i18n/avogadro_tr.ts, i18n/avogadro_uk.ts,
  i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Update with latest Launchpad
  translations.

  * scripts/installer/avogadro.ico: Update installer icon with much higher
  resolution one (from avogadro/src/icons/)

  * libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp: Set default filenames from
  molecule name and typical extension.

2009-02-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix bug with new Window menu and hide/show
  windows on Mac.

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/engines/orbitalengine.cpp: Fix bug with colors always
  appearing black. New gradient method was preferred over normal "set"
  function.

  * avogadro/src/mainwindow.cpp: Use fileName() instead of full path for Mac
  Window menu.

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Added a real
  "Window" menu on Mac OS X.

2009-02-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Add additional "polish" to menus -- eliminate
  trailing (or initial) separators. Remove any duplicate separators (i.e., two
  in a row)

  * avogadro/src/mainwindow.cpp: Fix Mac bug reported by Ian Davis -- when
  showing a "closed" window, reset the camera.

2009-02-16  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Save file dialog paths (e.g., default
  directory for open and save dialogs).

  * libavogadro/src/extensions/gaussianinputdialog.cpp: Default to using the
  molecule's filename + .com and rewrite checkpoint name to match.

  * authors.txt, authors.xml, avogadro/COPYING, avogadro/README, gpltemplate:
  Remove unused files.

  * CMakeLists.txt, cmake/modules/AvoCTestConfig.cmake,
  cmake/modules/CTestConfig.cmake: Look for cmake files as "modules"

  * libavogadro/src/extensions/shaderextension.h: Add identifier to shader
  extension. (Hopefully the last missing identifier.)

  * AvoCPack.cmake, CTestConfig.cmake, PythonDeps.cmake,
  cmake/modules/AvoCPack.cmake, cmake/modules/CTestConfig.cmake,
  cmake/modules/PythonDeps.cmake: Move cmake files into cmake directory (to
  clean up top-level directory). Adjust PythonDeps to handle Boost 1.38.

2009-02-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/moleculelist.cpp,
  libavogadro/src/python/moleculelist.h: Fix python module linking. Split
  MoleculeList into new compile unit. Ensure correct moc file is included
  (previously used any "molecule.moc"!)

  * libavogadro/src/CMakeLists.txt: ignore libavogadro translations right now
  -- need to split library vs. app i18n

2009-02-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt, libavogadro/src/engines/iso.cpp,
  libavogadro/src/engines/iso.h: Removed the retired iso code, superseded by
  new MeshGenerator class.

  * AvoCPack.cmake, CMakeLists.txt, avogadro/CMakeLists.txt,
  avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  libavogadro/CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/extensions/CMakeLists.txt, libavogadro/src/primitive.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/tests/CMakeLists.txt: Clean
  ups to the build system, bumped the version number to 0.9.1 and a few small
  fixes.

2009-02-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/mesh.cpp, libavogadro/src/primitive.cpp: Small improvements
  to initialisation.

  * libavogadro/src/molecule.cpp: Removed superfluous locking code.

  * libavogadro/src/extensions/orbitalextension.cpp: Cleaned up the destructor
  and setMolecule code a little.

  * libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Finally tracked down that bug, I had
  not propagated through my improvements in the underlying engine code to this
  engine. Working much better now.

2009-02-16  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/qlist.cpp: Rename
  "long int" to simply "long" 

  * libavogadro/src/engines/bsdyengine.cpp: Fix problem with half-checked "Show
  Multiple Bonds" checkbox and default of transparency after recent patch. 

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt:
  Obey -DENABLE_PYTHON=FALSE for building python-free even when dependencies
  are present. 

2009-02-15  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/qlist.cpp: Rename
  "long int" to simply "long"

  * libavogadro/src/engines/bsdyengine.cpp: Fix problem with half-checked "Show
  Multiple Bonds" checkbox and default of transparency after recent patch.

2009-02-15  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, libavogadro/src/atom.cpp,
  libavogadro/src/atom.h, libavogadro/src/bond.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/selectextension.cpp, libavogadro/src/fragment.cpp,
  libavogadro/src/fragment.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/neighborlist.cpp,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h,
  libavogadro/src/residue.cpp, libavogadro/src/residue.h,
  libavogadro/src/tools/selectrotatetool.cpp: Several fixes to type names and a
  few clean ups.

2009-02-15  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt:
  Obey -DENABLE_PYTHON=FALSE for building python-free even when dependencies
  are present.

2009-02-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdysettingswidget.ui: Applied an adapted patch from
  Magnus Lundborg. Corrected some issues with render order and indentation.
  Adds transparency support to the ball and stick engine.

  * avogadro/src/mainwindow.cpp: Previous layout was not perfect. This one
  looks about the same as before.

  * avogadro/src/mainwindow.cpp: Fixed the layout issues I think. The tools and
  engines dialogs should always use the minimum amount of space.

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h: The position function
  should take unsigned ints.

  * libavogadro/src/extensions/orbitalextension.cpp: Some cleanups for the
  progress dialogs, added experimental electron density calculation for GTOs
  although there is a problem with the calculation.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp: Now reading the SCF density
  matrix, added the code to calculate the electron density. There is a problem
  and so I need to go back and take another look at the equations. Made quite a
  few optimisations to the MO calculations and improved the data layout
  significantly.

  * libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: Corrected incorrect calculation of
  the electron density for slaters.

  * libavogadro/src/extensions/orbitaldialog.cpp: Fixed a typo causing the
  combos not to remember the last position.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Use guarded pointers to store the
  current mesh objects, fixes potential crashes if the mesh objects are
  removed.

2009-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/neighborlist.cpp, libavogadro/src/neighborlist.h:
  OrbitalExtension: use NeighborList class for ESP approximation...

2009-02-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/neighborlist.h, libavogadro/src/pluginmanager.cpp: A few
  small fixes for issues pointed out by krazy2.

2009-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pythonengine.cpp: bug fix for PythonEngine

  * libavogadro/src/extensions/python/example.py,
  libavogadro/src/pythonextension.cpp: Add message(const QString &) signal to
  PythonExtension

  * libavogadro/src/pythonengine.cpp, libavogadro/src/pythonengine.h,
  libavogadro/src/pythontool.cpp, libavogadro/src/pythontool.h: Add read/write
  Settings to PythonTool & PythonEngine

  * libavogadro/src/extensions/python/example.py,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythonextension.h: Add
  dockWidget to PythonExtension

  * libavogadro/src/python/engine.cpp, libavogadro/src/python/main.cpp: minor
  python improvements

2009-02-15  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Better adjustment for minimizing tool and
  display docks. Rather than using fixed size, use QSizePolicy on the
  underlying widgets. 

2009-02-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Better adjustment for minimizing tool and
  display docks. Rather than using fixed size, use QSizePolicy on the
  underlying widgets.

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h,
  libavogadro/src/colors/residuecolorsettings.ui, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/surfaceengine.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/povpainter.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/line.cpp, libavogadro/src/line.h, libavogadro/src/plugin.cpp,
  libavogadro/src/plugin.h, libavogadro/src/point.cpp, libavogadro/src/point.h,
  libavogadro/src/python/plugin.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/eyecandy.h, libavogadro/src/tools/manipulatetool.cpp:
  Update to add color settings (e.g., residue coloring). Required change of
  Plugin to inherit QObject, plus a variety of changes to assigning Color
  objects.

2009-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/sip.cpp, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythonextension.h: Add readSettings/writeSettings to
  pythonextension (TODO: Tool & Engine)

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/python/example.py: Python Extension example

  * libavogadro/src/engines/python/cubepoints.py,
  libavogadro/src/python/main.cpp, libavogadro/src/python/molecule.h,
  libavogadro/src/python/sip.cpp: more python...

2009-02-14  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/molecule.cpp, libavogadro/src/pythonengine.cpp,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythoninterpreter.cpp,
  libavogadro/src/pythontool.cpp: More python stuff

  * libavogadro/src/python/molecule.cpp, libavogadro/src/python/molecule.h:
  Remove unneeded function

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/molecule.h, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/swig.cpp, libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/camera.py,
  libavogadro/src/python/unittest/color.py,
  libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/extension.py,
  libavogadro/src/python/unittest/fragment.py,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/python/unittest/primitivelist.py,
  libavogadro/src/python/unittest/residue.py,
  libavogadro/src/python/unittest/tool.py,
  libavogadro/src/python/unittest/toolgroup.py,
  libavogadro/src/pythonengine.cpp, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythontool.cpp: Various python updates. All ownership issues
  should be solved now...

2009-02-14  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colors/elementcolor.h, libavogadro/src/colors/indexcolor.h,
  libavogadro/src/colors/residuecolor.h, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.h, libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h, libavogadro/src/extension.h,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/fileimportextension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/povrayextension.h,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/pythonterminal.h,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/vibrationextension.h, libavogadro/src/plugin.h,
  libavogadro/src/python/plugin.cpp, libavogadro/src/pythonengine.cpp,
  libavogadro/src/pythonengine.h, libavogadro/src/pythonextension.cpp,
  libavogadro/src/pythonextension.h, libavogadro/src/pythontool.cpp,
  libavogadro/src/pythontool.h, libavogadro/src/tool.h,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h: Add unique, untranslated
  identifiers for plugins and factories. These will be used to ensure config
  files do not crash when changing languages.

2009-02-12  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/tools/autoopttool.cpp: Fix layout of auto-opt tool. Looked
  horrible on Mac. 

2009-02-11  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: Display a warning if no
  displacements exist (e.g. Gaussian output with OB-2.2.0)

2009-02-11  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/tools/autoopttool.cpp: Fix layout of auto-opt tool. Looked
  horrible on Mac.

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

  * libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/orbitalextension.cpp: Adapted orbital extension to
  use the slimmed down BasisSet class.

  * libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h: Added in a function to read in the
  SCF density matrix.

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h: Big changes to the Gaussian type basis
  sets. Flattened out the data structure in order to be more efficient and
  flexible. Got rid of most structs and also removed old experimental code that
  is no longer used. Some of the variable names possibly need improvements and
  I still need to add the electron density calculation in.

2009-02-10  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h: Handle Q-Chem checkpoints with
  16-character fields. (Grrr.)

  * libavogadro/src/extensions/orbitalextension.cpp: Go through the current
  directory to look for a .fchk or .aux or similar file. Now you can open .out
  or .g03 and find the right orbital file. Still needs a warning if we're not
  opening our current file!

  * libavogadro/src/extensions/orbitalextension.cpp: Add TODO on reading
  different filenames.

  * avogadro/src/mainwindow.cpp: Add size policies to tools and engines --
  minimum sizes to maximize GLWidget space. Seems to fix layout problems I had
  with Qt-4.5.

2009-02-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitalextension.cpp: Fixed another crasher -
  only modify engine settings if one of the correct type exists.

2009-02-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/molecule.cpp: Add python bindings for Molecule's
  copy constructor.

2009-02-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Removed a few more functions that
  are not used anymore.

2009-02-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/pythonextension.cpp, libavogadro/src/pythonextension.h: Move
  PythonExtension to libavogadro

2009-02-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Added some extra hooks to
  colour by ESP estimated from partial charges. More mappings onto surfaces to
  come, tested on several test VdW surfaces.

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Removed most of the old code, this
  has been migrated to the orbital extension. This engine is now much simpler
  and should probably remain this way.

2009-02-07  Marcus D. Hanwell <marcus@cryos.org>

  * AvoCPack.cmake, CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/pluginsettings.cpp, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/pluginmanager.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp: Move our Windows packaging to
  CPack. Various improvements and changes to the Windows build process,
  bringing it more into line with other architectures.

2009-02-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h: Some cleanups on the unit
  cell code, cannot use trunc as Windows does not have this function. Static
  cast to induce rounding seems to be an acceptable subsititute.

2009-02-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix crash when opening files on Mac from the
  command line.

  * libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp: A variety of cleanups in
  the vibration extension, including UI layout fixes, calls for molecule/widget
  update, etc.

  * libavogadro/src/engines/bsdysettingswidget.ui: Fix layout of ball-and-stick
  settings (should all go together when sized to a larger box -- matches
  default OS layout).

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/vibrationdialog.cpp,
  libavogadro/src/extensions/vibrationdialog.h,
  libavogadro/src/extensions/vibrationdialog.ui,
  libavogadro/src/extensions/vibrationextension.cpp,
  libavogadro/src/extensions/vibrationextension.h: New extension to begin
  animating vibrations. Right now, will add force vectors for viewing by the
  force engine. Data is read in through Q-Chem files currently and latest 2.2.x
  branch of Open Babel. More formats (and animations) to come.

  * libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h: Clean up code a bit to more modular
  calls, less casting pointers.

  * libavogadro/src/extensions/h2methylextension.cpp: Fix typo with plugin
  declared as hydrogen, not h2methyl

  * avogadro/src/aboutdialog.cpp, avogadro/src/aboutdialog.h,
  avogadro/src/addenginedialog.cpp, avogadro/src/addenginedialog.h,
  avogadro/src/application.cpp, avogadro/src/application.h,
  avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/enginecolorswidget.cpp, avogadro/src/enginecolorswidget.h,
  avogadro/src/engineitemmodel.cpp, avogadro/src/engineitemmodel.h,
  avogadro/src/enginelistview.cpp, avogadro/src/enginelistview.h,
  avogadro/src/engineprimitiveswidget.cpp,
  avogadro/src/engineprimitiveswidget.h, avogadro/src/flattabwidget.cpp,
  avogadro/src/flattabwidget.h, avogadro/src/icontabwidget.cpp,
  avogadro/src/icontabwidget.h, avogadro/src/importdialog.cpp,
  avogadro/src/importdialog.h, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/pluginitemmodel.cpp, avogadro/src/pluginitemmodel.h,
  avogadro/src/pluginlistview.cpp, avogadro/src/pluginlistview.h,
  avogadro/src/pluginsettings.cpp, avogadro/src/pluginsettings.h,
  avogadro/src/primitivetreeview.cpp, avogadro/src/primitivetreeview.h,
  avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/atomdelegate.h,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.h,
  avogadro/src/projectdelegates/labeldelegate.cpp,
  avogadro/src/projectdelegates/labeldelegate.h,
  avogadro/src/projectdelegates/moleculedelegate.cpp,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.h,
  .../src/projectdelegates/selectiondelegate.cpp,
  avogadro/src/projectdelegates/selectiondelegate.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreeitem.cpp,
  avogadro/src/projecttreeitem.h, avogadro/src/projecttreemodel.cpp,
  avogadro/src/projecttreemodel.h, avogadro/src/projecttreemodeldelegate.cpp,
  avogadro/src/projecttreemodeldelegate.h, avogadro/src/savedialog.cpp,
  avogadro/src/savedialog.h, avogadro/src/settingsdialog.cpp,
  avogadro/src/settingsdialog.h, libavogadro/src/atom.cpp,
  libavogadro/src/atom.h, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/boxcontrol.cpp, libavogadro/src/boxcontrol.h,
  libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h, libavogadro/src/colors/indexcolor.cpp,
  libavogadro/src/colors/indexcolor.h, libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h, libavogadro/src/cube.cpp,
  libavogadro/src/cube.h, libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h, libavogadro/src/elementtranslate.cpp,
  libavogadro/src/elementtranslate.h, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h, libavogadro/src/engines/iso.cpp,
  libavogadro/src/engines/iso.h, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationdialog.h,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.h,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/constraintsmodel.h,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/fileimportextension.h,
  libavogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/extensions/forcefielddialog.h,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  .../src/extensions/gamessefpmatchdialog.cpp,
  libavogadro/src/extensions/gamessefpmatchdialog.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/highlighter.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/liganddialog.cpp,
  libavogadro/src/extensions/liganddialog.h,
  libavogadro/src/extensions/linmorphdialog.cpp,
  libavogadro/src/extensions/linmorphdialog.h,
  libavogadro/src/extensions/linmorphextension.cpp,
  libavogadro/src/extensions/linmorphextension.h,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/pocketdialog.cpp,
  libavogadro/src/extensions/pocketdialog.h,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/povrayextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaderextension.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vdwsurface.h,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/extensions/wiitrackextension.h,
  libavogadro/src/filetreeitem.cpp, libavogadro/src/filetreeitem.h,
  libavogadro/src/fragment.cpp, libavogadro/src/fragment.h,
  libavogadro/src/global.cpp, libavogadro/src/global.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/idlist.cpp, libavogadro/src/idlist.h,
  libavogadro/src/line.cpp, libavogadro/src/line.h, libavogadro/src/mesh.cpp,
  libavogadro/src/mesh.h, libavogadro/src/meshgenerator.cpp,
  libavogadro/src/meshgenerator.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/navigate.cpp,
  libavogadro/src/navigate.h, libavogadro/src/neighborlist.cpp,
  libavogadro/src/neighborlist.h, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h, libavogadro/src/painterdevice.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/plugin.cpp, libavogadro/src/plugin.h,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/point.cpp, libavogadro/src/point.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h,
  libavogadro/src/pythonengine.cpp, libavogadro/src/pythonengine.h,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythoninterpreter.h,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h,
  libavogadro/src/pythontool.cpp, libavogadro/src/pythontool.h,
  libavogadro/src/residue.cpp, libavogadro/src/residue.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/aligntool.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/quaternion.cpp, libavogadro/src/tools/quaternion.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/tools/skeletontree.h,
  libavogadro/src/undosequence.cpp, libavogadro/src/undosequence.h,
  libavogadro/tests/moleculetest.cpp, libavogadro/tests/neighborlisttest.cpp:
  Fix homepage URL in headers and other URL strings.

2009-02-03  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix crash with copy and nothing selected.
  Thanks to Marek Freindorf.

2009-02-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/pluginitemmodel.cpp, avogadro/src/pluginitemmodel.h,
  avogadro/src/pluginsettings.cpp: PluginSettings: detect if plugins need to be
  reloaded 

2009-02-03  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/molecule.cpp: Quick fixes for silly crashes when dealing
  with OBGenericData syncing.

2009-02-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/pluginitemmodel.cpp, avogadro/src/pluginitemmodel.h,
  avogadro/src/pluginsettings.cpp: PluginSettings: detect if plugins need to be
  reloaded

2009-02-03  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/icons/avogadro.ico: Another ICO file with multiple
  resolutions, including Windows Vista.

  * avogadro/src/icons/avogadro.ico: Updated windows icon.

2009-02-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/molecule.cpp: Cache any OBVibrationData in an OBMol

  * libavogadro/src/molecule.cpp: Sync OBPairData in a molecule to and from the
  OBMol

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/forceengine.cpp, libavogadro/src/molecule.cpp:
  Brought back the force engine, including support for Atom::forceVector()
  which will be used as well by vibrations.

2009-02-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp: Fix crash with new custom data
  support when opening molecules without custom data. 

2009-02-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp: Fix crash with new custom data
  support when opening molecules without custom data.

2009-02-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/protein.cpp,
  libavogadro/src/protein.h: Various updates to Protein class + basic rendering
  of 3 and 4 turn helixes in ribbon engine 

2009-02-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/protein.cpp: various updates to Protein class 

  * libavogadro/include/avogadro/protein.h, libavogadro/src/molecule.cpp,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h: * Add Protein class
  to handle proteins specific molecule properties (2nd Structure) * Molecule:
  Fix chainNumbers 

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/protein.cpp,
  libavogadro/src/protein.h: Various updates to Protein class + basic rendering
  of 3 and 4 turn helixes in ribbon engine

  * libavogadro/src/protein.cpp: various updates to Protein class

2009-02-03  Geoff Hutchison <geoff@geoffhutchison.net>

  * testfiles/ch3oh-nmr.qcout: Added Q-Chem NMR example -- works only with
  latest OB-2.2.1 code.

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Add "custom data" atom label,
  which will show custom data, when present. (Eventually should also add names
  of custom data to combo box.) Works perfectly with code requested by Q-Chem
  for NMR shifts.

  * libavogadro/src/atom.cpp: Add custom properties to atoms based on sync
  to/from OBPairData.

  * libavogadro/src/molecule.cpp: Fix iterators -- no need to use
  OBNodeBase/OBEdgeBase and casts anymore.

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  libavogadro/src/atom.h, libavogadro/src/extensions/constraintsmodel.h,
  libavogadro/src/primitive.h, libavogadro/src/primitiveitemmodel.h: Remove
  un-necessary #include <QAbstractItemModel> in primitive.h We should make a
  pass to remove un-needed #includes.

2009-02-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/include/avogadro/protein.h, libavogadro/src/molecule.cpp,
  libavogadro/src/protein.cpp, libavogadro/src/protein.h: * Add Protein class
  to handle proteins specific molecule properties (2nd Structure) * Molecule:
  Fix chainNumbers

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

  * avogadro/src/pluginsettings.h: Removed symbol export as this is not part of
  libavogadro.

  * CMakeLists.txt, PythonDeps.cmake, cmake/modules/FindAllPython.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/pluginmanager.cpp: Tidied up
  our build files a little more, ensured that Avogadro will build without
  Python.

2009-02-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h: HBondEngine: use new NeighborList
  class

2009-02-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/propextension.cpp, libavogadro/src/molecule.cpp:
  Fix some compiler warnings...

2009-02-01  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/pluginsettings.ui: Fixed include header location.

2009-02-01  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/pluginsettings.ui: change header for PluginListView from
  avogadro/pluginlistview.h to pluginlistview.h in the .ui file

  * avogadro/src/mainwindow.cpp, avogadro/src/pluginitemmodel.cpp,
  avogadro/src/pluginitemmodel.h, avogadro/src/pluginlistview.cpp,
  avogadro/src/pluginlistview.h, avogadro/src/pluginsettings.cpp,
  avogadro/src/pluginsettings.h, avogadro/src/pluginsettings.ui,
  avogadro/src/settingsdialog.cpp,
  libavogadro/include/avogadro/pluginlistview.h,
  libavogadro/include/avogadro/pluginsettings.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/neighborlist.cpp,
  libavogadro/src/neighborlist.h, libavogadro/src/pluginitemmodel.cpp,
  libavogadro/src/pluginitemmodel.h, libavogadro/src/pluginlistview.cpp,
  libavogadro/src/pluginlistview.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/pluginsettings.cpp,
  libavogadro/src/pluginsettings.h, libavogadro/src/pluginsettings.ui,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h: Move Plugin
  settings widget to avogadro.

  * libavogadro/src/pythonengine.cpp, libavogadro/src/pythonengine.h: Forgot
  pythonengine.*

  * libavogadro/src/python/engine.cpp: Add readSettings/writeSettings to
  Engine's python bindings

  * libavogadro/include/avogadro/neighborlist.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/neighborlist.cpp,
  libavogadro/src/neighborlist.h, libavogadro/tests/CMakeLists.txt,
  libavogadro/tests/neighborlisttest.cpp: Add NeighborList class + unit tests
  (for this class). To Marcus: Feel free to change the
  libavogadro/tests/CMakeLists.txt file

  * libavogadro/src/engine.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.h, libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/engines/pythonsettingswidget.ui,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/pythontool.h,
  libavogadro/src/tools/CMakeLists.txt: Move PythonEngine to libavogadro

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreeeditor.h,
  avogadro/src/projecttreeeditor.ui, avogadro/src/settingsdialog.cpp,
  avogadro/src/settingsdialog.h, libavogadro/include/avogadro/pluginsettings.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/plugindialog.cpp,
  libavogadro/src/plugindialog.h, libavogadro/src/plugindialog.ui,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/pluginsettings.cpp, libavogadro/src/pluginsettings.h,
  libavogadro/src/pluginsettings.ui: New configuration dialog

  * avogadro/src/settingsdialog.ui: Create the icon list based configuration
  dialog.

2009-01-31  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h,
  libavogadro/src/pythontool.cpp: Add toolTip support to the PythonTool &
  remove some debug msgs

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythontool.cpp,
  libavogadro/src/pythontool.h: Continue moving PythonTool to libavogadro.
  Re-added the PythonToolFactory which allow us to use python tools just like
  any other C++ tools. In other words, we create a PythonToolFactory for each
  script and the ..Factory gets the name and description from running the
  script. You can now enable/disable python tools.  still TODO: * set the
  activate action's tooltip * icons??

2009-01-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/CMakeLists.txt: Move pythontool to libavogadro

  * avogadro/src/importdialog.cpp,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/plugin.cpp,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/manipulatetool.cpp: Fix compiler warnings

2009-01-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.cpp: Fixed compiler warning and improved the logic a
  little in the primitives() function.

2009-01-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/python.png,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h,
  libavogadro/src/pythontool.cpp, libavogadro/src/pythontool.h,
  libavogadro/src/pythontool.qrc, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/python.png, libavogadro/src/tools/pythontool.cpp,
  libavogadro/src/tools/pythontool.h, libavogadro/src/tools/pythontool.qrc:
  Move PythonTool (1)

2009-01-28  Albert DeFusco <albert@defusco.msg.chem.iastate.edu>

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.ui: I like more precision in my
  input files. I also like yellow hydrogen bonds

2009-01-28  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, CTestConfig.cmake: Added some initial CDash support, see
  http://www.cdash.org/CDashPublic/index.php?project=Avogadro for our new
  CDash.

2009-01-28  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/unitcellextension.cpp: Fixed up Fill Unit Cell
  -- creates all symmetry-defined atoms. Bonds may look strange, since
  "rebonding" is not attempted.

2009-01-27  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/unitcellextension.cpp: Updated fillUnitCell code
  which looks for duplicates. Still seems to miss a few "corner" cases with
  atoms at the corner of the unit cell.

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/glpainter.cpp: Fixes for Eigen cast warnings with
  Eigen-2.0rc1

2009-01-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianinputdialog.cpp: Fixed bug 2540166 -
  z-matrix is now generated correctly.

2009-01-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * CMakeLists.txt, cmake/modules/FindAllPython.cmake,
  cmake/modules/FindNumpy.cmake, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/sip.cpp,
  libavogadro/src/tools/CMakeLists.txt: Change the python dependency detection:
  All python dependencies are now in the cmake/modules/FindAllPython.cmake.
  Python support is only enabled when all dependencies (python interp+libs,
  boost python, sip, numpy) are found. Also, in the message saying X can't be
  found, I added the package names for debian/ubuntu. Perhaps we should do
  something similar for other distros/dependencies.

  * cmake/modules/FindBoostPython.cmake: remove old FindBoostPython.cmake (was
  needed for cmake 2.4)

  * libavogadro/src/python/sip.cpp: Python SIP initialization: Add more verbose
  error output...

2009-01-26  Geoff Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindOpenBabel2.cmake: From Carsten: KDE Commit from:
  Christian Ehrlicher <Ch.Ehrlicher@gmx.de> it's openbabel-2 on windows 

2009-01-25  Geoff Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindOpenBabel2.cmake: From Carsten: KDE Commit from:
  Christian Ehrlicher <Ch.Ehrlicher@gmx.de> it's openbabel-2 on windows

2009-01-24  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp: When picking, add a bit of a "slop"
  factor to make it easier to hit an atom. Helps make drawing easier. 

  * libavogadro/src/tools/quaternion.cpp: Update to use squaredNorm for current
  Eigen. 

2009-01-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp: When picking, add a bit of a "slop"
  factor to make it easier to hit an atom. Helps make drawing easier.

  * libavogadro/src/tools/quaternion.cpp: Update to use squaredNorm for current
  Eigen.

2009-01-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp: MainWindowPrivate does require
  EIGEN_WITH_ALIGNED...

2009-01-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/python/eigen.cpp: replace WithAlignedOperatorNew with
  EIGEN_MAKE_ALIGNED_OPERATOR_NEW. This macro is available from version
  Eigen2-beta5 and up.

2009-01-23  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  Draw tool refinements. Do not add/delete hydrogens when manually drawing
  bonds with a new H atom. Do not bond to hydrogen atoms when dragging unless H
  atoms are manually selected as the new element. 

2009-01-22  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  Draw tool refinements. Do not add/delete hydrogens when manually drawing
  bonds with a new H atom. Do not bond to hydrogen atoms when dragging unless H
  atoms are manually selected as the new element.

  * avogadro/src/enginecolorswidget.cpp, avogadro/src/enginecolorswidget.ui:
  Add support for color settings widgets when present. 

2009-01-21  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/enginecolorswidget.cpp, avogadro/src/enginecolorswidget.ui:
  Add support for color settings widgets when present.

2009-01-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Listen for the Molecule::destroyed() signal to stop the AutoOpt Tool.
  (prevents crashes when closing avogadro while AutoOpt is running) 

2009-01-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Listen for the Molecule::destroyed() signal to stop the AutoOpt Tool.
  (prevents crashes when closing avogadro while AutoOpt is running)

  * scripts/installer/setup.nsi: update NSI installer script (windows) 

  * scripts/installer/setup.nsi: update NSI installer script (windows)

2009-01-20  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/engineitemmodel.cpp: Add tooltips to engine list. Engine
  descriptions need a lot of updating. 

2009-01-18  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/dipolesettingswidget.ui: Updated dipole engine which
  updates on-the-fly and handles recent changes. 

2009-01-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/molecule.cpp: Properly import dipole moments from Open
  Babel. 

2009-01-19  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/engineitemmodel.cpp: Add tooltips to engine list. Engine
  descriptions need a lot of updating.

2009-01-17  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/dipolesettingswidget.ui: Updated dipole engine which
  updates on-the-fly and handles recent changes.

  * libavogadro/src/molecule.cpp: Properly import dipole moments from Open
  Babel.

2009-01-15  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/unitcellextension.cpp: Minor fix to ensure all
  transformed atoms stay in the unit cell. 

2009-01-16  Carsten Niehaus <cniehaus@kde.org>

  * libavogadro/src/engines/CMakeLists.txt: Fix the build with Python. If
  Python is disabled Python-Boost should obviously also be disabled 

  * libavogadro/src/engines/CMakeLists.txt: Fix the build with Python. If
  Python is disabled Python-Boost should obviously also be disabled

2009-01-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp: Forgot to add test for whether there was a
  unit cell... Fixed a crash when loading molecules with no unit cell.

2009-01-14  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/extensions/unitcellextension.cpp: Minor fix to ensure all
  transformed atoms stay in the unit cell.

2009-01-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp: Make deep copies of the unit cell.

2009-01-14  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp: Fix broken signals BondAdded and BondUpdated.

  * libavogadro/src/tools/python.png: Updated python tool icon with real
  transparency. Found from:
  
  n-logo-master-v3-icon-32flat.png

2009-01-12  Marcus D. Hanwell <marcus@cryos.org>

  * INSTALL: Updated the install instructions.

2009-01-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/autoopttool.cpp: Remove "little red ball" in auto-opt
  tool and fix compile warning.

2009-01-12  Tim Vandermeersch <tim@ubuntu.(none)>

  * libavogadro/src/engine.cpp: add extra check to make sure m_pd is not 0
  (Engine::primitives())

  * libavogadro/src/python/eigen.cpp, libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/camera.py,
  libavogadro/src/python/unittest/eigen.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/glwidget.py: update python unit tests

2009-01-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.cpp: Changed signal to listen to
  for sliders - should capture all relevant changes now.

  * libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfacesettingswidget.ui,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.ui: Disabled parts of the dialog
  that need to be (re)implemented, removed obsolete parts. Fixed a bug with VdW
  surface generation.

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp: Improved the metadata put
  into the meshes - orbital engines can infer the pairs and also draw cube
  extents again.

  * libavogadro/src/mesh.h: Added extra metadata so that the engines and
  extensions can function more smoothly.

  * avogadro/src/mainwindow.cpp: Disabled detached views for now - needs more
  work to be useful.

  * libavogadro/src/tools/autoopttool.cpp: Changed so that all mouse release
  events also go to the navigate tool.

2009-01-12  Geoff Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/propextension.cpp: Remove separator (now added
  by hydrogens extension).

  * libavogadro/src/extensions/orbitaldialog.ui: Add a default value for
  isosurface cutoff. Should work OK for most orbitals.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Implement
  translation of molecules. Solves PR#2497081.

2009-01-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povpainter.cpp: Fixed a bug where the aspect
  ratio of the image was not saved correctly.

2009-01-10  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added extra slots
  for atom and bond changes. Fixes bug 2497037.

2009-01-09  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.ui: Change name of project dock to "Project Tree"
  to match "Project Tree Editor".

  * libavogadro/src/tools/autoopttool.cpp: Use UFF for the default force field
  (instead of Ghemical!). Should handle pretty much any element and
  coordination number.

  * libavogadro/src/tools/insertfragmentdialog.cpp: Expand fragments list to
  first level. (We should probably figure out how to save the expanded state.)

2009-01-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/main.cpp, libavogadro/src/global.cpp: Add correct paths for
  translation files on windows.

2009-01-09  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.ui: Add short tooltip about
  clicking to insert a fragment. Should address PR#1971923.

2009-01-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianextension.cpp: A few tweaks to the
  extension - should be renamed or split to reflect different input dialogs.

  * libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h: Various updates to the
  Gaussian dialog.

  * libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui: Various improvements to the
  Q-Chem dialog.

  * libavogadro/src/extensions/highlighter.cpp: Cleaned up the includes a
  little.

2009-01-09  Simon Ochsenreither <soc@desktop06.(none)>

  * avogadro/src/main.cpp: Translations-usable-without-install fix 

  * avogadro/src/main.cpp: export AVOGADRO_TRANSLATIONS if you don't want to
  install avo 

2009-01-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/primitive.cpp: Removed Eigen Regression include where not
  needed, changed it to the new Eigen/LeastSquares in molecule.cpp.

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/periodictableview.cpp, libavogadro/src/tools/drawtool.cpp:
  Ported to use the static ElementTranslator function rather than the global
  instance.

  * libavogadro/src/elementtranslate.cpp, libavogadro/src/elementtranslate.h:
  Changed to use a static member function rather than instantiating a global
  instance.

  * libavogadro/src/global.cpp, libavogadro/src/global.h: Some documentation
  updates and a little tidying up.

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/main.cpp, libavogadro/src/global.cpp: Added some extra debug
  output when translation files cannot be found.

  * avogadro/include/avogadro/extension.h: Removed orphaned include - moved to
  libavogadro months ago.

2009-01-08  Tim Vandermeersch <tim@ubuntu.(none)>

  * libavogadro/src/extensions/selectextension.h: Remove more code

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/namedselectionmodel.cpp,
  libavogadro/src/extensions/namedselectionmodel.h,
  libavogadro/src/extensions/selectextension.cpp: Remove obsolete code (named
  selections moved to project tree)

  * .../src/projectdelegates/selectiondelegate.cpp,
  avogadro/src/projectdelegates/selectiondelegate.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreemodel.cpp: Add a
  ProjectDelegate for named selections.

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Add a signal to
  the GLWidget to notify the project tree the named selections have changed
  (added, removed, renamed)

  * avogadro/src/mainwindow.cpp: call GLWidget::update() after setting the
  selection from the project tree

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/colorbutton.h: Reverted previous doc change on this file.
  Is this intended to be outside of our namespace?

  * Doxyfile, libavogadro/src/atom.h, libavogadro/src/bond.h,
  libavogadro/src/colorbutton.h, libavogadro/src/fragment.h,
  libavogadro/src/mesh.h, libavogadro/src/molecule.h,
  libavogadro/src/pythoninterpreter.h, libavogadro/src/residue.h,
  libavogadro/src/textrenderer.h: Various updates to improve the API
  documentation.

2009-01-08  Tim Vandermeersch <tim@ubuntu.(none)>

  * avogadro/src/projecttreeeditor.cpp: Add ';' on line 455...

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * doc/pdf/index.pdf: Removed PDF - it is autogenerated on the web site now.

  * libavogadro/src/CMakeLists.txt: Added global.h to installed headers.

2009-01-08  Tim Vandermeersch <tim@ubuntu.(none)>

  * libavogadro/src/global.h, libavogadro/src/python/eigen.cpp: define
  EIGEN_WORK_AROUND_QT_BUG_CALLING_WRONG_OPERATOR_NEW_FIXED_IN_QT_4_5 in
  global.h and include it where needed (only python/eigen.cpp)

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp: Found a divide by zero bug. Molecule radius
  was zero unless there was more than one atom in the molecule. Caused the
  camera perpective to break.

  * libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Removed the duplicate button
  from the dialog, changed the menu entry name to surfaces and cleaned up a few
  compiler warnings.

  * libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h:
  Updated the API docs and removed an unused function.

2009-01-08  Geoff Hutchison <babel@geoffhutchison.net>

  * Doxyfile, Doxyfileext, doc/mainpage.dox, libavogadro/src/global.cpp:
  Doxygen changes. Move mainpage documentation out of global.cpp and into
  doc/mainpage.dox. Updated to output to doc/api and be a bit more consistent
  with Eigen and other projects.

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

2009-01-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Few small fixes
  and updates. I think some of the new functions may need a little work but do
  seem to be working quite well.

2009-01-08  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/projectdelegates/atomdelegate.h,
  avogadro/src/projectdelegates/bonddelegate.h,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projecttreeeditor.h, avogadro/src/projecttreemodel.h,
  avogadro/src/projecttreemodeldelegate.h, avogadro/src/savedialog.cpp: A
  variety of small krazy fixes.

2009-01-08  Tim Vandermeersch <tim@ubuntu.(none)>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/dockingextension.h: remove obsolete files (Docking
  extension)

  * libavogadro/src/extensions/forcefieldextension.cpp: remove debugging output

  * avogadro/src/mainwindow.cpp: Make MainWindowPrivate inherit
  Eigen::WithAlignedOperatorNew

  * libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h: * Add the properties extension again
  (including conformers)  * update force field extension to make use of the
  added conformers code.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Small bug fixes
  for conformers + Add energies/setEnergies

  * avogadro/src/projecttreeeditor.cpp: Add ';' on line 455...

2009-01-07  Marcus D. Hanwell <marcus@cryos.org>

  * Doxyfile, Doxyfileext, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt:
  Version changed to 0.9.0.

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/runkrazy.rb, scripts/runkrazy.rb: Removed
  the krazy subdirectory, will be autogenerated from now on. Also moved the
  script into our scripts directory.

2009-01-07  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/projecttreeeditor.cpp: Fix compile error.

  * libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/hydrogensextension.cpp: Update extensions to add
  some menu separators

2009-01-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/trajvideomaker.cpp: Initial porting of the
  animation tool to the new API.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Made the
  conformer support actually work now!

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Set the version to
  0.9_beta1 in preparation for the release.

2009-01-07  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreemodel.cpp: Find a
  few more un-translated strings.

  * avogadro/src/CMakeLists.txt, avogadro/src/mac/lang.sh: Cleanup of Mac
  .lproj (language directories) creation. Should improve translations.

  * krazy/runkrazy.rb: Run Krazy in colors and projectdelegates subdirectories
  too

2009-01-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: First attempt at
  adding conformer support, needs some testing.

  * doc/index.docbook: Updated the docs a little, added contributors etc. Will
  look at moving tutorials across from the wiki soon.

2009-01-06  Geoff Hutchison <babel@geoffhutchison.net>

  * i18n/avogadro.pot, scripts/extract-messages.sh, scripts/extractrc.sh:
  Modified scripts and POT file to keep similar format for UI files as CPP and
  H

2009-01-05  Geoff Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_fr.ts: Updated
  en_GB de and fr TS files from Launchpad. All translations should now be using
  Launchpad.

2009-01-05  Geoff Hutchison <babel@geoffhutchison.net>

  * cmake/modules/FindEigen2.cmake: Updated FindEigen2 from KDE (and Benoit).
  Should fix PR#2372569.

  * i18n/avogadro.pot: Updated avogadro.pot with 0.9 strings.

  * scripts/extract-messages.sh: Update to clean up avogadro.pot a bit, grab
  version from CMakeLists.txt, etc.

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version number
  for 0.9.0 beta.

  * i18n/avogadro_ar.ts, i18n/avogadro_ca.ts, i18n/avogadro_cs.ts,
  i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sv.ts, i18n/avogadro_tr.ts,
  i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Updated
  translation strings.

  * avogadro/src/aboutdialog.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/fileimportextension.h,
  libavogadro/src/extensions/povrayextension.cpp: Fix some un-translated (or
  confused) strings.

  * avogadro/src/CMakeLists.txt: Silence Mac command-line calls using
  EXECUTE_PROCESS.

2009-01-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/bond.cpp, libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/glgraphicsview.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/periodictableview.cpp,
  libavogadro/src/plugindialog.cpp, libavogadro/src/pythoninterpreter.h,
  libavogadro/src/textrenderer.cpp: Made a start on fixing issues pointed out
  by krazy2.

2009-01-05  Geoff Hutchison <babel@geoffhutchison.net>

  * cmake/modules/FindLinguist.cmake: Don't drop "unfinished" translations --
  this is how translations come from Launchpad.

2009-01-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/painterengine.cpp, libavogadro/src/painterengine.h: Removed
  orphaned source files.

  * libavogadro/src/engines/dipoleengine.cpp: Ported to access atoms using the
  new functions.

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added some
  functions to set and get the dipole moment of the molecule. Copying the
  dipole moment seems to cause segfaults here, so it is commented out for now.

2009-01-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt: Mac build: Test for directory before creating
  it.

  * i18n/avogadro_ar.ts, i18n/avogadro_ca.ts, i18n/avogadro_cs.ts,
  i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_es.ts,
  i18n/avogadro_fr.ts, i18n/avogadro_it.ts, i18n/avogadro_ja.ts,
  i18n/avogadro_ko.ts, i18n/avogadro_nb.ts, i18n/avogadro_nl.ts,
  i18n/avogadro_pl.ts, i18n/avogadro_pt.ts, i18n/avogadro_pt_BR.ts,
  i18n/avogadro_ru.ts, i18n/avogadro_sv.ts, i18n/avogadro_tr.ts,
  i18n/avogadro_uk.ts, i18n/avogadro_zh_CN.ts, i18n/avogadro_zh_TW.ts: Updated
  translations. Still need to work out a clean po -> ts solution.

  * CMakeLists.txt: Drop obsolete translations when running
  "update-translations"

  * avogadro/src/CMakeLists.txt: Mac build: Test for directory before creating
  it.

2009-01-04  Carsten Niehaus <cniehaus@kde.org>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Pretty big update as I didn't run those tests for
  ages and Krazy2 improved a lot

2009-01-04  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt: Add additional translations to Mac list (i.e.,
  ensure Apple strings are auto- translated).

  * i18n/avogadro_ar.ts, i18n/avogadro_cs.ts, i18n/avogadro_de.ts,
  i18n/avogadro_ja.ts, i18n/avogadro_ko.ts, i18n/avogadro_nb.ts,
  i18n/avogadro_nl.ts, i18n/avogadro_sv.ts, i18n/avogadro_tr.ts,
  i18n/avogadro_uk.ts: Add new translations from Launchpad plus
  "update-translations" for new strings.

2009-01-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.cpp: Ensure that newly added engines get initialised
  with the molecule properly.

2009-01-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * CMakeLists.txt: define ENABLE_PYTHON (used in mainwindow.cpp)

2009-01-02  Carsten Niehaus <cniehaus@kde.org>

  * cmake/modules/FindBoostPython.cmake: Support Python 2.6 for Boost

2009-01-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gamessextension.cpp: Some improvements to get
  EFP stuff working again. Still has some issues with SMARTS errors.

2009-01-01  Albert DeFusco <albert@albert-defuscos-macbook.local>

  * libavogadro/src/extensions/gamessinputdata.cpp: Fixed $EFRAG group.  This
  is now consistent with the EFP1 potentials H2ODFT and H2ORHF.

  * libavogadro/src/extensions/gamessinputdata.cpp: The atomicNumber is not
  used in EFP1

  * libavogadro/src/extensions/gamessinputdata.cpp: Modified the $EFRAG group
  to be consistent with EFP1 potentials

2009-01-01  Geoff Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/macchempasteboard.cpp,
  avogadro/src/macchempasteboard.cpp.disabled,
  avogadro/src/macchempasteboard.h, avogadro/src/macchempasteboard.h.disabled:
  Disable Mac ChemPasteboard until we can fix it completely.

  * libavogadro/src/extensions/CMakeLists.txt: Build and install the unit cell
  extension. Remove references to supercell.

2009-01-01  Geoffrey Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mac/MacOSXBundleInfo.plist.in: Fix strange crash -- remove
  LSUIElement from Info.plist template. Tracing using Qt debug libraries and
  source code found the problem. 

  * CMakeLists.txt: Don't search for Python bits unless it's enabled and Boost
  Python is found. 

2008-12-31  Geoffrey Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mac/MacOSXBundleInfo.plist.in: Fix strange crash -- remove
  LSUIElement from Info.plist template. Tracing using Qt debug libraries and
  source code found the problem.

  * CMakeLists.txt: Don't search for Python bits unless it's enabled and Boost
  Python is found.

2008-12-31  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.cpp: Finished the porting of the
  GAMESS input deck generator. Only performed cursory testing so far for quite
  a number of changes. Basic input deck generation seems to work at least.

  * avogadro/src/main.cpp: Moved the version and help function calls to the top
  of main.

  * libavogadro/src/tools/bondcentrictool.cpp: Improved consistency of
  bondcentric unit display to other tools.

2008-12-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/eigen.cpp,
  scripts/cmake-vs2005.bat: Some win32 specific changes

  * libavogadro/src/extensions/shaderextension.cpp: Add search path for windows
  + don't try to load shaders when there is no shader support (needed for win32
  installer, GLSL always enabled, support detected at runtime)

2008-12-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/bondcentrictool.cpp: Fix molecule updates. Probably
  not optimal, but no worse than it was before.

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Reduction of includes that are not
  needed.

  * libavogadro/src/tools/bondcentrictool.cpp: Removed the navigation functions
  which are duplicated there.

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/tools/skeletontree.h:
  Initial work to port the bondcentrictool to the new framework. This seems to
  mostly work, has some issues with atom updates that should not be too hard to
  sort out.

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h: Added a new function to
  return the bond between the atom and any other. Returns 0 if no bond between
  them exists.

2008-12-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/python/atom.cpp: Removed calls to private API that should
  not be exposed.

  * libavogadro/src/tools/drawtool.cpp: Some minor changes to make it work
  properly with the modified Atom and Bond classes.

  * libavogadro/src/atom.h, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/cube.h, libavogadro/src/fragment.h, libavogadro/src/global.h,
  libavogadro/src/mesh.cpp, libavogadro/src/mesh.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h: Added a little
  access control and friend classes. Id and index should only be set by the
  containing Molecule and are not part of our public API. They reflect internal
  state of the molecule.

  * CMakeLists.txt, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Updated the build system, now require
  CMake 2.6.0. Clean ups in several places.

  * libavogadro/src/CMakeLists.txt: Explicitly set the headers that should be
  installed. Only those headers exporting symbols and part of our public API
  should be installed.

  * libavogadro/src/python/atom.cpp, libavogadro/src/python/molecule.cpp:
  Ported to use the new API, new -> add and delete -> remove.

2008-12-29  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/atom.h, libavogadro/src/molecule.h: Documentation updates
  with previous syntax change.

  * avogadro/src/editcommands.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/python/atom.cpp, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/color.py,
  libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/extension.py,
  libavogadro/src/python/unittest/fragment.py,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/python/unittest/primitivelist.py,
  libavogadro/src/python/unittest/residue.py, libavogadro/src/pythonerror.cpp,
  libavogadro/src/pythonerror.h, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/tests/moleculetest.cpp: Change syntax of atoms and molecules. All
  references to "new" are now "add" and all references to "delete" are now
  "remove." So it's "addAtom" or "removeAtom" for consistency with Qt and the
  rest of our API.

  * CMakeLists.txt: For CMake 2.6 (which is recommended anyway) we can look for
  newer versions of boost (e.g., the recent 1.37 release.

2008-12-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pluginmanager.cpp: replace getenv(...) with
  QProcess::systemEnvironment() 

  * libavogadro/src/elementtranslate.h: Replace "A_DECL_EXPORT extern ..." with
  "A_EXPORT extern ..." 

  * CMakeLists.txt: use /MD compiler flag for MSVC 

  * libavogadro/src/tools/pythontool.cpp: Add the search path for the python
  tool on win32

  * libavogadro/src/pluginmanager.cpp: replace getenv(...) with
  QProcess::systemEnvironment()

  * libavogadro/src/elementtranslate.h: Replace "A_DECL_EXPORT extern ..." with
  "A_EXPORT extern ..."

2008-12-28  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/python/molecule.cpp: Lots of documentation updates,
  reorganised the functions and grouped in Doxygen tags. Some minor changes
  too, more are needed for const correctness.

2008-12-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * CMakeLists.txt: use /MD compiler flag for MSVC

2008-12-28  Geoff Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Only embed SMILES graphics if available.

2008-12-28  Marcus D. Hanwell <marcus@cryos.org>

  * testfiles/multicubes.cube.gz: Removed from our source as it is the same
  size as all the other files put together. May be we should provide a more
  extensive sample of files in a separate distribution.

  * libavogadro/src/engines/bsdyengine.cpp: Ported to use the new bond position
  functions.

  * libavogadro/src/bond.cpp, libavogadro/src/bond.h: Added functions to
  retrieve bond positions, still need to implement the mid-point function.

  * libavogadro/src/bond.h: Documentation updates.

  * libavogadro/src/python/bond.cpp: Added missing Atom include.

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h: Documentation updates,
  added member function groupings and a destructor.

  * libavogadro/src/atom.cpp, libavogadro/src/bond.cpp, libavogadro/src/bond.h:
  Added some atom accessor functions to the Bond class. This should make using
  bonds easier. Fixed assignment order in Atom constructor.

2008-12-28  Geoffrey Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/colors/residuecolor.cpp: Update to work with the new
  residue/atom updates. Much cleaner.

2008-12-28  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp: Fixed PR 2353831 - crash when closing a
  molecule with selected items

  * libavogadro/src/engines/labelengine.cpp: Added back in the Residue
  functions. Labels for residues are now displayed when requested.

  * libavogadro/src/atom.cpp, libavogadro/src/fragment.cpp,
  libavogadro/src/fragment.h, libavogadro/src/residue.cpp,
  libavogadro/src/residue.h: Made the classes aware of their parent. Added in
  calls in Residue to set and unset the Residue of its child atoms.

2008-12-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h: Added methods to set and
  get at the residue an atom belongs to.

2008-12-27  Geoffrey Hutchison <babel@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Temporarily remove crash when exporting
  graphics(!?)

  * ChangeLog: Removed ChangeLog -- not updated. Instead, use Git logs

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: Fix
  glpainter and wireframe to bring back stipple for h-bond engine. (oops!)

2008-12-27  Geoff Hutchison <babel@geoffhutchison.net>

  * libavogadro/src/colors/residuecolor.cpp: Fix crash in residue coloring.
  (Bad news -- residues are not avail. in new framework.) Need to sync residues
  with Molecule.

2008-12-27  Geoffrey Hutchison <babel@geoffhutchison.net>

  * cmake/modules/FindNumpy.cmake: Fix to FindNumpy to fail properly when Numpy
  is not available.

2008-12-27  Simon Ochsenreither <soc@desktop06.(none)>

  * libavogadro/src/pluginmanager.cpp: Fixed a typo preventing the extensions
  from being loaded

2008-12-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/python/pluginmanager.cpp: Added missing includes since I
  removed them from the pluginmanager header.

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h:
  Environment variable redux - move from four environment variables to one.
  AVOGADRO_PLUGINS can be set to point to Avogadro plugins.

2008-12-24  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp: Fixed triangle windings for
  negative electron isosurfaces, changed default tab in the dialog.

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/vdwsurface.cpp: Added the ability to generate VdW
  surfaces, and variants thereof. Still needs some work to tidy up the UI.

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Start of the simplification in the
  surface engine. Need to add back in coloured surfaces, currently draws
  surface meshes in the specified colour.

  * libavogadro/src/engines/orbitalengine.cpp: Added more safety checks here.

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui: Added Van der Waals surface tab
  and associated functions.

  * libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Added
  the option to reverse the winding of the generated mesh. This depends upon
  what you consider to be inside and outside of your isosurface.

  * libavogadro/src/extensions/vdwsurface.cpp,
  libavogadro/src/extensions/vdwsurface.h: Added a VdWSurdface class that uses
  QtConcurrent to calculate a VdW cube. It may need further optimisation with
  binning etc.

  * libavogadro/src/engine.cpp, libavogadro/src/meshgenerator.cpp: Got rid of a
  few unused variables in function calls.

2008-12-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/highlighter.cpp,
  libavogadro/src/extensions/highlighter.h,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/pythonterminal.cpp,
  libavogadro/src/extensions/pythonterminal.h: Split python extension into 2
  extensions. One handles python extension scripts and the other one provied
  the terminal. Also add syntax highlighting to the terminal widget :P

2008-12-24  Jordan Mantha <jordan.mantha@gmail.com>

  * libavogadro/src/extensions/gaussianfchk.cpp: fixed missing quotation 

  * libavogadro/src/extensions/gaussianfchk.cpp: read in orbital energies from
  gaussian fchk files 

2008-12-23  Jordan Mantha <jordan.mantha@gmail.com>

  * libavogadro/src/extensions/gaussianfchk.cpp: fixed missing quotation

  * libavogadro/src/extensions/gaussianfchk.cpp: read in orbital energies from
  gaussian fchk files

2008-12-24  unknown <AB@.(none)>

  * libavogadro/src/camera.cpp: Make CameraPrivate inherit from
  Eigen::WithAlignedOperatorNew 

  * libavogadro/src/camera.cpp: Make CameraPrivate inherit from
  Eigen::WithAlignedOperatorNew

2008-12-24  Jordan Mantha <jordan.mantha@gmail.com>

  * doc/index.docbook: updateded minimum required versions of Qt and cmake.
  Also mention eigen2 and git. 

2008-12-23  Jordan Mantha <jordan.mantha@gmail.com>

  * doc/index.docbook: updateded minimum required versions of Qt and cmake.
  Also mention eigen2 and git.

2008-12-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h: PythonTerminalWidget: Allow
  python code indentation  

2008-12-23  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/supercellbuilder.cpp,
  libavogadro/src/extensions/supercellbuilder.h,
  libavogadro/src/extensions/supercelldialog.cpp,
  libavogadro/src/extensions/supercelldialog.h,
  libavogadro/src/extensions/supercelldialog.ui: Remove supercell for now,
  until it can be finished for public use. 

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h, libavogadro/src/molecule.cpp:
  Add back unit cell extension. 

  * libavogadro/src/glwidget.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, testfiles/ZnO.fract: Added back basic support for
  unit cells. (e.g., open testfiles/ZnO.fract) 

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt: Fix build
  error when ENABLE_PYTHON = false 

2008-12-23  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/stickengine.cpp: Fixed a bug causing crashes if a
  color map has not been set for the stick engine. 

  * libavogadro/src/engines/stickengine.cpp: Fixed a bug causing crashes if a
  color map has not been set for the stick engine.

  * AUTHORS, INSTALL, authors.txt, authors.xml: Updated the author files, added
  a new authors.txt that can be used by Git to map SVN users to Git authors. 

  * avogadro/src/mainwindow.cpp: Significantly simplified the timer logic for
  the center view animation. This should get rid of any problems compiling this
  code on Windows too. 

  * libavogadro/src/engines/ringengine.cpp, libavogadro/src/glpainter.cpp:
  Noticed that the drawTriangle function was recalculating normals when it was
  given one. 

2008-12-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: Some
  tidying up. Remove unnecessary GL calls. Still an issue with transparency in
  the ring engine. 

2008-12-22  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/iso.cpp: Eigen2 fix -- add casts to floats. 

2008-12-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/selectextension.cpp: Ported the engines, and
  extension to use the new API introduced. Please let me know if you notice any
  new issues arising from all the changes. Hopefully the API changes can be
  kept to a minimum now. 

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h: Removed includes that
  should not be in the Engine header. Added a molecule member pointer that can
  be used to more efficiently take care of the lazy copying of lists. Separated
  atoms and bonds from general primitives. This allows for engines to
  specialise further, i.e. engines with no atoms/bonds can ignore these signals
  and avoid copying these pointer lists when custom primitives are to be
  rendered. Added new Engine slots for the new molecule signals. 

  * libavogadro/src/python/glwidget.cpp: Changes necessary for updates in the
  GLWidget class. 

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Changed the
  transparent rendering. Enable GL_BLEND for the rendering cycle as everything
  in there currently enables/disables this. Also removed the depth mask stuff
  as this did not look good with any of the engines. Removed more calls to the
  PrimitiveList, there is no point in keeping two copies of this list and it
  will be phased out. Actually emit the moleculeChanged signal when the
  molecule is changed. Adding a new toggleSelected function which toggles the
  selection with no list. 

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added greater
  granularity to the Molecule. Separate atom and bond signals are emitted. All
  other primitives go in the old signals. Atoms and bonds are the most
  susceptible to change and in general the most numerous. 

  * libavogadro/src/extensions/povpainter.h: Added missing include. 

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Some improvements to the behaviour
  of the selection tool. 

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Only draw eye candy when the view is
  moving. 

2008-12-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/python/example.py: Add a QUndoCommand derived
  class to example.py and use it... 

  * libavogadro/src/extensions/pythonextension.cpp: pythonextension.cpp: Add
  some more error checking 

  * libavogadro/include/avogadro/pythonerror.h: forgot avogadro/pythonerror.h 

  * avogadro/src/mainwindow.cpp: Use the new python error handling 

  * libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/pythonerror.cpp, libavogadro/src/pythonerror.h,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h: Improve
  python error reporting, all errors are now printed to the messages log... 

2008-12-22  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Add a Mac window icon proxy:
  http://labs.trolltech.com/blogs/2007/12/28/spotlight-on-little-things/ 

2008-12-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/pythonextension.cpp: Added missing include. 

  * libavogadro/src/tools/autoopttool.cpp: Simplified the call, culling calls
  to GLWidget::primitives(), the molecule should be used instead. 

  * libavogadro/src/extensions/basisset.cpp, libavogadro/src/glpainter.cpp:
  norm2() -> squaredNorm() due to deprecation in Eigen2. 

  * libavogadro/src/engines/wireengine.cpp: Removed the unnecessary GL_BLEND
  calls. 

2008-12-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: MainWindow: Use the
  new Extension::actionsChanged() slot to reload an extension's actions when
  needed. 

  * libavogadro/src/python/sip.cpp: python/sip.cpp: Add from python converter
  for QList<QAction*> 

  * libavogadro/src/extensions/python/deleteAll.py,
  libavogadro/src/extensions/python/example.py,
  libavogadro/src/extensions/python/test.py,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h: PythonExtension: Make python
  extensions more like real extensions. Still needs some work but actions(),
  menuPath() & peroformAction are working... TODO: dockWidgets, work out
  example with QUndoCommand, ... 

  * libavogadro/src/pythonscript.cpp: pythonscript.cpp: Always reload the
  python script file in the constructor. 

  * libavogadro/src/extension.h: extension.h: Add actionsChanged() signal to
  notify the MainWindow (or similar classes) when an extensions QActions have
  changed. 

  * libavogadro/src/engines/pythonengine.cpp: pythonengine.cpp: improve error
  output 

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: MainWindow: * Add
  slot to handle plugin reloading * replace strcasestr with equivalent QString
  functions * TODO: make smooth transitions work on win32 

2008-12-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/main.cpp: main.cpp: move include avogadro/global.h to top of
  the file 

  * libavogadro/src/engine.h: engine.h: Remove Eigen include, moved global.h to
  top of the file (global defines some things to make std::min & std::max
  available) 

  * libavogadro/src/engine.h: engine.h: include Eigen/Core 

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: GLWidget:
  initialize m_navigateTool to 0 and check if it exists before trying to let it
  handle unaccepted events from other Tools. Add a toolsDestoryed() slot to set
  d->tool and d->activeTool to 0, connect the toolGroup::toolsDestroyed()
  signal to this slot in GLWidget::setToolGroup(...). 

  * libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h: ToolGroup: Add
  ToolGroup::removeAllTools() to clear the current list of tools + emit
  toolsDestroyed() when 1 or more tools are destroyed. 

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h:
  PluginManager: Add a reload slot and reloadPlugins signal. The reload slot is
  called from the PluginDialog when accepted, PluginManager::reload() writes
  the settings, deletes the instances and emits reloadPlugins. Classes such as
  MainWindow and GLWidget connect to this signal to invalidate their current
  plugins and reload them.  Nore: MainWindow & GLWidget follow later, reloading
  plugins without restarting is only working for Tools & Extensions at the
  moment 

2008-12-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp:
  Further refinements to wireframe, including optimization and aromatic dashed
  bonds.   

2008-12-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/global.h: global.h: include <limits> on win32 + add 'f' for
  float declarations 

  * libavogadro/src/plugindialog.cpp, libavogadro/src/plugindialog.h:
  PluginDialog: Add a signal to inform the PluginManager when the plugins have
  changed. 

  * libavogadro/src/meshgenerator.cpp: meshgenerator.cpp: Add include
  <Eigen/Geometry> (needed for win32 build) 

  * libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h:
  PythonScript: improve error handling 

  * libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h: pythonengine.*: Add win32 search
  paths + improve error handling 

  * libavogadro/src/extensions/pythonextension.cpp: pythonextension.cpp: Add
  win32 search path + delete the Terminal Widget in destructor 

2008-12-21  Simon Ochsenreither <simon@ochsenreither.de>

  * doc/index.docbook: Added some paragraphs to the avo handbook ... trying to
  understand docbook 

  * i18n/avogadro_de.ts: German ttranslations, some of them taken from
  Launchpad. 

2008-12-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.h, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/python/molecule.cpp: Added some code so that bond aromaticity
  can be exposed. 

2008-12-20  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/importdialog.cpp: Minor correction for people using case
  sensitive file systems. 

2008-12-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/importdialog.cpp, avogadro/src/importdialog.h,
  avogadro/src/importdialog.ui, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h: New "import file" dialog to set specific Open
  Babel format and conversion options. In particular, turning off bond orders
  should be helpful with nanotubes / graphite or really large files. 

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: More
  wireframe refinements. Getting there. 

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp:
  Somewhat more refined multiple bonds for wireframe. Also made multi-bond
  wireframe the default to address bug report. Still need "aromatic" stipple. 

  * avogadro/src/mainwindow.cpp: Ignore tabs for primitives and colors when the
  engines don't configure those. 

2008-12-19  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Finally got the new way of
  generating meshes working. It still has a few rough edges but on the whole is
  much improved. Adding color by another cube is now relatively simple. 

2008-12-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added new Mesh
  functions so that the Molecule can manage meshes properly too. 

  * libavogadro/src/glwidget.cpp: Tweaked the rendering order - now the tools
  draw before transparent parts of the scene. Much more visually correct for
  eye candy etc. 

  * libavogadro/src/cube.h, libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Working on adding
  the mesh generation to the extension and simplifying the orbital/surface
  engines. This will also ensure the molecule is cleared properly as engines
  should not be storing their own primitives to render. 

2008-12-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/engine.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/std_vector.cpp: some small syntax changes in the
  python module to make it compile with MSVC (not -> !) 

  * avogadro/src/projecttreeeditor.h, avogadro/src/projecttreemodel.h,
  avogadro/src/projecttreemodeldelegate.h: avogadro/src/*.h: Remove some more
  A_EXPORT 

  * avogadro/src/projectdelegates/atomdelegate.h,
  avogadro/src/projectdelegates/bonddelegate.h,
  avogadro/src/projectdelegates/labeldelegate.h,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projectdelegates/residuedelegate.h:
  avogadro/src/projectdelegates/*.h: These classes are not in libavogadro
  anymore, remove A_EXPORT from their declaration. 

  * libavogadro/src/extensions/povpainter.h: povpainter.h: this file is not in
  libavogadro anymore, remove the A_EXPORT from POVPainter and
  POVPainterDevice. 

2008-12-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/extensions/povpainter.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/python/engine.cpp: Engine flag overhaul. New flags: Layers
  (opaque, transparent, overlay) Primitives (atoms, bonds, etc.) Colors (none,
  indexed, plugins, etc.)  This should simplify the display settings windows,
  as well as new users. I've probably missed some engines, but I'll make
  another pass tomorrow. 

  * libavogadro/src/camera.cpp: Fix for PR#1964674 -- more space for the view
  with no molecule loaded. 

  * avogadro/src/mainwindow.cpp: Fix PR#1965004 -- don't show the main toolbar
  on the Mac. Period. 

2008-12-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Tidied up the extension a
  little, fixed an initialisation issue. 

  * libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: PQNs are actually integers, cache the
  effective PQNs in the loop - simplified slaterPoint. 

  * libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: Spotted that the exponential factor
  could be cached outside of the loop in electron density calculations - nearly
  three times faster. I still want it to go faster though! 

2008-12-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: Fix PR#2396701 -- when clicking
  again on an atom, remove it from the list. This prevents NaN measurements and
  makes it efficient to check out multiple measurements in a large molecule. 

2008-12-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/slaterset.cpp: Increased the default step size to
  a more relaxed 0.18, reduced the default padding to 2.5 and added some logic
  to skip calculations where the factor is very small. 

  * libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: Added calculation of electron density
  to the MOPAC code, this should be quite simple to translate to the Gaussian
  type orbitals too. Fixed normalization of the MOs too. ESP calculation might
  be next... 

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Added the option to calculate
  all MOs. 

2008-12-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindLinguist.cmake: Fix to FindLinguist for PR#2089508 --
  FindQt4 sets lupdate and lrelease variables, but does not consider that users
  may have lrelease -> Qt3 and should prefer lrelease-qt4 in that case. (This
  is really a Cmake bug, but we need a workaround for now.) 

  * cmake/modules/FindLinguist.cmake: Added -removeidentical to further
  compress translations. Still trying to sort out PR#2089508. 

2008-12-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Initial save/read settings to CML files. Right
  now, it will save *everything* under our QSettings (with some Mac-specific
  filtering to ignore Apple, etc. requests). There does seem to be one key
  (engineDocks) which also causes problems. The "plumbing" is done. 

2008-12-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/slaterset.cpp: Forgot to initialize the
  initialization variable - doh! 

2008-12-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, libavogadro/src/CMakeLists.txt,
  libavogadro/src/avogadroformat.cpp, libavogadro/src/xml.cpp: Remove useless
  Avogadro format and XML code -- we can't get this to work with the current
  Open Babel 2.2 architecture. 

2008-12-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/slaterset.cpp: Added un the d-type orbitals.
  These need to be verified somehow but seem to work at first glance. 

2008-12-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianinputdialog.cpp: Only listen when the
  edit has been changed, do not warn if not visible. Should hopefully get rid
  of this bug. 

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: Added a renderPick to the ball and
  stick engine. Should be much quicker when picking in large scenes. 

  * libavogadro/src/navigate.cpp, libavogadro/src/tools/navigatetool.cpp: Fixed
  up the translation of the view by keyboard - much better now. 

  * libavogadro/src/navigate.cpp, libavogadro/src/navigate.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  Added key press events for the navigate tool - now you can use the keyboard
  to modify the view. 

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/orbitalengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/painterdevice.h,
  libavogadro/src/python/engine.cpp, libavogadro/src/python/glwidget.cpp: Pass
  the primitives list by reference in the primitives() return type. All engines
  just render the primitive list unless otherwise instructed by the user - only
  one copy of the list normally. Introduced a renderPick() function to the
  engines, this allows a specialised function for picking that can omit
  extraneous details. 

2008-12-13  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tool.cpp, libavogadro/src/tool.h: Added key press and
  release events to the tools - keyboard interaction! 

2008-12-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindEigen2.cmake: Take a stab at PR#2372569.  

2008-12-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/pythontool.cpp: Fix crashes with Python tool and no
  scripts (e.g., PyQt is not installed) 

  * libavogadro/src/engine.h: Added a few needed flags. 

2008-12-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/mopacaux.cpp,
  libavogadro/src/extensions/mopacaux.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/slaterset.cpp,
  libavogadro/src/extensions/slaterset.h: Added support for MOPAC AUX file
  parsing, and more generally Slater Type Orbitals. Features are still very
  new. I need to add in support for d-type orbitals and do further testing. 

2008-12-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/pythonengine.cpp, libavogadro/src/python/sip.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/python.png,
  libavogadro/src/tools/python/template.py,
  libavogadro/src/tools/pythonsettingswidget.ui,
  libavogadro/src/tools/pythontool.cpp, libavogadro/src/tools/pythontool.h,
  libavogadro/src/tools/pythontool.qrc: Add Python Tool  

2008-12-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/CMakeLists.txt: Avoid newline at the end of
  PYTHON_LIB_PATH  

2008-12-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/CMakeLists.txt: use python to find site-packages
  directory like Geoff demonstrated.  

2008-12-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/python/CMakeLists.txt: Update python module. Added note for
  finding site-packages dir (using Python) Changed to build a "MODULE" which
  works better on Mac. 

  * avogadro/src/mainwindow.ui: Fix "import" and "export" submenu items (don't
  repeat words) and added ... when menu commands will bring up windows/dialogs.

  * avogadro/src/CMakeLists.txt: Revert "quiet" Mac changes -- EXECUTE_PROCESS
  has strange syntax. 

2008-12-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/python/cubepoints.py,
  libavogadro/src/engines/python/pythonTestEngine.py,
  libavogadro/src/engines/python/wireframe.py,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/engines/pythonsettingswidget.ui,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythoninterpreter.h,
  libavogadro/src/pythonscript.cpp: * libavogadro/src/pythoninterpreter.*: Make
  sure we don't call Py_Finalize() before all instances are destroyed. *
  libavogadro/src/engines/pythonengine.*: Allow python engines to have a
  settingsWidget, flags, transparencyDepth and changed() signal. *
  libavogadro/src/engines/python/wireframe.py: work out an example engine with
  a python settings widget.  

2008-12-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.cpp: Off by one when setting up
  the cubes. 

  * libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added the ability to save
  the dialog settings that make sense, added LANL2DZ and improved the routines
  to check if the new molecule coordinates should be used. 

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/tools/eyecandy.cpp: Give the user more control over the cube
  size to be calculated. Also reduced the size of the eye candy a little. 

  * libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tool.h, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Make the navigate tool a super tool
  - one tool to rule them all (when they do not accept the mouse event). 

  * CMakeLists.txt, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt:
  Adjusted the build files a little. Qt 4.4.0 is required now as we are using
  QtConcurrent. Bumped the version in preparation for 0.9 release. 

2008-12-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp: Fix a bug I reintroduced a few days ago  

2008-12-08  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp: Forgot to remove the FIXME comment, it is now
  fixed... 

  * avogadro/src/editcommands.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/atom.cpp, libavogadro/src/molecule.cpp: Fixed copy and
  pasting. 

2008-12-08  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/orbitalengine.cpp: Minor fix for orbital dialog --
  prevent crashes when no cubes exist. 

2008-12-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h, libavogadro/src/molecule.cpp:
  Fixes to the modality of the calculation, small fix to molecule and its
  setOBMol function. 

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h: Improved locking
  of the cube - too slow to make the class thread safe. Best solution is for
  users of it to lock/unlock. Orbitals now sees new cubes and updates the combo
  again. 

  * libavogadro/src/cube.h, libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/python/cube.cpp: Added a map form calculation - uses a lot
  less memory for large molecules. In my tests it is a little slower than whole
  cube but uses a lot less memory. On balance this is probably the best
  implementation for most people to use. 

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/savedialog.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added the coveted export to vector graphics
  option, provided by the GL2PS C library which is not built into Avogadro.
  Seems to work quite well and everyone loves vector graphics. 

  * avogadro/gl2ps/COPYING.GL2PS, avogadro/gl2ps/COPYING.LGPL,
  avogadro/gl2ps/TODO, avogadro/gl2ps/gl2ps.c, avogadro/gl2ps/gl2ps.h,
  avogadro/gl2ps/gl2ps.pdf, avogadro/gl2ps/gl2psTest.c,
  avogadro/gl2ps/gl2psTestSimple.c: Added a snapshot of GL2PS to build against.

2008-12-08  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt: Made Mac build/install commands silent. 

2008-12-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/sip.cpp, libavogadro/src/python/unittest/suite.py: Add
  unit test for Camera  

  * libavogadro/src/python/TODO, libavogadro/src/python/bond.cpp,
  libavogadro/src/python/cube.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/qlist.cpp, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/std_vector.cpp,
  libavogadro/src/python/unittest/glwidget.py,
  libavogadro/src/python/unittest/suite.py: update python bindings, including
  cube, fix bond & atom errors in unit tests, add std::vector<double>* to
  converter, unit test for GLWidget, simplify & document sip.cpp implementation
  a bit. Wrap GLHit and add QList<GLHit> to python converter.  

  * libavogadro/src/glwidget.h: forgot .h file  

  * libavogadro/src/glwidget.cpp: * libavogadro/src/glwidget.*: Replace
  QStringList with QList<QString> for GLWidget::namedSelections()  

2008-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/extension.cpp: Add QDockWidget & QUndoCommand  

2008-12-07  Marcus D. Hanwell <marcus@cryos.org>

  * testfiles/benzene.fchk, testfiles/co.fchk: Added a couple of formatted
  checkpoint examples. 

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Quite a few optimisations. I
  got the mapped reduce feature working. I am still a little concerned about
  memory usage on really big molecules with lots of cores. It looks good on
  some of the molecules I have tested it on though. Scales quite linearly now
  with two cores. 

  * libavogadro/src/cube.cpp, libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h: Quite a few optimisations to the
  calculation. Memory grows out of control when calculating large molecules,
  this needs map reduce but have not been able to get that working... 

  * libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/orbitalextension.cpp: Rewritten many of the
  calculation routines in an attempt to improve speed. Using QtConcurrent to
  actually calculate the cube on a shell by shell basis. Seems to be working
  quite well here. Still more tidying up/optimisation to do. 

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h,
  libavogadro/src/python/cube.cpp: Several modifications to the Cube class in
  order to make it more efficient and add flexibility. 

2008-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/sip.cpp: We now have signals/slots in python :-)  

2008-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/sip.cpp,
  libavogadro/src/python/unittest/atom.py: Fix Atom::valence and update unit
  test  

  * libavogadro/src/CMakeLists.txt, libavogadro/src/python/CMakeLists.txt,
  libavogadro/src/python/TODO, libavogadro/src/python/extension.cpp,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/python/main.cpp,
  libavogadro/src/python/plugin.cpp, libavogadro/src/python/qtlib.cpp,
  libavogadro/src/python/sip.cpp, libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/extension.py,
  libavogadro/src/python/unittest/suite.py: More python classes & unit tests.
  Also add converters to allow us to return PyQt (SIP) wrapped objects and
  accept them as parameters.  

2008-12-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitalextension.cpp: Added QDebug to includes
  as it was used but not included. 

  * libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Added a
  clear() function. 

2008-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/meshgenerator.cpp: *
  libavogadro/src/engines/orbitalengine.cpp: Add extra check for
  m_settingsWidget in OrbitalEngine::updateOrbitalCombo *
  libavogadro/src/meshgenerator.cpp: Add extra check in ::initialize to make
  sure the Cube and Mesh pointer are valid  

2008-12-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.h, libavogadro/src/engines/orbitalengine.cpp: Fixed
  up the update engine a little and added a new entry into the Egine enum for
  surfaces. 

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h: Added minimum and maximum
  value functions to the Cube class, corrected some off by one errors in the
  Cube initialization functions. 

  * libavogadro/src/cube.cpp: Small fix for latest Eigen2, casting is needed
  now. 

2008-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/engine.cpp,
  libavogadro/src/python/plugin.cpp, libavogadro/src/python/pluginmanager.cpp,
  libavogadro/src/python/primitivelist.cpp,
  libavogadro/src/python/unittest/engine.py,
  libavogadro/src/python/unittest/pluginfactory.py,
  libavogadro/src/python/unittest/pluginmanager.py,
  libavogadro/src/python/unittest/suite.py: Added python unit tests for engine
  and updated the pluginmanager bindings  

2008-12-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h:
  libavogadro/src/pluginmanager.*: Some additional functions to make plugin
  loading easier from python (or for 3rd party viewers which use libavogadro)  

2008-12-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Updated the orbital engine to use
  the new MeshGenerator class. It should be fixed to only render meshes,
  leaving generation to an exntension or tool. 

  * libavogadro/src/cube.cpp, libavogadro/src/cube.h: Fixes for the Cube class
  to work with the new MeshGenerator class. 

  * libavogadro/include/avogadro/meshgenerator.h,
  libavogadro/src/meshgenerator.cpp, libavogadro/src/meshgenerator.h: Added a
  new MeshGenerator class. The basic code is derived from that found at
  http://local.wasp.uwa.edu.au/~pbourke/geometry/polygonise/ Specifically the
  marchingsource.cpp file authored by Cory Bloyd and placed in the public
  domain (thanks Cory). I then made it play nice with the new Avogadro classes
  and put it in its own thread. I have not actually added the duplicate vertex
  detection yet. This new class is able to generate meshes significantly faster
  that the previous code. 

2008-12-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/color.cpp,
  libavogadro/src/python/glwidget.cpp, libavogadro/src/python/main.cpp,
  libavogadro/src/python/plugin.cpp, libavogadro/src/python/qtlib.cpp,
  libavogadro/src/python/tool.cpp, libavogadro/src/python/unittest/color.py,
  libavogadro/src/python/unittest/suite.py,
  libavogadro/src/python/unittest/tool.py: Add python unit tests for Tool and
  Color  

  * libavogadro/src/extensions/pythonextension.cpp: *
  libavogadro/src/extensions/pythonextension.cpp: Make the python command stack
  persistent across sessions (using QSettings)  

  * libavogadro/src/python/TODO,
  libavogadro/src/python/unittest/pluginfactory.py,
  libavogadro/src/python/unittest/suite.py: Add python unit test for
  PluginFactory  

  * libavogadro/src/python/TODO, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/plugin.cpp,
  libavogadro/src/python/pluginmanager.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/toolgroup.cpp,
  libavogadro/src/python/unittest/pluginmanager.py,
  libavogadro/src/python/unittest/suite.py,
  libavogadro/src/python/unittest/toolgroup.py: Wrap PluginManager & ToolGroup
  classes and added unit tests for them  

  * libavogadro/src/plugin.h, libavogadro/src/toolgroup.cpp: *
  libavogadro/src/plugin.h: Remove ProjectPlugin from the Type enum. *
  libavogadro/src/toolgroup.cpp: Add index checking in
  ToolGroup::setActiveTool(int index).  

  * libavogadro/src/toolgroup.cpp: * libavogadro/src/toolgroup.cpp: Add index
  checking to ToolGroup::tool(int index)  

  * libavogadro/src/python/TODO, libavogadro/src/python/main.cpp,
  libavogadro/src/python/primitivelist.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/unittest/primitivelist.py,
  libavogadro/src/python/unittest/suite.py: Add python unit test for
  PrimitiveList  

  * libavogadro/src/python/TODO, libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/mesh.cpp,
  libavogadro/src/python/std_vector.cpp,
  libavogadro/src/python/unittest/mesh.py,
  libavogadro/src/python/unittest/suite.py: *
  libavogadro/src/python/std_vector.cpp: Add std::vector<Vector3f>, needed for
  mesh * libavogadro/src/python/eigen.cpp: Add more typechecking, there was
  some pointer arithmatic going on with the wrong types  Python seems to use
  long and double here as default, but we also accept int and float. An array
  from python with doubles can now correctly be converted to a Vector3f.    

  * libavogadro/src/python/TODO, libavogadro/src/python/residue.cpp,
  libavogadro/src/python/unittest/residue.py,
  libavogadro/src/python/unittest/suite.py: Add python unit test for Residue  

  * libavogadro/src/residue.cpp: * libavogadro/src/residue.cpp: Bugfix in
  Residue::setAtomId(id, string_id)  

  * libavogadro/src/cube.cpp, libavogadro/src/python/TODO,
  libavogadro/src/python/cube.cpp, libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/std_vector.cpp,
  libavogadro/src/python/unittest/cube.py,
  libavogadro/src/python/unittest/fragment.py,
  libavogadro/src/python/unittest/molecule.py,
  libavogadro/src/python/unittest/suite.py,
  libavogadro/src/python/unittest/template.py: *
  libavogadro/src/python/unittest/*: Add template & cube tests *
  libavogadro/src/python/*: Add std::vector wrapper, bug fix for eigen.cpp &
  cube.cpp * libavogadro/src/cube.cpp: Bugfix in setLimits(Molecule*, double,
  double), don't assume any atom will have coordinates < (0,0,0)  

2008-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/extensions/shaderdialog.ui,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/python/glwidget.cpp: Added a view option to turn quick
  rendering on and off, for those times when you want eye candy all of the
  time. 

2008-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/engines/bsdyengine.cpp: elementcolor.cpp: give atoms with
  atomicNumber 0 a drak grey color bsdyengine.cpp: give them a radius  Helps
  with interactive python scripting: molecule.newAtom() will show the atom when
  the bsdy engine using element coloring is enabled (=default)  

  * libavogadro/src/python/TODO, libavogadro/src/python/bond.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/primitive.cpp,
  libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/suite.py: Python bindings unit tests for
  Atom, Bond & Molecule complete  

  * libavogadro/src/engines/python/cubepoints.py,
  libavogadro/src/engines/python/pythonTestEngine.py,
  libavogadro/src/python/atomTest.py: Replace import Numeric with import numpy 

  * libavogadro/src/molecule.cpp: small bug fix in Molecule::deleteBond(),
  don't try to remove the bond from the begin & end atom if the atoms don't
  exists. (was causing a segfault in the python unit test)  

2008-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, libavogadro/src/CMakeLists.txt: Removed the AVO_LINK_LIBS
  status message. Fixed up the Find LibXml2 call for those of us with case
  sensitive file systems. 

  * libavogadro/src/extensions/shaderdialog.ui,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaderextension.h: Fixed the rest of the shader
  calls that had not been ARBified. Added the ability to load shader programs. 

2008-12-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt, cmake/modules/FindGLEW.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt:
  Updates to GLEW includes for those of us with non-standard paths.  

  * libavogadro/src/avogadroformat.cpp, libavogadro/src/xml.cpp: Draft attempts
  at an avogadro format.  

  * libavogadro/src/extensions/povrayextension.cpp: Fix a Qt connect() warning.
   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  libavogadro/src/extensions/fileimportextension.cpp: Reorganize menus -- add
  an "Import" submenu on the File menu. (There should be a default to open
  files with strange extensions by specifying the Open Babel format.)  

2008-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/glwidget.cpp: Ported to use the ARB syntax, should work on
  older graphics cards. Still works the same here. 

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/mesh.cpp, libavogadro/src/mesh.h: The quest for greater
  stability continues, I think this is a reasonable solution for things like
  meshes. 

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Only use OpenGL
  2.0 functions when GLEW finds OpenGL 2.0 capabilities. 

  * libavogadro/src/bond.cpp, libavogadro/src/bond.h: Implemented the bond
  length member function. I hope LaserJock is happy now. 

2008-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h: Always call Molecule::update()
  when a user enters a command in the python terminal widget, makes the
  scripting terminal much more interactive...  

2008-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaders/phong.params,
  .../src/extensions/shaders/x-ray-cryos.frag,
  .../src/extensions/shaders/x-ray-cryos.params,
  .../src/extensions/shaders/x-ray-cryos.vert,
  libavogadro/src/extensions/shaders/x-ray.frag,
  libavogadro/src/extensions/shaders/x-ray.params,
  libavogadro/src/extensions/shaders/x-ray.vert, libavogadro/src/glwidget.cpp:
  Added a few new shaders along with their parameter files. Added the ability
  to load parameter files into shaders and got the x-ray shader working. 

2008-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * sip/README, sip/avogadro.sip, sip/camera.sip, sip/color.sip,
  sip/configure.py, sip/eigen.sip, sip/engine.sip, sip/glwidget.sip,
  sip/openbabel.sip, sip/painter.sip, sip/painterdevice.sip, sip/plugin.sip,
  sip/pluginmanager.sip, sip/primitive.sip, sip/primitivelist.sip, sip/test.py,
  sip/test.sdf, sip/test_Transform3d.py, sip/test_Vector3d.py, sip/tool.sip,
  sip/toolgroup.sip: Delete obsolete sip python bindings  

  * libavogadro/src/python/CMakeLists.txt: python bindings CMakeLists.txt: find
  the site-packages dir and use it to install the module  

2008-12-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/TODO, libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/unittest/atom.py,
  libavogadro/src/python/unittest/bond.py,
  libavogadro/src/python/unittest/eigen.py,
  libavogadro/src/python/unittest/suite.py: * libavogadro/src/python/eigen.cpp:
  add converters for all to/from Tranform3d objects. Add a class with get/set
  functions for all combinations of Vector3x/Tranform3d, used for unit testing.
   * libavogadro/src/python/unittest/*: Unit tests for python bindings.
  Currently atom, bond and the Eigen converters are covered.  To run test
  suite: $python libavogadro/src/python/unittest/suite.py  

  * avogadro/src/mainwindow.cpp, libavogadro/src/pluginitemmodel.cpp,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h:
  pluginmanager.*: Add static method PluginManager::instance(), replaces the
  global instance pluginManager pluginitemmodel.cpp, mainwindow.cpp: update to
  use PluginManager::instance()  

2008-12-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/shaderdialog.ui,
  libavogadro/src/extensions/shaderextension.cpp: Made the shaders more
  flexible hopefully more robust. 

  * libavogadro/src/engines/surfaceengine.cpp, libavogadro/src/glpainter.cpp:
  Port to use squaredNorm() as norm2() is deprecated now. 

  * libavogadro/src/engines/surfaceengine.cpp: Need to cast to float now as
  Eigen2 has become pickier about types.  

  * libavogadro/src/glwidget.cpp: Fixed a bug I reintroduced - listen to the
  comment in future. Affected the Mac build, but not Linux. 

  * libavogadro/src/engine.h: Fixed a bad include when not using GLSL... 

  * libavogadro/src/extensions/CMakeLists.txt: Improved the shader GLOBs. 

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/shaderdialog.ui,
  libavogadro/src/extensions/shaderextension.cpp,
  libavogadro/src/extensions/shaderextension.h,
  libavogadro/src/extensions/shaders/clip.frag,
  libavogadro/src/extensions/shaders/clip.vert,
  libavogadro/src/extensions/shaders/gooch.frag,
  libavogadro/src/extensions/shaders/gooch.vert,
  libavogadro/src/extensions/shaders/light.frag,
  libavogadro/src/extensions/shaders/light.vert,
  libavogadro/src/extensions/shaders/marble.frag,
  libavogadro/src/extensions/shaders/marble.vert,
  .../src/extensions/shaders/per-pixel-lighting.frag,
  .../src/extensions/shaders/per-pixel-lighting.vert,
  libavogadro/src/extensions/shaders/per_pixel2.frag,
  libavogadro/src/extensions/shaders/per_pixel2.vert,
  .../src/extensions/shaders/phong-use-diffuse.frag,
  .../src/extensions/shaders/phong-use-diffuse.vert,
  libavogadro/src/extensions/shaders/phong.frag,
  libavogadro/src/extensions/shaders/phong.vert,
  libavogadro/src/extensions/shaders/plasma.frag,
  libavogadro/src/extensions/shaders/plasma.vert,
  libavogadro/src/extensions/shaders/vmd.frag,
  libavogadro/src/extensions/shaders/vmd.vert, libavogadro/src/glwidget.cpp:
  Added the ShaderExtension which allows you to assign a shader to an engine.
  Still not implemented shader loading from arbitrary files - will do it soon.
  It currently loads all shader pairs in share/libavogadro/shaders, probably
  not optimal but it allows people to check out shaders now while I finish up a
  few bits. 

  * avogadro/src/mainwindow.cpp, libavogadro/include/avogadro/glgraphicsview.h,
  libavogadro/src/glgraphicsview.cpp, libavogadro/src/glgraphicsview.h: Added
  experimental GLGraphicsView detachment, more a proof of concept right now,
  performance is quite poor, antialiasing is disabled and text does not render
  correctly. It does however draw widgets etc on top of the GLWidget. 

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added a new
  member function for the GLGraphicsView, added GLEW initialisation in order to
  check for shader support and hopefully did not break anything in the process.

  * libavogadro/src/python/eigen.cpp: Fixed a compilation error here, also I
  think this is a better solution that using reinterpret_cast and should
  probably be adopted elsewhere. Still need to figure out where these objects
  get deleted. 

  * libavogadro/src/CMakeLists.txt: Ensure that all Python related source files
  are removed when Python support is disabled. 

2008-12-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * CMakeLists.txt, cmake/modules/FindGLEW.cmake,
  cmake/modules/FindNumpy.cmake, libavogadro/src/python/CMakeLists.txt: Minor
  Cmake magic to get everything compiling on Mac. (Silly Apple, stick to
  traditional paths more often!)  

2008-12-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/eigen.cpp: python/eigen.cpp: make drawSphere work
  with numpy  

  * libavogadro/src/boost.h, libavogadro/src/engines/python/cubepoints.py,
  libavogadro/src/engines/python/pythonTestEngine.py,
  libavogadro/tests/CMakeLists.txt: * libavogadro/tests/CMakeLists.txt: remove
  ${EXECUTABLE_OUTPUT_PATH}, "make test" now works here... *
  libavogadro/src/engines/python/cubepoints.py: Another example engine, renders
  cubes as 10x10x10 points colored red/blue for -/+    

  * libavogadro/src/python/TODO, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/color.cpp, libavogadro/src/python/engine.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/mesh.cpp,
  libavogadro/src/python/molecule.cpp, libavogadro/src/python/painter.cpp,
  libavogadro/src/python/tool.cpp: Various updates to python bindings  

  * libavogadro/src/python/eigen.cpp: Use numpy, Add Vector3f, Vector3i,
  Transform3d.  Altough it now works with numpy, I get lots of warnings from
  numpy/arrayobject.h...  

2008-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/pluginmanager.cpp: * pluginmanager.cpp: Rmove projectplugin
  loading, these have moved to avogadro   

  * libavogadro/src/engines/python/wireframe.py,
  libavogadro/src/python/color.cpp, libavogadro/src/python/main.cpp,
  libavogadro/src/python/plugin.cpp: * libavogadro/src/python/*: Wrap Plugin
  and Color classes. * libavogadro/src/engines/python/wireframe.py: Use Color
  class   

  * libavogadro/src/engines/pythonengine.cpp: pythonengine.cpp: catch the
  error_already_set exception from python, print the error to stderr and
  continue...  

2008-12-02  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/pythonengine.h: Does not need to include QGLWidget
  here. 

  * avogadro/src/main.cpp, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h: Changes needed in order
  to compile libavogadro with GLEW, needs to be included before gl.h/QGLWidget.

  * CMakeLists.txt, cmake/modules/FindGLEW.cmake, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt: Build system updates. Some clean ups and also
  added an option for GLSL using the GLEW library. 

  * libavogadro/src/extensions/povraydialog.cpp: Changed some of the command
  line options around a little. Pause at the end of rendering and other bits. 

2008-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/pythonengine.cpp: pythonengine.cpp: small bug fix:
  don't reset the script (set by readSettings) when creating the settingsWidget
   

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/python/engine.py,
  libavogadro/src/engines/python/pythonTestEngine.py,
  libavogadro/src/engines/python/wireframe.py,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h,
  libavogadro/src/engines/pythonsettingswidget.ui: Improve python engine and
  add a more realistic example: a wireframe engine  

2008-12-02  Marcus D. Hanwell <marcus@cryos.org>

  * cmake/modules/FindEigen2.cmake: Added some default paths and cleaned up a
  little, this should now find Eigen2 in the two standard installation
  locations at least. 

2008-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/python/engine.py,
  libavogadro/src/engines/pythonengine.cpp,
  libavogadro/src/engines/pythonengine.h: * libavigadro/engines/pythonengine.*:
  Initial attempt to create a python engine, still needs some work but it works
  \o/  * libavogadro/engines/python/engine.py: example engine (note: for now,
  the python engine uses the first script it finds...)  

  * libavogadro/src/pythoninterpreter.cpp: pythoninterpreter.cpp: Use an
  exception to make sure we keep running even when the module isn't correctly
  installed  

  * libavogadro/include/avogadro/pythonscript.h,
  libavogadro/src/extensions/python/deleteAll.py,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/pythonscript.cpp, libavogadro/src/pythonscript.h: *
  libavogadro/src/pythonscript.*: Moved here from pythonextension.* *
  src/extensions/pythonextension.*: remove PythonScript, now in libavogadro. *
  src/extensions/python/deleteAll.py: update this script to work with new API  

  * libavogadro/src/molecule.cpp: * libavogadro/src/molecule.cpp: Allocate
  posistions in newAtom so calling atomPos before setAtomPos just returns a
  Eigen::Vector3d:Zero()  

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/TODO,
  libavogadro/src/python/atom.cpp, libavogadro/src/python/atomTest.py,
  libavogadro/src/python/bond.cpp, libavogadro/src/python/cube.cpp,
  libavogadro/src/python/fragment.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/painter.cpp, libavogadro/src/python/painterdevice.cpp,
  libavogadro/src/python/primitive.cpp, libavogadro/src/python/qlist.cpp,
  libavogadro/src/python/qstring.cpp, libavogadro/src/python/residue.cpp: *
  libavogadro/src/python/*: update boost python bindings (QString, QList<T>,
  QList<T*>, Painter, PainterDevice, ...)   

2008-12-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povpainter.cpp: Made several improvements to the
  POV-Ray Painter. Using rgbt instead of rgbf, I think this is the right way to
  go now and provides more visually pleasing results. Engine renders are put
  inside unions for opaque objects and merges for transparent objects. Much
  nicer output that might make Geoff happy with the rainbow effect and VdW
  spheres. 

  * libavogadro/src/mesh.cpp: Added quite a bit of locking to the setters and
  getters - seems very stable here. 

  * libavogadro/src/engines/sphereengine.cpp: Corrected a minor rendering bug,
  renderTransparent actually renders all spheres twice in order to achieve a
  nice visual effect in OpenGL. This makes POV-Ray merges look terrible. This
  tweak seems to fix it although it is not ideal... 

  * libavogadro/src/glwidget.cpp: Initialise clickedPrimitive to zero, fixes
  bug when detaching views. 

2008-12-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Fix minor bug with
  Mac and project tree editor.  

  * libavogadro/src/plugin.cpp, libavogadro/src/plugin.h: Add support for *all*
  plugins to have settings widgets (e.g., colors too)  

2008-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Added some very initial support for detached
  views. Still needs more work, cannot set engines etc right now. It does work
  in the basic sense though and can be amazingly useful for some work. I will
  hopefully smooth this out a little more very soon. 

  * libavogadro/src/molecule.cpp: Fixed a bug I introduced in some of the new
  atom position initialisation. 

2008-11-30  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix for "export graphics" filename bug.  

2008-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/tests/CMakeLists.txt: Removed the install target - we do not
  want test binaries littering the filesystem. 

2008-11-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/wrapper.cpp: delete wrapper.cpp, compile should now
  work  

2008-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/molecule.cpp, libavogadro/tests/moleculetest.cpp: Updated
  with some new tests, noticed an initialisation bug in setAtomPos. There might
  be something in this unit testing thing... 

2008-11-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/python/CMakeLists.txt, libavogadro/src/python/atom.cpp,
  libavogadro/src/python/bond.cpp, libavogadro/src/python/camera.cpp,
  libavogadro/src/python/cube.cpp, libavogadro/src/python/eigen.cpp,
  libavogadro/src/python/fragment.cpp, libavogadro/src/python/glwidget.cpp,
  libavogadro/src/python/main.cpp, libavogadro/src/python/molecule.cpp,
  libavogadro/src/python/primitive.cpp, libavogadro/src/python/residue.cpp:
  split boost python bindings into multiple files  

2008-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/tests/moleculetest.cpp: Updated MoleculeTest class - added a
  member variable and use that between tests. Seems to work quite well, still
  needs more tests. 

  * libavogadro/src/molecule.cpp: Fixed partial charge caching logic. 

  * CMakeLists.txt, libavogadro/CMakeLists.txt,
  libavogadro/tests/CMakeLists.txt, libavogadro/tests/moleculetest.cpp: Added
  some initial unit testing using QTestLib and CTest. Use make test for basic
  reporting, or run ctest -V in the build directory for more detailed output.
  Test coverage is currently terrible, but it gives a template and I will flesh
  it out. We need unit testing for core functionality. 

2008-11-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp,
  avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  avogadro/src/projecttreemodel.cpp, avogadro/src/projecttreemodel.h,
  libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h, libavogadro/src/glwidget.h,
  libavogadro/src/molecule.cpp, libavogadro/src/python/CMakeLists.txt,
  libavogadro/src/python/wrapper.cpp, libavogadro/src/pythoninterpreter.cpp,
  libavogadro/src/pythoninterpreter.h: * libavogadro/src/python: Compile the
  boost python bindings seperatly so they can also be used from outside
  avogadro.  * libavogadro/src/pythoninterpreter.*: remove the boost.h
  include...  * libavogadro/src/molecule.cpp: Don't segfault when you call
  atomPos before setPos.  * libavogadro/src/glwidget.h: remove undefined
  function toolManger (we have a toolGroup/setToolGroup.  *
  libavogadro/src/extensions/pythonextension.*: remove boost.h include...  *
  avogadro/src/projecttreemodel.*, avogadro/src/projectdelegates/*: some small
  improvements  * avogadro/src/mainwindow.cpp: Use QPixmap::grapWidget to
  export png images. (Should work on more platforms. If it causes problems on
  other platforms we can still use
  QGLFramebufferObject::hasOpenGLFramebufferObjects() to detect which method to
  use.)   

2008-11-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/aligntool.cpp: Fixed a bug I introduced to the align
  tool when porting earlier. Works properly again now. 

2008-11-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h, libavogadro/src/colors/indexcolor.cpp,
  libavogadro/src/colors/indexcolor.h, libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h: Updated color plugins, including new
  "color by index" -- rainbow based on atom index.  

  * libavogadro/src/molecule.cpp: Fix unsigned compiler warning.  

2008-11-27  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.cpp, libavogadro/src/bond.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawtool.cpp: Chased down the bonding bugs and
  hopefully optimized some of this code a little. Please test and report any
  issues I might have missed. 

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h, libavogadro/src/bond.cpp,
  libavogadro/src/bond.h, libavogadro/src/molecule.cpp: Some optimizations and
  tweaks to the atom, bond and molecule classes. Still some drawing bugs I am
  tracking down... 

2008-11-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/fileimportdialog.ui,
  libavogadro/src/extensions/fileimportextension.cpp,
  libavogadro/src/extensions/fileimportextension.h: Added a new file import
  dialog, initially concentrating purely on xyz files and amber parameter
  files. Still pretty rough around the edges. 

  * libavogadro/src/atom.cpp, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/molecule.cpp: Some updates to the bond, atom and molecule
  classes. Hopefully improving speed a little. 

2008-11-25  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp: Tweaked the fog parameters a little. I think
  this works quite well - feedback and suggestions are of course welcome. 

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  avogadro/src/settingsdialog.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added a fog setting to the GLWidget. The numbers
  still need tweaking but it demonstrates the effect. 

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added partial
  charge calculation and caching. Also made a start on adding locking to the
  molecule class. I did not find any deadlocks but please report if you do.
  Still more locking needed, finer granularity may be necessary. 

  * libavogadro/src/extensions/forcefieldextension.cpp: Removed molecule
  locking - the molecule takes care of locking and unlocking itself in a more
  granular form. 

2008-11-24  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/editcommands.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/molecule.h,
  libavogadro/src/tools/autoopttool.cpp: * libavogadro/src/molecule.*: Add
  Molecule::residue(index) and Molecule::residueById(id).  *
  avogadro/src/editcommands.cpp: Handle Bond and Residue primitives in
  ClearCommand and CutCommand.  *
  avogadro/src/projectdelegates/residuedelegate.cpp: Also add the residue
  itself to the primitives (for selection).  *
  libavogadro/src/tools/autoopttool.cpp: optimize the way we retreive
  coordinates from the OBMol object.   

  * libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h: Add the force field
  extension again, conformers not handled at the moment and marked with FIXME. 

2008-11-24  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.ui: Few tweaks to tab order, added
  the fileName widget to the signals connected to the updateCommandLine slot. 

  * libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povrayextension.cpp: Several improvements to the
  POV-Ray extension, update the command line more frequently, use the supplied
  path and work from the directory specified. 

2008-11-23  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povrayextension.cpp: Set the working directory of
  the process, only use relative paths as POV-Ray can be paranoid. Should
  improve rendering success on systems configured in quite restrictive ways. 

  * libavogadro/src/glpainter.cpp: Add a check to ensure that the
  vertices/normals/colors are of the correct size. Should reduce some crashes
  caused by this. 

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h, libavogadro/src/cube.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/painter.h,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Main change is having the
  molecule manage the atom's coordinates. This should open up the possibility
  of quickly changing the coordinate set and redrawing. The main practical
  difference is Vector3d being a pointer rather than a reference. Everything
  else is pretty much porting to the new API. Small fix to the molecule
  constructor to assign a default file name. 

2008-11-23  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp,
  avogadro/src/projectdelegates/residuedelegate.cpp: * small bug fix for
  ResidueDelegate * remove obsolete connect() call from mainwindow.cpp  

  * avogadro/src/projectdelegates/moleculedelegate.cpp,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projectdelegates/residuedelegate.cpp,
  avogadro/src/projectdelegates/residuedelegate.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreemodel.cpp: * Add
  ResidueDelegate  

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/projectdelegates/atomdelegate.cpp,
  avogadro/src/projectdelegates/atomdelegate.h,
  avogadro/src/projectdelegates/bonddelegate.cpp,
  avogadro/src/projectdelegates/bonddelegate.h,
  avogadro/src/projectdelegates/labeldelegate.cpp,
  avogadro/src/projectdelegates/labeldelegate.h,
  avogadro/src/projectdelegates/moleculedelegate.cpp,
  avogadro/src/projectdelegates/moleculedelegate.h,
  avogadro/src/projectplugin.cpp, avogadro/src/projectplugin.h,
  avogadro/src/projectplugins/atomitems.cpp,
  avogadro/src/projectplugins/atomitems.h,
  avogadro/src/projectplugins/bonditems.cpp,
  avogadro/src/projectplugins/bonditems.h,
  avogadro/src/projectplugins/labelitems.cpp,
  avogadro/src/projectplugins/labelitems.h,
  avogadro/src/projectplugins/moleculeitems.cpp,
  avogadro/src/projectplugins/moleculeitems.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreeeditor.h,
  avogadro/src/projecttreeitem.cpp, avogadro/src/projecttreeitem.h,
  avogadro/src/projecttreemodel.cpp, avogadro/src/projecttreemodel.h,
  avogadro/src/projecttreemodeldelegate.cpp,
  avogadro/src/projecttreemodeldelegate.h: * Some renaming in the Project Tree
  area:  There is now the ProjectTreeModel which delegates its work to various
  ProjectTreeModelDelegate objects.  * Dynamic initialization of the model: 
  \o/  Using QAbstractItemModel::hasChildren(), canFecthMore() and fetchMore()
  it is possible to delay the initialization (and connecting of singals) until
  the user actually expands the item.  * Still need to update some
  documentation and add a ResidueDelegate, ...   

2008-11-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/CMakeLists.txt, avogadro/src/back.png, avogadro/src/down.png,
  avogadro/src/forward.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/minus.png, avogadro/src/plus.png,
  avogadro/src/projectplugin.cpp, avogadro/src/projectplugin.h,
  avogadro/src/projectplugins/atomitems.cpp,
  avogadro/src/projectplugins/atomitems.h,
  avogadro/src/projectplugins/bonditems.cpp,
  avogadro/src/projectplugins/bonditems.h,
  avogadro/src/projectplugins/labelitems.cpp,
  avogadro/src/projectplugins/labelitems.h,
  avogadro/src/projectplugins/moleculeitems.cpp,
  avogadro/src/projectplugins/moleculeitems.h,
  avogadro/src/projecttreeeditor.cpp, avogadro/src/projecttreeeditor.h,
  avogadro/src/projecttreeeditor.qrc, avogadro/src/projecttreeeditor.ui,
  avogadro/src/projecttreeitem.cpp, avogadro/src/projecttreeitem.h,
  avogadro/src/projecttreemodel.cpp, avogadro/src/projecttreemodel.h,
  avogadro/src/up.png, libavogadro/include/avogadro/projectplugin.h,
  libavogadro/include/avogadro/projecttreeeditor.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/cube.cpp, libavogadro/src/projectplugin.cpp,
  libavogadro/src/projectplugin.h,
  libavogadro/src/projectplugins/CMakeLists.txt,
  libavogadro/src/projectplugins/selectionitem.cpp,
  libavogadro/src/projectplugins/selectionitem.h,
  libavogadro/src/projectplugins/smartsitems.cpp,
  libavogadro/src/projectplugins/smartsitems.h,
  libavogadro/src/projectplugins/smartsitems.ui,
  libavogadro/src/projecttreeeditor.cpp, libavogadro/src/projecttreeeditor.h,
  libavogadro/src/projecttreeeditor.ui: * move Project Tree stuff from
  libavogadro to avogadro * implement a QAbstractItemModel for the tree * lots
  of bug fixes   

2008-11-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.cpp, libavogadro/src/extensions/povpainter.cpp: Fixed
  up the POV-Ray drawColorMesh function - looks very nice. 

  * libavogadro/src/atom.cpp, libavogadro/src/atom.h,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/engines/iso.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/mesh.cpp,
  libavogadro/src/mesh.h, libavogadro/src/molecule.cpp,
  libavogadro/src/painter.h: Ported the surface engine to the new API, added
  multiple color support to the GLPainter. added partial charge importing to
  Atom and a few minor cleanups. 

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glwidget.cpp: Commented out the new ProjectTree stuff for now
  - it was causing build failures. Also Avogadro should be able to build
  independently of LibAvogadro. Depending on the ui header generation in
  libavogadro from avogadro should not be done as it will not necessarily
  exist. 

  * libavogadro/src/boxcontrol.cpp: Disabled the call to removePrimitives in
  the destructor. Is this needed? It was causing Avogadro to segfault when I
  quit the second instance of Avogadro to return to the first. 

2008-11-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h: Port
  patch from Carsten with const iterators.  

  * libavogadro/src/projectplugins/CMakeLists.txt: Temporarily comment out
  smarts -- causes build problems for me.  

2008-11-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/projecttreeeditor.cpp, libavogadro/src/projecttreeeditor.h:
  update the project tree widget without needing a restart  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/include/avogadro/projectplugin.h,
  libavogadro/include/avogadro/projecttreeeditor.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/molecule.cpp,
  libavogadro/src/plugin.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/projectplugin.cpp,
  libavogadro/src/projectplugin.h,
  libavogadro/src/projectplugins/CMakeLists.txt,
  libavogadro/src/projectplugins/selectionitem.cpp,
  libavogadro/src/projectplugins/selectionitem.h,
  libavogadro/src/projectplugins/smartsitems.cpp,
  libavogadro/src/projectplugins/smartsitems.h,
  libavogadro/src/projectplugins/smartsitems.ui,
  libavogadro/src/projecttreeeditor.cpp, libavogadro/src/projecttreeeditor.h,
  libavogadro/src/projecttreeeditor.ui: * libavogadro/src/projectplugin.*: A
  new plugin type to create a user configurable tree view with various items
  (User Selections, Chains/Residues, smarts, ...)  *
  libavogadro/src/pluginmanager.*: load the new ProjectPlugins.  *
  libavogadro/src/molecule.cpp: Add a check in ::OBMol() to make sure the both
  bond atoms exist before adding the bond. This was causing a problem when
  functions, invoked by the Molecule::primitive*() signals, called it.  *
  libavogadro/src/projectplugins/smartsitems.*: A ProjectPlugin for smarts
  patterns. This is the only plugin working at the moment, still some
  performance issues too.  * libavogadro/src/projectplugins/selectionitem.*:
  still need to update this, not build right now...  *
  libavogadro/src/projecttreeeditor.*: The tree editor. Still need to add the
  arrow images...  * libavogadro/src/plugin.h: Add the new type to the Type
  enum.  * avogadro/src/mainwindow.*: Use the Project Tree View system. The old
  Project dock is replaced, the editor is available through Settings > Project
  Tree Editor.  The code still has some rough edges, but it works well enough
  to illustrate what it could become....  

2008-11-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/atom.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h: Added the polygon engine back in. I
  think valency needs implementing properly but this works for now... Next is
  adding multiple colour support into the Mesh class. 

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/extensions/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/molecule.cpp, libavogadro/src/residue.cpp,
  libavogadro/src/residue.h: Improved residue support, added back in the
  GLWidget and ported the ribbon engine. 

  * libavogadro/src/extensions/propmodel.cpp: Began porting the properties. 

  * libavogadro/src/primitiveitemmodel.cpp: Corrected bug when displaying bonds
  in the engine dialog. 

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/namedselectionmodel.cpp,
  libavogadro/src/extensions/selectextension.cpp: Ported the select extension.
  Seems to work quite well but had to comment out some bits in the
  namedselectionmodel class. Tim - I think that might need a little TLC. 

2008-11-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/selectrotatetool.cpp: *
  libavogadro/src/tools/selectrotatetool.cpp: Make residue selection work again
  and handle clicks on bonds in "residue" and "molecule" selection mode  

  * libavogadro/src/molecule.cpp: * libavogadro/src/molecule.cpp: Fix another
  index issue, bonds in OB are indexed starting from 0 :-)  

2008-11-19  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/fragment.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/residue.cpp, libavogadro/src/residue.h: First attempt at
  fleshing out the Residue class. It probably still needs to bring more data
  across from the OBMol. Also fleshed out the setOBMol function a little, needs
  adding to OBMol in Molecule to save the Residues too. 

2008-11-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/selectrotatetool.cpp: *
  libavogadro/src/tools/selectrotatetool.cpp: Fix atom index issue to make
  molecule selection work again.  

2008-11-19  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/mainwindow.cpp: Make file saving actually save the file again,
  did not catch the cast in the saveFile function. 

  * libavogadro/src/tools/aligntool.cpp: Fixed the align tool, still needs
  fragments adding back in. 

2008-11-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Made the orbital extension
  much cleverer. It now uses the molecules file name, determines if it can
  process it and then imports it. Also unhidden the fields where the cube size
  can be set. 

  * avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/povrayextension.h: Added the setFileName call to
  the MainWindow class. Ported POVRayExtension to take advantage of the
  fileName parameter. 

  * libavogadro/src/molecule.cpp, libavogadro/src/molecule.h: Added fileName as
  a property of the molecule. Gives extensions etc access to this information
  if set. Also added various objects to the destructor and removed some
  debugging. Added more documentation for the new API. 

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povraydialog.ui,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/povrayextension.h: Added lots more options to the
  POV-Ray dialog, it now saves its settings (as can all extensions now). Should
  be more robust. 

  * avogadro/src/mainwindow.cpp: Connected up the extensions read and write
  settings functions. 

2008-11-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h: OK, I spotted the silly mistake. A
  bool is not a double! I think this update also makes it simpler for users to
  change the aspect ratio themselves. 

  * libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povrayextension.cpp: Some updates to respect the
  requested image dimensions. The aspect ratio is still not getting through and
  so many images come out distorted. Any ideas? 

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, avogadro/src/savedialog.cpp,
  libavogadro/include/avogadro/atom.h, libavogadro/include/avogadro/bond.h,
  libavogadro/include/avogadro/boxcontrol.h,
  libavogadro/include/avogadro/cube.h, libavogadro/include/avogadro/fragment.h,
  libavogadro/include/avogadro/line.h, libavogadro/include/avogadro/mesh.h,
  libavogadro/include/avogadro/molecule.h,
  libavogadro/include/avogadro/point.h, libavogadro/include/avogadro/residue.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/atom.cpp,
  libavogadro/src/atom.h, libavogadro/src/bond.cpp, libavogadro/src/bond.h,
  libavogadro/src/boost.h, libavogadro/src/boxcontrol.cpp,
  libavogadro/src/boxcontrol.h, libavogadro/src/camera.cpp,
  libavogadro/src/color.h, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/residuecolor.cpp, libavogadro/src/cube.cpp,
  libavogadro/src/cube.h, libavogadro/src/engine.cpp,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/hbondengine.cpp, libavogadro/src/engines/iso.cpp,
  libavogadro/src/engines/iso.h, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/povpainter.cpp,
  libavogadro/src/extensions/povpainter.h,
  libavogadro/src/extensions/povraydialog.cpp,
  libavogadro/src/extensions/povraydialog.h,
  libavogadro/src/extensions/povraydialog.ui,
  libavogadro/src/extensions/povrayextension.cpp,
  libavogadro/src/extensions/povrayextension.h,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/fragment.cpp, libavogadro/src/fragment.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/line.cpp, libavogadro/src/line.h, libavogadro/src/mesh.cpp,
  libavogadro/src/mesh.h, libavogadro/src/molecule.cpp,
  libavogadro/src/molecule.h, libavogadro/src/painter.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/point.cpp, libavogadro/src/point.h,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitivelist.cpp,
  libavogadro/src/primitivelist.h, libavogadro/src/pythoninterpreter.cpp,
  libavogadro/src/residue.cpp, libavogadro/src/residue.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: MERGE the primitive branch with
  trunk. There are still quite a few extensions not ported, some engines and
  tools too. I would appreciate testing, comments and help with porting. There
  are some big changes to the API, some disabled functions and likely some new
  bugs introduced. 

2008-09-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * sip/primitive.sip: * sip/primitive.sip: remove invalid function  

  * sip/avogadro.sip: Rename the sip python module from Avogadro to AvoSIP so
  it can be used with boost::python interpreter code.  

  * ChangeLog, libavogadro/src/colors/CMakeLists.txt, sip/README,
  sip/avogadro.sip, sip/color.sip, sip/configure.py, sip/eigen.sip,
  sip/engine.sip, sip/glwidget.sip, sip/openbabel.sip, sip/plugin.sip,
  sip/pluginmanager.sip, sip/primitive.sip, sip/test.py, sip/test.sdf,
  sip/test_Transform3d.py, sip/test_Vector3d.py, sip/toolgroup.sip: *
  libavogadro/src/colors/CMakeLists.txt: remove elementcolor, this is
  statically linked into libavogadro.  * sip/*: Update SIP python bindings.   

2008-09-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp: *
  libavogadro/src/engines/surfaceengine.cpp: Don't try to compute and render a
  surface when there are no atoms. This was also causing a crash when starting
  avogadro with the surface engine enabled on one of my computers here.   

2008-09-07  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp: patch by Gael Guennebaud, use slerp in
  View->Center   

2008-09-02  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt: Fixed line endings. 

2008-08-31  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/primitive.cpp: adapt to Eigen API change   

2008-08-26  Benoit Jacob <jacob.benoit.1@gmail.com>

  * CMakeLists.txt: Do not disable eigen asserts in default buildtype.  I tried
  with avogadro and with isolated benchmarks, and it turns out that Eigen2
  asserts are far less costly than Eigen1 asserts. This is because eigen now
  bypasses them for its own internal computations (except in unit-tests where
  we re-enable them).  Moreover since we use fixed-size matrices and vectors,
  most assert conditions evaluate at compile-time.  Fun fact: gcc produces
  smaller code when eigen asserts are left enabled. Apparently that prevents
  some excessive function inlining.   

2008-08-25  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/clickmeasuretool.cpp: Print *1... labels on top of
  atoms, not aside them. That didn't really work and often made it difficult to
  know to which atom they were corresponding. I think we did that a long time
  ago before we had good text outlining.   

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/residuecolor.cpp, libavogadro/src/cylinder.cpp,
  libavogadro/src/glpainter.cpp: - make color store its channels as an array.
  Otherwise, there's no guarantee that they're adjacent in memory so usage of
  glColor4fv is dangerous.  - make use of the 'v' GL functions like glVertex3dv
  instead of glVertex3d everywhere in GLPainter.  - some cosmetic fixes in
  Cylinder.   

  * CMakeLists.txt, INSTALL, avogadro/src/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, cmake/modules/FindEigen.cmake,
  cmake/modules/FindEigen2.cmake,
  cmake/modules/FindPackageHandleStandardArgs.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/camera.cpp,
  libavogadro/src/camera.h, libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/iso.h, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/supercellbuilder.cpp,
  libavogadro/src/glpainter.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/painterengine.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/sphere.h, libavogadro/src/textrenderer.h,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/manipulatetool.cpp, libavogadro/src/tools/quaternion.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h, scripts/cmake-vs2005.bat,
  sip/camera.sip, sip/eigen.sip: * Port to Eigen2 * Some misc simplifications
  and optimizations * CMakeLists: use CMAKE_BUILD_TYPE is the same way as KDE
  does   

2008-08-15  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Fixed
  compilation errors introduced with the new setQuickRenderEnabled and
  isQuickRenderEnabled. Is the Enabled part needed? 

2008-08-14  Naomi Fox <naomi.fox@gmail.com>

  * libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  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: * animationextension.* :
  added functionality to read xyz trajectory file as defined here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html  *
  linmorphextension.* : added functionality to write xyz trajectory file.  *
  linmorphdialog.ui: removed save-pov-snapshots button and replaced with
  save-xyz-trajectory button.  * animationdialog.ui : added *.xyz extension for
  open file option.   

2008-08-14  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h:
  Removed "stable" attribute from the glwidget.  There was a reason we had this
  but I can't remember anymore.  Updated the ChangeLog 

2008-08-14  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp: Revert the settingsWindow from
  being instantiated as a child of MainWindow - caused issues here. 

2008-08-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/enginecolorswidget.cpp, avogadro/src/enginecolorswidget.h,
  avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  avogadro/src/settingsdialog.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/plugin.cpp, libavogadro/src/plugin.h,
  libavogadro/src/plugindialog.cpp, libavogadro/src/pluginitemmodel.cpp,
  libavogadro/src/pluginitemmodel.h, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/toolgroup.h: Rehauled the PluginManager to be much easier to
  use.  By default all Factories are loaded and retrieved through the
  PluginManager.  In addition, instances of Colors, Tools, and Extensions can
  be retrieved from the manager by creating an instance and using the
  appropriate function.  This fixed a bug where every MainWindow was sharing
  the same set of Plugins.  Added an option in the settings to select which
  direction the tabs on the tabbed widget should go {top, bottom, left, right}.
   Fixed up a few other things to utilize the new pluginmanager architecture.
  There was some refactoring done. 

2008-08-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/boost.h,
  libavogadro/src/pluginmanager.cpp: Fixed a bug in the animated "center"
  command.  Added some extra functions to the Python module.  Added a *.so
  filter to the plugin manager for when loading plugins on linux. 

2008-08-11  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.ui: Added
  settings to disabled smooth transitions on the GLwidget.  This is really the
  animation of certain movements.  Right now only "center view" is animated.
  These additions animate the camera movement and don't work so well with the
  surface engine. 

  * avogadro/src/mainwindow.cpp: Fixed so the camera placement is also modified
  as a result of movement.  Also fixed "Center" so that the x and y axis are
  placed right and up respectively. 

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: "Center" command is
  now more fluid.  This is the first step into having more fluid movement. 
  While this is "eyecandy" some people might find it more intuitive and nice
  when using the program.  Soon to have an option this is just my testing code.

2008-08-09  Naomi Fox <naomi.fox@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationdialog.h,
  libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h: * Fixed a bug in
  libavogadro/src/extensions/CMakeLists.txt where a needed source
  (linmorphdialog) was absent from the linmorph sources.  * Added a progress
  dialog to trajectory video maker.  * Added trajectory video making capability
  to the animation extension.   

2008-08-08  Naomi Fox <naomi.fox@gmail.com>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  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/trajvideomaker.cpp,
  libavogadro/src/extensions/trajvideomaker.h, testfiles/tyr-33-conf1.pdb,
  testfiles/tyr-33-conf2.pdb: * Took functionality of making a video of a
  trajectory from linmorph and placed into a separate class, TrajVideoMaker,
  with static functions. This way it can be reused with other trajectories.  *
  Fixed a bug in linmorph so now the number of frames and the number of
  conformations match.   

2008-08-06  Naomi Fox <naomi.fox@gmail.com>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt: Merged revisions
  1520-1542,1544-1549 via svnmerge from
  https://avogadro.svn.sourceforge.net/svnroot/avogadro/branches/animate 
  ........ r1523 | naomifox | 2008-06-17 12:28:56 -0400 (Tue, 17 Jun 2008) | 11
  lines  LinMorph - first take. To run, open up testfiles/tyr-33-conf1.pdb,
  then under extensions --> animate mol, load file testfiles/tyr-33-conf2.pdb
  and press play.  These two conformations were taken from:
  http://molmovdb.org/cgi-bin/morph-classic.cgi?ID=035639-9827  I took out all
  extensions from CMakeLists.txt other than the linmorph extension. ........
  r1526 | naomifox | 2008-06-24 13:35:55 -0400 (Tue, 24 Jun 2008) | 3 lines 
  linmorphextension now inherits from extension.  not animatemolextension.
  ........ r1527 | naomifox | 2008-06-24 13:37:37 -0400 (Tue, 24 Jun 2008) | 6
  lines  linmorph now has its own dialog window and does not use
  animatemolextension's dialog (which will be removed).  added a button for
  saving a trajectory as a file. ........ r1528 | naomifox | 2008-06-24
  13:42:18 -0400 (Tue, 24 Jun 2008) | 3 lines  Initialized merge tracking via
  "svnmerge" with revisions "1-1518" from
  https://avogadro.svn.sourceforge.net/svnroot/avogadro/trunk ........ r1529 |
  naomifox | 2008-06-25 10:32:21 -0400 (Wed, 25 Jun 2008) | 3 lines  Ran
  svn-merge with branch. ........ r1531 | naomifox | 2008-07-01 10:09:05 -0400
  (Tue, 01 Jul 2008) | 7 lines  linmorph has feature to save a series of .pov
  snapshots that can later be compiled into a movie.  also fixed the "player"
  so that numframes is adjusted correctly. ........ r1532 | naomifox |
  2008-07-01 10:25:56 -0400 (Tue, 01 Jul 2008) | 3 lines  Neatened up.  Added
  headers for files. ........ r1533 | naomifox | 2008-07-01 10:40:18 -0400
  (Tue, 01 Jul 2008) | 5 lines  Fixed the order of initialization of member
  variables in the constructor to be the same ordering as that in the class
  declaration so we don't get compiler warnings.  ........ r1534 | naomifox |
  2008-07-01 11:02:40 -0400 (Tue, 01 Jul 2008) | 9 lines  (1) removed any
  reference to animatemol (was going to be an abstract class for animations,
  but decided it was oo-overkill).  (2) copied animation.qrc to linmorph.qrc. 
  this is the file for those buttons (originally from Tim V).  (3) updated
  linmorphdialog.ui to use linmorph.qrc, not animatemol.qrc ........ r1544 |
  naomifox | 2008-07-23 11:06:02 -0400 (Wed, 23 Jul 2008) | 5 lines  1. did
  svnmerge.py merge with the trunk 2. fixed linmorphextension and
  applyforceextension factories so that they now inhert from plugin factory and
  use the correct macros. ........ r1545 | naomifox | 2008-07-28 16:24:22 -0400
  (Mon, 28 Jul 2008) | 3 lines  Added ability to make a video of linmorph using
  povray and mencoder. ........  

2008-07-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/addenginedialog.cpp, avogadro/src/enginecolorswidget.cpp,
  avogadro/src/engineitemmodel.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/include/avogadro/plugin.h,
  libavogadro/include/avogadro/pluginlistview.h,
  libavogadro/include/avogadro/pluginmanager.h, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/colorplugin.cpp,
  libavogadro/src/colorplugin.h, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h,
  libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/extension.cpp,
  libavogadro/src/extension.h, libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/supercellbuilder.h,
  libavogadro/src/extensions/templateextension.h,
  libavogadro/src/extensions/unitcellextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/plugin.cpp, libavogadro/src/plugin.h,
  libavogadro/src/plugindialog.ui, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h: Remove ColorPlugin cause it really doesn't need to be
  there.  Also eliminated some un-needed functions in the engine class. 
  Everything should rock now.  I wish i could tell you more. 

2008-07-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/addenginedialog.cpp,
  avogadro/src/addenginedialog.h, avogadro/src/enginecolorswidget.cpp,
  avogadro/src/enginecolorswidget.ui, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.h, libavogadro/src/colorplugin.cpp,
  libavogadro/src/colorplugin.h, libavogadro/src/colors/CMakeLists.txt,
  libavogadro/src/colors/elementcolor.cpp,
  libavogadro/src/colors/elementcolor.h,
  libavogadro/src/colors/residuecolor.cpp,
  libavogadro/src/colors/residuecolor.h, libavogadro/src/elementcolor.cpp,
  libavogadro/src/elementcolor.h, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/forceengine.h, libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/overlayengine.cpp,
  libavogadro/src/engines/overlayengine.h,
  libavogadro/src/engines/overlaysettingswidget.ui,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.h, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.h, libavogadro/src/extension.cpp,
  libavogadro/src/extension.h, libavogadro/src/extensions/animationextension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/namedselectionmodel.cpp,
  libavogadro/src/extensions/namedselectionmodel.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/supercellbuilder.h,
  libavogadro/src/extensions/unitcellextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/plugin.cpp,
  libavogadro/src/plugin.h, libavogadro/src/plugindialog.cpp,
  libavogadro/src/plugindialog.ui, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h, libavogadro/src/residuecolor.cpp,
  libavogadro/src/residuecolor.h, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.h,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h: * avogadro/src/addenginedialog.*:
  Use new PluginFactory class. * avogadro/src/enginecolorswidget.*: Use new
  ColorPlugin class. * avogadro/src/main.cpp: Load the plugins here... *
  avogadro/src/mainwindow.cpp: Remove call to PluginManager::loadExtensions().
  * libavogadro/src/CMakeLists.txt: Statically link ElementColor in
  libavogadro. * libavogadro/src/color.h: Move settingsWidget() to ColorPlugin.
  * libavogadro/src/elementcolor.*: Moved to colors/. *
  libavogadro/src/engine.*: Use new Plugin base class. *
  libavogadro/src/engines/CMakeLists.txt: Add overlay engine. *
  libavogadro/src/engines/*engine.h: Use new PluginFactory class. *
  libavogadro/src/extension.*: Use new Plugin base class. *
  libavogadro/src/extensions/*extension.h: Use new PluginFactory class. *
  libavogadro/src/glwidget.*: Use new PluginFactory class. *
  libavogadro/src/plugindialog.*: Use the PluginFactory's descriptions. Added
  Colors to the combo box. * libavogadro/src/pluginmanager.*: Load all plugins
  in the same generic function, PluginFactory::type() is used to determine the
  plugin type. * libavogadro/src/residuecolor.*: Moved to colors/. *
  libavogadro/src/tool.*: Use new Plugin base class. *
  libavogadro/src/toolgroup.cpp: Remove call to PluginManager::loadTools(). *
  libavogadro/src/tools/*tool.h: Use new PluginFactory class. *
  libavogadro/src/colorplugin.*: Add new ColorPlugin class for Color plugins. *
  libavogadro/src/colors/: New directory for color plugins. ElementColor and
  ResidueColor can now be found here. *
  libavogadro/src/engines/overlayengine.*,
  libavogadro/src/engines/overlaysettingswidget.ui: Replaces overlay extension.
  There is an initial delay when creating the QPainter on the QGLWidget... :( *
  libavogadro/src/plugin.*: New Plugin base class.  

2008-07-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/mainwindow.cpp, libavogadro/src/pluginmanager.cpp,
  libavogadro/src/pluginmanager.h: * libavogadro/src/pluginmanager.*: Added
  support for extensions.  * avogadro/src/mainwindow.cpp: Use PluginManager for
  extensions.  

  * ChangeLog: add some info about possible compile problems...  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  libavogadro/src/CMakeLists.txt, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/overlayextension.cpp,
  libavogadro/src/extensions/overlayextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/plugindialog.cpp,
  libavogadro/src/plugindialog.h, libavogadro/src/plugindialog.ui,
  libavogadro/src/pluginitemmodel.cpp, libavogadro/src/pluginitemmodel.h,
  libavogadro/src/pluginlistview.cpp, libavogadro/src/pluginlistview.h,
  libavogadro/src/pluginmanager.cpp, libavogadro/src/pluginmanager.h,
  libavogadro/src/toolgroup.cpp: Plugin Manager: -------------- *
  libavogadro/src/pluginmanager.*: The PluginManager class. This class is now a
  central class to handle the loading of plugins.  *
  libavogadro/src/pluginitemmodel.*: The PluginItemModel class.  *
  libavogadro/src/pluginlistview.*: The PluginListView class.  *
  libavogadro/src/plugindialog.*: The PluginManager dialog.  *
  libavogadro/src/glwidget.*: Use PluginManager.  *
  libavogadro/src/toolgroup.cpp: Use PluginManager.  *
  avogadro/src/mainwindow.ui, avogadro/src/mainwindow.cpp: Use the
  PluginManager. Added the menu entry "Settings > Plugin Manager".  TODO: -
  Avogadro needs to be restarted at the moment in order for the changes to take
  effect. - Not yet used for extensions. - Better descriptions, download
  updates, ...  Compiling problems? - run cmake again to include the new *.h,
  *.cpp and *.ui files... - if mainwindow.cpp can't find
  <avogadro/pluginmanager.h>, copy the file to /usr/(local/)include/avogadro  

2008-07-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/painter.h, libavogadro/src/painterdevice.h,
  sip/README, sip/avogadro.sip, sip/camera.sip, sip/color.sip,
  sip/configure.py, sip/eigen.sip, sip/engine.sip, sip/glwidget.sip,
  sip/openbabel.sip, sip/painter.sip, sip/painterdevice.sip, sip/primitive.sip,
  sip/primitivelist.sip, sip/test.py, sip/tool.sip, sip/toolgroup.sip: * sip/*:
  Initial attempt to make SIP python bindings.  *
  libavogadro/src/painter(device).h: export Painter and PainterDevice. See
  sip/README for more info (revert if this is wrong)   

2008-07-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/enginecolorswidget.cpp,
  avogadro/src/enginecolorswidget.h, avogadro/src/enginecolorswidget.ui,
  avogadro/src/mainwindow.cpp, libavogadro/src/engine.cpp: *
  avogadro/src/enginecolorswidget.*: Widget for setting an engine's color map. 
  * avogadro/src/mainwindow.cpp: Add the color widget to engine settings
  window.  * libavogadro/src/engine.cpp: emit changed() when
  Engine::setColorMap() is called.  

2008-07-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp: Use some of the newer
  OBGridData API - requires OpenBabel trunk/OpenBabel 2.2.0 release. 

2008-06-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/primitiveitemmodel.cpp: Remove invalid "void" in
  destructor.  

2008-06-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/color.cpp, libavogadro/src/povpainter.cpp,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitiveitemmodel.h:
  port a fix by Laurent Montel fixing 2 memleaks, in PrimitiveItemModel and in
  POVPainter.  See: http://websvn.kde.org/?view=rev&revision=822121  By the
  way, this made me re-read the Color class. Why do we have all these virtual
  methods? Is there any reason why we might want to subclass Color? Or is it
  not-performance-critical? Also there now are many members to this class. That
  might be fine but one just needs to keep that in mind, don't allocate a whole
  array of objects of Color class, and don't create a new Color object too
  frequently (i.e. every few drawn triangles! i hope e.g. the Surface engine is
  not doing that).   

2008-06-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h,
  libavogadro/src/engines/dipolesettingswidget.ui: Added some initial dipole
  engine settings. Klunky.  

2008-06-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/boost.h: * libavogadro/src/boost.h: Add
  extract_swig_wrapped_ptr to convert SWIG object (from openbabel) to be
  converted to boost::python/C++ objects. Still very limited, but you can now
  do: >>> atom = obcore.OBAtom() >>> atom.SetAtomicNum(6) >>>
  Avogadro.molecule.AddAtom(atom)   

2008-06-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/qcheminputdialog.cpp,
  libavogadro/src/extensions/qcheminputdialog.h,
  libavogadro/src/extensions/qcheminputdialog.ui: Added a new QChem input deck
  generator. The input file generated is still not correct but VLANs and the
  fact that it compiles mean it is better to add it now.  

2008-06-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Added bond length label.  

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp: Remove Mac
  pasteboard converter -- currently prevents drag-and-drop.  

  * libavogadro/src/extensions/supercellbuilder.cpp,
  libavogadro/src/extensions/unitcellextension.cpp: Update to unit cell support
  -- update molecule to reflect changes in unit cell and translate properly to
  show super cell planes.  

  * libavogadro/src/camera.h: Allow public normalize() call.  

2008-06-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp: When
  opening a 2D file, ask to do a quick conversion to 3D. (scale bonds, wedge ->
  Z+1, hash -> Z-1, UFF 100 steps, should we add hydrogens?)   

2008-06-11  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp: Fixed initialisation of the
  QVarLengthArray.  

2008-06-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/supercellbuilder.cpp: Minor fixes for Miller
  rotations.  

  * libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/supercellbuilder.cpp,
  libavogadro/src/extensions/supercellbuilder.h,
  libavogadro/src/extensions/supercelldialog.cpp,
  libavogadro/src/extensions/supercelldialog.h,
  libavogadro/src/extensions/supercelldialog.ui: Initial "super cell builder."
  For now, simply rotate the camera to expose a partiacular Miller plane of the
  crystal.  

2008-06-09  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added a compact form of
  the z-matrix as an option.  

2008-06-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/namedselectionmodel.cpp,
  libavogadro/src/extensions/namedselectionmodel.h: forgot files :(  

  * ChangeLog, libavogadro/src/boost.h: * libavogadro/src/glwidget.*: Functions
  for named selections.  * libavogadro/src/extensions/selectextension.*,
  libavogadro/src/extension/namedselectionmodel.*: Use them. At the moment the
  model is a simple list. I needed this functionality for specifying
  interaction groups in the force field setup dialog. This would be expanded in
  the future (tree view).  * libavogadro/src/boost.h: adjust
  OBMol::AddHydrogens() for added pH paramter.   

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: * libavogadro/src/glwidget.*: Functions for named
  selections.  * libavogadro/src/extensions/selectextension.*,
  libavogadro/src/extension/namedselectionmodel.*: Use them. At the moment the
  model is a simple list. I needed this functionality for specifying
  interaction groups in the force field setup dialog. This would be expanded in
  the future (tree view).   

2008-06-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/extensions/CMakeLists.txt: remove namedselectionmodel.cpp  

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/overlayextension.cpp,
  libavogadro/src/extensions/overlayextension.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: * libavogadro/src/glwidget.*: Add resized()
  signal.  * libavogadro/src/extensions/overlayextension.*: 2D overlay
  extension for displaying ESP gradient, 2D representations, ???   

2008-06-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * scripts/installer/setup.nsi: don't use the version number in start menu &
  desktop shortcuts. 

  * scripts/avogadro.nsi, scripts/cmake-vs2005.bat,
  scripts/installer/Changelog.txt, scripts/installer/avogadro.ico,
  scripts/installer/dist/gpl.txt,
  scripts/installer/installer_languages/english.nsh,
  scripts/installer/installer_languages/german.nsh,
  scripts/installer/setup.nsi: New win32 installer. 

2008-06-07  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bumped
  version number of trunk to 0.8.2 now that trunk is open again.  

2008-06-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro.pot: Updated PO template.  

  * i18n/avogadro_pt_BR.ts: Translation updates from Launchpad.  

2008-06-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/tools/selectrotatetool.cpp: *
  libavogadro/src/tools/selectrotatetool.cpp: When selecting residues, also
  select the bonds.  * libavogadro/src/extensions/hydrogenextension.*: Added
  "Add Hydrogens for pH...".   

2008-06-06  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Added calls to
  tr for i18n, thanks to Louis Ricard in bug 1986689.  

  * ChangeLog, libavogadro/src/primitive.cpp: Tweaked the calling order for the
  signals.  

2008-06-05  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h: Fixed copyright lines to
  give credit to Michael Banck for his contribution.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Finally added the z-matrix
  support from Michael Banck in bug 1954332.  

  * CMakeLists.txt: Relax our CMake version requirement a little - Benoit
  reported 2.4.7 worked fine.  

  * ChangeLog, libavogadro/src/extensions/gamessinputdialog.ui: Reduced the
  vertical size of the GAMESS dialog, fixes bug 1982113.  

2008-06-05  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts: french translation: added last missing strings and
  improved existing ones thanks to Louis and Geoff   

2008-06-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Added more verbosity to engine
  loading in order to diagnose engine loading issues.  

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp: Fixed issue with the
  atom IDs not getting trimmed and so the ribbon not being displayed.  

2008-06-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp: Fixed the rendering mode code
  calls.  

2008-06-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/surfaceengine.cpp: surfaceengine.cpp: Use 3.0 for
  padding  

2008-06-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Actually draw the extents of the
  cube if requested to.  

2008-06-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/gaussianinputdialog.ui: Remove "Deck Generator"
  from dialog title. Let's stick to "Gaussian Input" or something like this.
  "Input Deck" sounds like we're using punch cards...  

  * avogadro/src/CMakeLists.txt, scripts/extract-messages.sh: Minor Mac
  localization improvements.  

2008-06-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp: *
  libavogadro/src/engines/surfaceengine.cpp: Scale numBoxes with quality.   

2008-06-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Added a quick render and render
  transparent function.  

  * ChangeLog, libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h: Added a quick render function to fix
  rendering when quick draw is used.  

2008-06-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp: *
  libavogadro/src/engines/surfaceengine.cpp: Instead of iterating over all
  atoms for each grid point, iterate over all atoms once and only update grid
  points around the atom. This is 100-200x times faster...   

2008-06-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/addenginedialog.cpp: Fixes bug 1984080 - the added
  engine was somewhat random before.  

2008-06-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts: just realized that i had misread "checkpoint" as
  "breakpoint". I have no clue what a checkpoint is, so leaving untranslated.  

  * i18n/avogadro_fr.ts: update french translation (1067/1076 strings)   

2008-06-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro-pt.ts, i18n/avogadro_pt.ts: Fix name of Portuguese
  translation.  

  * ChangeLog, avogadro/src/CMakeLists.txt, i18n/avogadro-pt.ts,
  i18n/avogadro.pot, i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts,
  i18n/avogadro_es.ts, i18n/avogadro_fr.ts,
  libavogadro/src/extensions/animationdialog.ui, scripts/extract-messages.sh: *
  i18n/*, scripts/extract-messages.sh: Added additional resources for .pot and
  .po file generation to integrate with Rosetta/Launchpad. Includes pt and es
  initial translations.  * avogadro/src/CMakeLists.txt: Use a file glob for ts
  files to build into qm files.   

2008-06-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindLinguist.cmake, i18n/avogadro.pot, i18n/avogadro_de.ts,
  i18n/avogadro_en_GB.ts, i18n/avogadro_fr.ts,
  libavogadro/src/extensions/selectextension.cpp, scripts/extract-messages.sh,
  scripts/extractrc.sh: Minor i18n improvements and scripts for generating
  po/pot files.  

2008-06-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engine.h, libavogadro/src/extension.h,
  libavogadro/src/tool.h: Bumped our plugin version to 1.1 - should help with
  bugs 1973909 and 1982102 - warning a make clean is needed.  

  * libavogadro/src/global.cpp: Added newline at the end of the file.  

2008-06-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/addenginedialog.ui: Remove "Engine" for user-visible text in
  favor of "Display Types"  

2008-06-02  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/dipoleengine.cpp,
  libavogadro/src/engines/dipoleengine.h: *
  libavogadro/src/engines/dipoleengine.*: New dipole moment engine -- needs
  more work, but displays dipole moments from Gaussian, GAMESS and Q-Chem
  output  with recent OB-trunk.   

  * avogadro/src/CMakeLists.txt: Fix syntax error in Mac document installation.
   

2008-06-02  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp: Fixed bug 1968565 -
  orbitals are now cleared correctly along with everything else.  

2008-05-31  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some translations, mostly missing element names. 

2008-05-30  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Implemented showing and
  hiding of the preview text - defaults to shown.  

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h: Fixed up the template
  extension so that it would actually compile, added an example minimal entry
  in the CMake file too (commented out).  

2008-05-30  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp: emit
  enableEngineSettingsButton(false) when you delete an engine. Otherwise when
  you pressed "Settings...", it would segfault. 

  * ChangeLog, avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/toolgroup.cpp: * libavogadro/src/glwidget.cpp,
  libavogadro/src/toolgroup.cpp, avogadro/src/mainwindow.cpp: In windows, use
  QCoreApplication::applicationDirPath() to find the plugins. (fixes #1977338) 

  * ChangeLog, libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.ui,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h: *
  libavogadro/src/extensions/constraintsdialog.ui: Disable unimplemented
  Save/Load buttons.  * libavogadro/src/extensions/forcefieldextension.*: Only
  create new dialogs when needed. (in performAction, not in constructor)  *
  libavogadro/src/extensions/constraintsdialog.cpp: Small GUI changes (min/max
  values, singleStep, ...)  * libavogadro/src/extensions/propmodel.cpp: Angle
  and Torsion properties are not editable, don't set writable flag.  *
  libavogadro/src/extensions/propextension.*: Only create dialogs (views) and
  models when needed. Call QObject::deleteLater() on both the model and the
  view in PropertiesView::hideEvent().  * libavogadro/src/tools/autoopttool.*:
  Exit, wait, and delete the thread in the destructor. Display the energy while
  running. Added conjugate gradients again.   

2008-05-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/insertfragmentdialog.cpp: *
  libavogadro/src/tools/insertfragmentdialog.cpp: workaround for bug #1977172.
  Create a new OBConversion object each time you insert a fragment from the
  library.   

2008-05-29  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/unitcellextension.cpp: Updated "fill" method to
  check for transformed atoms outside the unit cell.  

2008-05-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h: *
  libavogadro/src/tools/directorytreemodel.*: Invalidate persistent indexes.
  See this blogpost for details: last code block at the bottom
  http://der-dakon.net/blog/KDE/persistent-crash.html (This fixes the crashes I
  was having with the "Reset List" button.)   

2008-05-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/unitcellparamdialog.ui,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: *
  libavogadro/src/glwidget.*: Add method to clear unit cell data.  *
  libavogadro/src/extensions/unitcell*: Improved unit cell dialog. Added
  "Apply" button to change parameters. Automatically changes number of cells to
  display via signals/slots. Button to delete unit cells. New button to "fill"
  unit cells with symmetry-defined atoms via the space group.   

  * libavogadro/src/tools/manipulatetool.cpp: Found another Mac SelectAll
  cursor fix.  

  * libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Workaround for Qt/Mac cursor
  problems.  

2008-05-28  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/propmodel.cpp: *
  libavogadro/src/extensions/propmodel.cpp: Get energy for all conformers and
  only use OBMol::GetEnergy() if no ConformerData is available. (fixes
  #1976199)   

2008-05-28  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some translations. 

2008-05-27  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: show a QMessageBox on invalid opengl context 
   

2008-05-27  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/CMakeLists.txt: Removed the macchempasteboard.cpp file from
  the Avogadro application if it is not being compiled on an Apple system.  

  * ChangeLog, avogadro/src/mainwindow.cpp: Fixed PR 1973714 - removed the file
  ending from the file name passed to the save dialog. Also placed the
  macchempasteboard.h in a Mac ifdef to fix compilation on other OSes.  

2008-05-27  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: *
  libavogadro/src/tools/drawtool.cpp: Do not try to change the bond order for
  X-H bonds when adjust hydrogens is on. Not sure if we should ever have double
  bonds to hydrogens...   

2008-05-27  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/macchempasteboard.cpp,
  avogadro/src/macchempasteboard.h, avogadro/src/mainwindow.cpp: *
  avogadro/src/macchempasteboard.*: Add mime converter to supply MIME types for
  Mac chemical clipboard/pasteboard types (i.e. ChemDraw).  *
  avogadro/src/mainwindow.cpp: Add support for ChemDraw. Doesn't parse -- need
  more debugging.   

2008-05-26  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: Exit at initialization if the GL context is
  invalid, which happened to a user with broken nvidia driver setup, and which
  according to QGLWidget::context() documentation also happens if somehow the
  opengl implementation doesn't support the requested format (which for now
  shouldn't happen as we check for availability of features, but this check
  makes us more fool-proof for the future).   

2008-05-26  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, Doxyfile, avogadro/src/mainwindow.h, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/elementcolor.cpp,
  libavogadro/src/elementcolor.h, libavogadro/src/elementtranslate.h,
  libavogadro/src/engine.h, libavogadro/src/extension.h,
  libavogadro/src/global.cpp, libavogadro/src/global.h,
  libavogadro/src/glwidget.h, libavogadro/src/idlist.h,
  libavogadro/src/navigate.h, libavogadro/src/painter.h,
  libavogadro/src/primitive.h, libavogadro/src/residuecolor.h,
  libavogadro/src/textrenderer.h, libavogadro/src/toolgroup.h: * Doxyfile,
  avogadro/src/mainwindow.h, libavogadro/src/*: Update doxygen documentation.  

  * ChangeLog, avogadro/src/CMakeLists.txt,
  avogadro/src/mac/locversion.plist.in: * avogadro/src/CMakeLists.txt,
  avogaro/src/mac/locversion.plist.in: Add additional Mac i18n support, solving
  PR#1972467.   

2008-05-25  Benoit Jacob <jacob.benoit.1@gmail.com>

  * CMakeLists.txt, cmake/modules/TestIfWeNeedFPermissive.cmake: patch from
  Simon: improve and make use of TestIfWeNeedFPermissive.cmake This solves
  issues with gcc >= 4.3.1 being stricter than current boost code. In fact the
  present test is slightly stricter in that 4.3.0 also needs -fpermissive. GCC
  4.2 doesn't require it.   

2008-05-25  Simon Ochsenreither <simon@ochsenreither.de>

  * cmake/modules/TestIfWeNeedFPermissive.cmake: cmake module: c++ source code
  fails with gcc >= 4.3.1, sets var permissive_no  

  * CMakeLists.txt: Fixes 1968282. We check if we need -fpermissive c++
  compiler flags. 

  * i18n/avogadro_de.ts: Some results from the translation session with carsten
  and azeem :-) #4 

  * i18n/avogadro_de.ts: Some results from the translation session with carsten
  and azeem :-) #3 

  * i18n/avogadro_de.ts: Some results from the translation session with carsten
  and azeem :-) #2 

  * i18n/avogadro_de.ts: Some results from the translation session with carsten
  and azeem :-) 

2008-05-25  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Update for Krazy 

2008-05-23  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog: Bump our dependencies on CMake and Qt.  

2008-05-22  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/orbitaldialog.cpp: Fix PR#1968560. Allow both
  .fchk and .fch files. (Maybe we should also have an option for "all files?") 

2008-05-22  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/python/deleteAll.py: Fixed the
  deleteAll script to use the new DeleteAtom function signature.  

  * ChangeLog, libavogadro/src/extensions/pythonextension.cpp: Search the
  system path for Python plugins too.  

2008-05-22  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Minor Mac cleanup -- hide menubar icons with a
  semi-documented Qt call.  

2008-05-22  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/insertfragmentdialog.cpp: *
  libavogadro/src/tools/insertfragmentdialog.cpp: Fix insert smiles. Also
  disable the driectoryTreeView and smilesLineEdit while in insert mode. This
  makes it impossible to change the smiles and forget to press Stop/Start.   

2008-05-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Add help URLs to the website.  

  * libavogadro/src/elementtranslate.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/periodictableview.cpp, libavogadro/src/tools/drawtool.cpp:
  Change extern elementTranslate to ensure there's only one copy.  

2008-05-20  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: forwardport fix from kalzium: only enable
  second light when quality>=3.   

2008-05-20  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/hydrogensextension.cpp: Fixed PR
  1947734, now the number of hydrogrens most people would expect are added.... 

2008-05-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * CMakeLists.txt, ChangeLog, avogadro/src/main.cpp,
  libavogadro/src/cylinder.cpp, libavogadro/src/elementtranslate.cpp,
  libavogadro/src/engines/iso.cpp, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/periodictableview.cpp, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/drawtool.cpp: * CMakeLists.txt: Change "C:\Program
  Files\avogadro" into "C:\\Program Files\\avogadro".  * avogadro/src/main.cpp:
  Windows build had problems with printVersion/printHelp. Quick fix with cout &
  #ifdef WIN32.  * libavogadro/src/cylinder.cpp: Make sure M_PI isdefined.  *
  libavogadro/src/elementtranslate.cpp: Global instance should be extern.  *
  libavogadro/src/engines/iso.cpp: MSVC doesn't have __attribute__
  ((aligned(16)). Quick fix with #ifdef WIN32 and without the data alignment. 
  * libavogadro/src/engines/labelengine.cpp: Local instance should not be
  extern.  * libavogadro/src/engines/polygonengine.cpp: Change
  static_cast<const Atom*> into static_cast<Atom*>.  *
  libavogadro/src/periodictableview.cpp: Local instance should not be extern. 
  * libavogadro/src/tools/aligntool.cpp: Change static_cast<const Atom*> into
  static_cast<Atom*>.  * libavogadro/src/tools/bondcentrictool.cpp: This file
  defined its own isnan() function which resulted in a conflict with
  OpenBabel::IsNan(). Now uses OpenBabel::IsNan().  *
  libavogadro/src/tools/drawtool.cpp:  Local instance should not be extern.  *
  scripts/avogadro.nsi: update installer generating script.   

2008-05-19  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Fixed the bug where zoom would
  corrupt the camera matrix in the draw tool. Made the molecule check in the
  navigate tool a little safer.  

  * ChangeLog, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h: Made the manipulate tool a lot faster
  by only saving undo points on mouse up and mouse down.  

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Added back in target_link_libraries as
  they are needed on the Mac at least.  

  * CMakeLists.txt, ChangeLog, avogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/tools/CMakeLists.txt: Various changes to the build system.
  Added -DQT_NO_DEBUG to our release mode. Changed all plugins to be built as
  modules.  

2008-05-18  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some translations added. Does someone know a sane
  translation for dock & pocket? 

2008-05-18  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/CMakeLists.txt, libavogadro/src/CMakeLists.txt: Add
  the OpenBabel library directory to the linker path.  

  * CMakeLists.txt, ChangeLog: Respect the users CXXFLAGS.  

2008-05-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/engineitemmodel.cpp: Fix the other half of PR#1965779. Sort
  engine list from the beginning.  

  * avogadro/src/enginelistview.cpp: Initial pass at a sorting proxy model for
  the list of engines.  

2008-05-17  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: Add some caching in the tool so
  measurements are only echoed once.  

  * ChangeLog, avogadro/src/mainwindow.ui: Tweaks to the UI.  

2008-05-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/addenginedialog.cpp: Fix part of PR#1965779 -- add engine
  dialog is now sorted alphabetically.  

  * libavogadro/src/engines/hbondengine.h: Fix PR# 1965781 -- name for HBond
  engine should be Hydrogen Bond engine.  

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Propagate new grids through
  to the combo and some UI cleanup.  

2008-05-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/iso.cpp: *
  libavogadro/src/iengines/iso.cpp: Surfaces are now centered around atom
  again. The - 0.5 * m_stepSize correction is only needed for
  vMarchCube1(float,float,float). This is a bug in OBFloatGrid?   

  * ChangeLog, libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: *
  libavogadro/src/tools/drawtool.*: Use new OBForceField::SetIgnoreAtom() to
  make sure the new atom doesn't push away other fragment you want to connect
  with. Also fix the atom when you hit an atom that already exists. This makes
  drawing rings with AutoOpt enabled really easy.  *
  libavogadro/src/autoopttool.*: Use new OBForceField::SetFixAtom()  *
  libavogadro/src/extensions/animationdialog.ui: Make the dialog more compact.
  Removed the group boxes.   

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.ui: Hide more advanced options for
  now, cleanups.  

2008-05-16  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawcommand.cpp: Fix PR#1965449 with alchemy mode --
  one last OBMol::GetAtom existed -- changed to getAtomById. Kudos to Marcus
  for finding the spot.  

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/drawtool.cpp:
  Minor interface cleanups.  

  * INSTALL: Minor cleanups for requirements.  

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/extensions/animationextension.cpp: Small clean up.  

2008-05-16  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Krazy  

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog: ChangeLog entry got mangled...  

  * libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/aligntool.h:
  Added options to align everything or just the current molecule.  

2008-05-16  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version for 0.8
  release.  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/tools/autorotatetool.cpp: *
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/propextension.cpp, avogadro/src/mainwindow.ui,
  avogadro/src/mainwindow.cpp: More interface cleanup -- any menu item or
  button which brings up a dialog should have "..." at the end. (KDE, Windows,
  and Mac UI guidelines.)   

2008-05-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: More layout improvements.  

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: Layout improvements in the
  tool set up dialog.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added the ability to edit
  the input deck, revert etc.  

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: Added some extra signals on
  mouse release to ensure molecule is updated.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.ui: Fixed the tab
  ordering of the dialog.  

  * ChangeLog, libavogadro/src/periodictableview.cpp: Some changes to improve
  layout in Linux (and hopefully Windows).  

  * ChangeLog, cmake/modules/FindOpenBabel2.cmake: Hopefully a new and improved
  FindOpenBabel2 using the new PkgConfig functions.  

  * CMakeLists.txt, ChangeLog: Set the CMake policy for CMake 2.6.  

2008-05-16  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: * avogadro/mainwindow.h, avogadro/mainwindow.cpp:
  Changed engine configuration to a new button which brings up an extra
  "settings" window with tabs. Add signal/slot for enabling the Engine Settings
  window -- only enables button for engines with settings.   

  * avogadro/src/enginelistview.cpp, avogadro/src/primitivetreeview.cpp: *
  src/enginelistview.cpp, primitivetreeview.cpp: Add setUniformItemSizes(true)
  -- supposedly improves performance.   

  * avogadro/src/enginesetupwidget.cpp, avogadro/src/enginesetupwidget.h,
  avogadro/src/enginesetupwidget.ui: Removed deprecated code.  

2008-05-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/elementcombobox.cpp.disabled, avogadro/src/elementcombobox.h:
  Remove deprecated code.  

2008-05-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitive.cpp: Fixed primitive to not be so hacky when it
  comes to the unique IDs.  Should fix some signal problems.  

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  libavogadro/include/avogadro/idlist.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h, libavogadro/src/idlist.cpp,
  libavogadro/src/idlist.h, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h: Added the IDList class which holds an organized
  list of IDs like PrimitiveList except that you cannot iterate through them
  all since IDs are specific to the type they belong.  Moved id to be a
  property of all primitives.  Fixed the Hydrogens commands and the
  editcommands to use IDs instead of pointers which should alleviate much of
  the crashing.  See PR#1964661  

2008-05-15  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.cpp: Made some
  changes to the surface engine and the GLWidget to improve locking. Seems to
  have prevented crashes in the surface engine here. More locking is needed.  

  * ChangeLog, libavogadro/src/tools/selectrotatetool.cpp: Added Control
  modifier to the tool to fix PR 1962903 - toggle selected primitives.  

  * ChangeLog, libavogadro/src/color.h: Cast GLFloats to ints to suppress
  warning.  

  * ChangeLog, libavogadro/src/CMakeLists.txt: Only add the Boost_INCLUDE_DIR
  if boost is found - fixes a CMake error with CMake 2.6.  

2008-05-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  Added unique identifiers for each atom that is created and this helps us with
  adding and deleting atoms with our drawing tool.  

  * libavogadro/src/boost.h: update to fix newest const correctness in
  openbabel  

  * libavogadro/src/extensions/pythonextension.cpp: Cleaned up debugging code. 

2008-05-14  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/pythonextension.cpp: Fixed typo.  

2008-05-14  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts: update and improve french translation   

2008-05-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/animation.qrc,
  libavogadro/src/extensions/animationdialog.cpp,
  libavogadro/src/extensions/animationdialog.h,
  libavogadro/src/extensions/animationdialog.ui,
  libavogadro/src/extensions/animationextension.cpp,
  libavogadro/src/extensions/animationextension.h,
  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, testfiles/spc216.pdb,
  testfiles/spc216.xtc: * libavogadro/src/extensions/animation*.*: Basic
  animation extension.  * testfiles/spc216.*: Added pdb topology and xtc
  trajectory to test animation.   

2008-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog: Allow ENABLE_PYTHON variable to allow disabling
  of Python.  

2008-05-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: Fix
  PR#1839866 with graphical bugs and multiple bond wireframe view.  

  * libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp: Fixed PR#1959763.  

2008-05-13  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Krazy  

2008-05-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/insertfragmentdialog.cpp: typo:/usr/shareD/ should be
  /usr/share. Fixes #1959763  

2008-05-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/pythonextension.cpp: Mac fix for path to
  Avogadro script directory.  

  * libavogadro/src/glwidget.cpp: Make sure to remove the unit cell when
  setMolecule is called. Fixes PR# 1947737.  

  * libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp: Some Linux fixes for the
  insert fragment paths.  

2008-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: Fixed uninitialised
  variables.  

2008-05-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/primitiveitemmodel.cpp: A few minor "const" fixes for
  foreach() keyword.  

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfacesettingswidget.ui: Disable the "Custom Color"
  widget when using ESP coloring.  

2008-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * i18n/avogadro_de.ts, i18n/avogadro_en_GB.ts, i18n/avogadro_fr.ts,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/insertfragmentdialog.ui: Update some translation
  strings.  

  * ChangeLog, avogadro/src/mainwindow.cpp: Fix a potential file corruption
  problem if save file fails. Instead, save to a new name, then rename the
  file.  * avogadro/src/mainwindow.cpp: Implement save to a new file, then a
  rename. (If others have ways to improve this, please let me know.)   

2008-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp: Fixed the code to fail properly
  when the file to be opened does not exist.  

2008-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/residuecolor.cpp: Fix minor compiler warning --
  unintialized residue.  

  * avogadro/src/mainwindow.cpp: Fix minor bug -- hideMainWindow for Mac would
  disable select all and select none actions.  

  * avogadro/src/main.cpp: Fix PR#1849964. Unfortunately Qt docs fall down--
  you need to specify the path to the Qt translations. Ugh.  

2008-05-12  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Geoff fixed many many more issues. <10 left! 

2008-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp: *
  libavogadro/src/extensions/propmodel.cpp
  libavogadro/src/extensions/propextension.h
  libavogadro/src/extensions/propextension.cpp: Updates to fix some
  translations and to allow resizing the window without showing large amounts
  of empty space.   

  * Doxyfile, Doxyfileext: Update for 0.8 version number.  

  * avogadro/src/addenginedialog.h, avogadro/src/application.h,
  avogadro/src/editcommands.h, avogadro/src/elementcombobox.h,
  avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.h,
  avogadro/src/enginesetupwidget.h, avogadro/src/flattabwidget.h,
  avogadro/src/mainwindow.h, avogadro/src/primitivetreeview.h,
  avogadro/src/savedialog.h, avogadro/src/settingsdialog.h,
  libavogadro/src/boost.h, libavogadro/src/camera.h, libavogadro/src/color.h,
  libavogadro/src/colorbutton.h, libavogadro/src/cylinder.h,
  libavogadro/src/elementcolor.h, libavogadro/src/elementtranslate.h,
  libavogadro/src/engine.h, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/extension.h, libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/constraintsdialog.h,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/constraintsmodel.h,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/forcefielddialog.h,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/liganddialog.h,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitalextension.h,
  libavogadro/src/extensions/pocketdialog.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/extensions/wiitrackextension.h,
  libavogadro/src/filetreeitem.h, libavogadro/src/global.h,
  libavogadro/src/glpainter.h, libavogadro/src/glwidget.h,
  libavogadro/src/navigate.h, libavogadro/src/painter.h,
  libavogadro/src/painterdevice.h, libavogadro/src/painterengine.h,
  libavogadro/src/periodictableview.h, libavogadro/src/povpainter.h,
  libavogadro/src/primitive.h, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitivelist.h, libavogadro/src/pythoninterpreter.h,
  libavogadro/src/residuecolor.h, libavogadro/src/sphere.h,
  libavogadro/src/textrenderer.h, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.h, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/aligntool.h, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/quaternion.h, libavogadro/src/tools/selectrotatetool.h,
  libavogadro/src/tools/skeletontree.h, libavogadro/src/undosequence.h: More
  Krazy fixes.  

2008-05-12  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Update Krazy after Geoffs many fixes 

2008-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/flowlayout.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdialog.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/painterengine.cpp, libavogadro/src/painterengine.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/skeletontree.cpp,
  libavogadro/src/tools/skeletontree.h: * Many files: Fix a pile of Krazy
  warnings.   

2008-05-11  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed uninitialised undoStack
  pointer.  

2008-05-10  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/aligntool.cpp: Fixed for case where the
  molecule was already alined to the chosen axis.  

2008-05-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/directorytreemodel.cpp: Fix a silly nested directory
  bug.  

  * avogadro/src/mainwindow.cpp: Fix silly warning about end-of-file with gzip
  files. We can't seem to properly test, so check for ".gz" in the filename.  

  * CMakeLists.txt, ChangeLog, libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp: * CMakeLists.txt: Install our
  fragments. Destination may need tuning on Linux and Windows.  *
  libavogadro/src/tools/insertfragmentdialog.cpp: Update to include default
  fragment paths as much as possible. This will need tuning on Linux and
  Windows. Does Cmake set a -D define for an installation path, e.g. /usr vs
  /usr/local?  * libavogadro/src/tools/directorytreemodel.cpp: Ignore hidden
  files.   

  * fragments/coordination/3-trigonal-planar.cml,
  fragments/coordination/3-trigonal-pyramidal.cml,
  fragments/coordination/4-planar.cml,
  fragments/coordination/4-tetrahedral.cml,
  fragments/coordination/5-square-pyramidal.cml,
  fragments/coordination/5-trigonal-bipyramidal.cml,
  fragments/coordination/6-octahedral.cml: Add coordination fragments for metal
  centers  

2008-05-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/extensions/forcefieldextension.cpp: *
  libavogadro/src/extensions/forcefieldextension.cpp: Added a
  QMessageBox::information() box to display the energy when the user clicks
  "Calculate Energy". (#1947745)   

  * ChangeLog, libavogadro/src/extensions/forcefieldextension.cpp: *
  libavogadro/src/extensions/forcefieldextension.cpp: Move call to SetLogFile
  (fixes #1960307)   

2008-05-08  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * fragments/cyclic alkanes/adamantane.cml, fragments/cyclic
  alkanes/cyclobutane.cml, fragments/cyclic alkanes/cycloheptane.cml,
  fragments/cyclic alkanes/cyclohexane.cml, fragments/cyclic
  alkanes/cyclopentane.cml, fragments/cyclic alkanes/cyclopropane.cml: New
  alkane rings.  

2008-05-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * fragments/alcohols/ethanol.cml, fragments/alcohols/methanol.cml,
  fragments/alcohols/propan-1-ol.cml, fragments/alcohols/propan-2-ol.cml,
  fragments/aldehydes/acetaldehyde.cml, fragments/aldehydes/formaldehyde.cml,
  fragments/alkanes/2-methylpropane.cml, fragments/alkanes/ethane.cml,
  fragments/alkanes/methane.cml, fragments/alkanes/propane.cml,
  fragments/alkenes/but-1-ene.cml, fragments/alkenes/ethene.cml,
  fragments/alkynes/acetylene.cml, fragments/alkynes/propyne.cml,
  fragments/amides/N_N-dimethylacetamide.cml,
  fragments/amides/N_N-dimethylformamide.cml, fragments/amides/acetamide.cml,
  fragments/amides/ethyl_carbamate.cml, fragments/amides/oxamide.cml,
  fragments/amines/ammonia.cml, fragments/amines/azepane.cml,
  fragments/amines/ethylamine.cml, fragments/amines/methylamine.cml,
  fragments/amino_acids/D-alanine.cml,
  fragments/amino_acids/D-allo-threonine.cml,
  fragments/amino_acids/D-arginine.cml, fragments/amino_acids/D-asparagine.cml,
  fragments/amino_acids/D-aspartic_acid.cml,
  fragments/amino_acids/D-cysteine.cml,
  fragments/amino_acids/D-glutamic_acid.cml,
  fragments/amino_acids/D-glutamine.cml, fragments/amino_acids/D-histidine.cml,
  fragments/amino_acids/D-isoleucine.cml, fragments/amino_acids/D-leucine.cml,
  fragments/amino_acids/D-lysine.cml, fragments/amino_acids/D-methionine.cml,
  fragments/amino_acids/D-phenylalanine.cml,
  fragments/amino_acids/D-proline.cml, fragments/amino_acids/D-serine.cml,
  fragments/amino_acids/D-threonine.cml,
  fragments/amino_acids/D-tryptophan.cml, fragments/amino_acids/D-tyrosine.cml,
  fragments/amino_acids/D-valine.cml,
  fragments/amino_acids/L-4-nitrophenylalanine.cml,
  fragments/amino_acids/L-alanine.cml,
  fragments/amino_acids/L-allo-isoleucine.cml,
  fragments/amino_acids/L-arginine.cml, fragments/amino_acids/L-asparagine.cml,
  fragments/amino_acids/L-aspartic_acid.cml,
  fragments/amino_acids/L-cysteine.cml,
  fragments/amino_acids/L-glutamic_acid.cml,
  fragments/amino_acids/L-glutamine.cml, fragments/amino_acids/L-histidine.cml,
  fragments/amino_acids/L-isoleucine.cml, fragments/amino_acids/L-leucine.cml,
  fragments/amino_acids/L-lysine.cml, fragments/amino_acids/L-methionine.cml,
  fragments/amino_acids/L-phenylalanine.cml,
  fragments/amino_acids/L-proline.cml, fragments/amino_acids/L-serine.cml,
  fragments/amino_acids/L-threonine.cml,
  fragments/amino_acids/L-tryptophan.cml, fragments/amino_acids/L-tyrosine.cml,
  fragments/amino_acids/L-valine.cml, fragments/amino_acids/glycine.cml,
  fragments/aromatics/1H-indene.cml, fragments/aromatics/aniline.cml,
  fragments/aromatics/anisole.cml, fragments/aromatics/anthracene.cml,
  fragments/aromatics/benzaldehyde.cml, fragments/aromatics/benzene.cml,
  fragments/aromatics/benzoic_acid.cml,
  fragments/aromatics/benzoyl_chloride.cml, fragments/aromatics/caffeine.cml,
  fragments/aromatics/naphthalene.cml, fragments/aromatics/nitrobenzene.cml,
  fragments/aromatics/phenol.cml, fragments/aromatics/toluene.cml,
  fragments/buckminsterfullerene.cml, fragments/carbamides/urea.cml,
  fragments/carbohydrates/d-allose.cml, fragments/carbohydrates/d-altrose.cml,
  fragments/carbohydrates/d-arabinose.cml,
  fragments/carbohydrates/d-erythrose.cml,
  fragments/carbohydrates/d-erythrulose.cml,
  fragments/carbohydrates/d-fructose.cml,
  fragments/carbohydrates/d-galactose.cml,
  fragments/carbohydrates/d-glucose.cml,
  fragments/carbohydrates/d-glyceraldehyde.cml,
  fragments/carbohydrates/d-gulose.cml, fragments/carbohydrates/d-idose.cml,
  fragments/carbohydrates/d-lyxose.cml, fragments/carbohydrates/d-mannose.cml,
  fragments/carbohydrates/d-psicose.cml, fragments/carbohydrates/d-ribose.cml,
  fragments/carbohydrates/d-ribulose.cml,
  fragments/carbohydrates/d-sorbose.cml,
  fragments/carbohydrates/d-tagatose.cml, fragments/carbohydrates/d-talose.cml,
  fragments/carbohydrates/d-threose.cml, fragments/carbohydrates/d-xylose.cml,
  fragments/carbohydrates/d-xylulose.cml,
  fragments/carbohydrates/dihydroxyacetone.cml,
  .../carboxylic_acids/2_2-dichloroacetic_acid.cml,
  .../2_2_2-trichloroacetic_acid.cml, .../2_2_2-trifluoroacetic_acid.cml,
  fragments/carboxylic_acids/D-lactic_acid.cml,
  fragments/carboxylic_acids/D-malic_acid.cml,
  fragments/carboxylic_acids/D-tartaric_acid.cml,
  fragments/carboxylic_acids/L-ascorbic_acid.cml,
  fragments/carboxylic_acids/L-lactic_acid.cml,
  fragments/carboxylic_acids/L-malic_acid.cml,
  fragments/carboxylic_acids/L-tartaric_acid.cml,
  fragments/carboxylic_acids/acetic_acid.cml,
  fragments/carboxylic_acids/butanoic_acid.cml,
  fragments/carboxylic_acids/citric_acid.cml,
  fragments/carboxylic_acids/formic_acid.cml,
  fragments/carboxylic_acids/isobutyric_acid.cml,
  fragments/carboxylic_acids/oxalic_acid.cml,
  fragments/carboxylic_acids/propanoic_acid.cml, fragments/cyclic
  alkanes/cubane.cml, fragments/cyclic alkanes/norbornane.cml,
  fragments/ethers/di-tert-butylether.cml, fragments/ethers/dibutylether.cml,
  fragments/ethers/diethylether.cml, fragments/ethers/diisopropylether.cml,
  fragments/ethers/dimethylether.cml, fragments/ethers/dipropylether.cml,
  fragments/ethers/ethylmethylether.cml, fragments/ethers/tetrahydrofuran.cml,
  fragments/fatty acids/decanoic_acid.cml, fragments/fatty
  acids/hexanoic_acid.cml, fragments/fatty acids/lauric_acid.cml,
  fragments/fatty acids/linoleic_acid.cml, fragments/fatty
  acids/octanoic_acid.cml, fragments/fatty acids/oleic_acid.cml,
  fragments/fatty acids/palmitic_acid.cml, fragments/fatty
  acids/stearic_acid.cml, fragments/heteroaromatics/1H-indole.cml,
  fragments/heteroaromatics/1H-pyrazole.cml,
  fragments/heteroaromatics/1H-pyrrole.cml,
  fragments/heteroaromatics/1_2-oxazole.cml,
  fragments/heteroaromatics/1_2-thiazole.cml,
  fragments/heteroaromatics/1_3-oxazole.cml,
  fragments/heteroaromatics/1_3-thiazole.cml,
  fragments/heteroaromatics/benzofuran.cml,
  fragments/heteroaromatics/benzothiophene.cml,
  fragments/heteroaromatics/furan.cml, fragments/heteroaromatics/pyridine.cml,
  fragments/heteroaromatics/thiophene.cml, fragments/ketones/acetone.cml,
  fragments/ketones/butanone.cml, fragments/macrocycles/porphin.cml,
  fragments/nucleobases/adenine.cml, fragments/nucleobases/cytosine.cml,
  fragments/nucleobases/guanine.cml, fragments/nucleobases/thymine.cml,
  fragments/nucleobases/uracil.cml, fragments/steroids/cholesterol.cml,
  fragments/steroids/estradiol.cml, fragments/steroids/testosterone.cml,
  fragments/sulfoxides/dimethyl_sulfoxide.cml,
  fragments/thiols/ethanethiol.cml, fragments/thiols/methanethiol.cml,
  fragments/thiols/pentane-1-thiol.cml, fragments/water.cml: Added new fragment
  library based on chem-file Blue Obelisk repository. These are selected files,
  and I haven't added the CMakeLists.txt to install them. Suggestions welcome. 

2008-05-07  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt: Optionally use CMake 2.6 and the
  much improved FindBoost to check for and use Boost Python on more than just
  Linux - works great on the Mac.  

2008-05-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.h,
  libavogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/extensions/forcefielddialog.h,
  libavogadro/src/extensions/forcefielddialog.ui,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h: *
  libavogadro/src/extensions/forcefielddialog.*: Removed gradients option. Now
  handled OBForceField::HasAnalyticalGradients()  *
  libavogadro/src/extensions/conformersearchdialog.*: Same.  *
  libavogadro/src/extensions/forcefieldextension.*: Same.  *
  libavogadro/src/extensions/constraintsdialog.*: Update for static
  constraints. We now only need to set it once.  *
  libavogadro/src/tools/autoopttool.*: Replaced convergence spin box by steps
  per update spin box.   

2008-05-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Make sure "SaveAs" is always enabled, and
  exporting graphics and POV-Ray have default names and paths.  

2008-05-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/extensions/forcefieldextension.cpp: Warning if a force
  field cannot be set up for a molecule. (e.g., using MMFF94 on a molecule with
  metals)  

2008-05-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Set the navigate tool as the
  active tool after loading a file.  

2008-05-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: Added saving of the current
  element to the draw tool.  

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp: Add checks in for whether
  the force field was initialised correctly.  

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: More updates to the orbital engine
  to improve rendering consistency.  

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Fixed another
  crasher - when no basis set has been loaded.  

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Corrected the
  MO title in the cube title.  

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Added some settings persistence,
  improved the quickRender a little too.  

2008-05-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: More guarded pointers to prevent
  crashing caused by dangling pointers.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Only switch to quickRender on
  mouse move, not press.  

  * ChangeLog, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/aligntool.h: Used guarded pointers (QPointer) to make
  the align tool much harder to crash.  

2008-05-02  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp: Adding some extra detail on
  the cube parameters along with the ability to modify this. Also added a
  little extra debug output while support if improved.  

2008-05-01  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added several new options
  and modifications based upon discussion in bug 1954113. Editing of the text
  edit box still needs to be added.  

2008-04-30  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Update the display after axes or
  debug rendering is turned on or off.  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Updated
  with new view menu actions for axes and debug information.  

2008-04-30  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/savedialog.cpp: Make sure to always offer "untitled" as a
  default filename.  

2008-04-29  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/savedialog.cpp: *
  avogadro/src/mainwindow.cpp: Fix up Mac/Windows save dialogs. Also disable
  save/revert menu actions until the document is modified.  *
  avogadro/src/savedialog.cpp: Remove incorrect #ifdef for setting filters on
  Mac. Now done in mainwindow.cpp. Use static QFileDialog on Windows (and Mac).
    

  * libavogadro/src/tools/align.png, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/aligntool.qrc: New icon for the align tool.  

2008-04-29  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp: Several
  fixes suggested by Michael Banck in bugs 1954108, 1954101 and 1954099.  

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Only recalculate the
  isosurface when editing is finished, minimum spinner value of zero.  

  * ChangeLog, avogadro/src/mainwindow.cpp: Tracked the bug of the disappearing
  molecule - it was never set for extensions after the first window.  

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Return if the
  file name is empty.  

2008-04-28  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp: Also
  connected molecule signals to the dialog.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp: Made the
  reset button work.  

  * ChangeLog, libavogadro/src/extensions/gaussianinputdialog.cpp: Update the
  preview when setMolecule is called. Also added some logic to disable basis
  sets with certain theories.  

  * ChangeLog, libavogadro/src/extensions/basisset.cpp: Actually call the doD
  and doD5 functions - this really helps when trying to use d-type orbitals to
  generate cubes...  

2008-04-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: On Mac, will close the molecule when the
  window is "closed." Also disables "Revert to Saved" if the molecule is
  unmodified.  

2008-04-28  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/gaussianextension.cpp,
  libavogadro/src/extensions/gaussianextension.h,
  libavogadro/src/extensions/gaussianinputdialog.cpp,
  libavogadro/src/extensions/gaussianinputdialog.h,
  libavogadro/src/extensions/gaussianinputdialog.ui: Added a new Gaussian input
  deck generator. Still quite basic with a few bugs but is already generating
  valid input decks.  

2008-04-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/savedialog.cpp,
  avogadro/src/savedialog.h: Cleaned up Mac-specific save dialog (we can use
  the Qt static methods). Make sure to save the selected filter on all
  platforms -- we should remember what the user picked and make it the default
  next time.  

2008-04-27  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Found a few more cases where
  foreach loops needing fixing.  

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/toolgroup.cpp:
  Made changes to foreach loops as suggested by Albert Astals Cid, prevent
  unnecessary creation of temporary objects.  

2008-04-25  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Add back Mac-native file dialogs. Still needs
  more work.  

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: *
  avogadro/src/mainwindow.*: Add drag-and-drop support. Files dragged onto a
  window will be loaded.   

  * avogadro/src/mainwindow.ui: * avogadro/src/mainwindow.ui: Move export to a
  new submenu of File.   

  * libavogadro/src/moleculetreeview.cpp.disabled,
  libavogadro/src/moleculetreeview.h.disabled,
  libavogadro/src/primitiveitemmodel.cpp: *
  libavogadro/src/primitiveitemmodel.cpp: Added in layout change signals. Will
  hopefully prevent crashing.   

2008-04-25  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/orbitalextension.cpp: Ported to use std::vector to
  store everything. Changed the way normalisation is handled. Added d-type
  orbitals - this has not been verified yet.  

2008-04-24  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/basisset.cpp: Added destructor bits. 

2008-04-23  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Sorted out the
  units in the cube calculation initialisation...  

2008-04-22  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Also added a
  call to processEvents() to maintain interactivity.  

  * ChangeLog, libavogadro/src/extensions/orbitalextension.cpp: Work out the
  dimensions of the cube from the molecule, also clear the molecule.  

  * ChangeLog, libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/basisset.cpp,
  libavogadro/src/extensions/basisset.h,
  libavogadro/src/extensions/gaussianfchk.cpp,
  libavogadro/src/extensions/gaussianfchk.h,
  libavogadro/src/extensions/orbitaldialog.cpp,
  libavogadro/src/extensions/orbitaldialog.h,
  libavogadro/src/extensions/orbitaldialog.ui,
  libavogadro/src/extensions/orbitalextension.cpp,
  libavogadro/src/extensions/orbitalextension.h: Added a new orbital extension.
  This extension uses the new BasisSet class along with GaussianFchk to load a
  formatted checkpoint file and calculate MOs. Support for more programs and
  more features soon.  

2008-04-22  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some fragment translations added. Does someone know a
  sane translation for dock, ligand & pocket? 

2008-04-21  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts: update french translation   

  * avogadro/src/savedialog.cpp, avogadro/src/savedialog.h,
  libavogadro/src/tools/navigatetool.cpp: * fix bug: when using navigatetool on
  empty molecule, the camera got corrupted. * fix file comment in savedialog.* 
   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/savedialog.cpp, avogadro/src/savedialog.h,
  libavogadro/src/povpainter.cpp: * make the SaveDialog generic enough to be
  useful for more than just saving molecules. * move it to separate
  savedialog.* files * use it in "export graphics" and "export POV-Ray". * fix
  crash when doing "export POV-Ray" on empty molecule   

2008-04-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h: Fixed reloading of python
  script issue.  

  * libavogadro/src/filetreeitem.h: Added visibility keyword.  

2008-04-20  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Add SaveDialog
  class inheriting QFileDialog, currently in mainwindow.* but feel free to move
  to separate files. This class sets a default filename suffix based on the
  currently selected filter. Having our own class allows us to act on the
  filterSelected signal, which is necessary for a consistent behavior.  Closes
  avogadro-Bugs-1945955   

2008-04-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp: add filters to the file open / "save as"
  dialogs. This hopefully addresses avogadro-Bugs-1945955   

  * libavogadro/src/filetreeitem.cpp: fix compilation on case-sensitive
  filesystem. still the same linking error further in the build process,
  though.   

2008-04-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/include/avogadro/filetreeitem.h,
  libavogadro/include/avogadro/treeitem.h, libavogadro/src/filetreeitem.cpp,
  libavogadro/src/filetreeitem.h, libavogadro/src/treeitem.cpp,
  libavogadro/src/treeitem.h: Step two: FileTreeItem not TreeItem  

  * libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h, libavogadro/src/treeitem.cpp,
  libavogadro/src/treeitem.h: Step one of renaming TreeItem to FileTreeItem  

  * libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/insertfragmentdialog.ui: Fixed crashes with fragment
  window -- need to emit layoutChanged signals. Now also checks for duplicate
  directories and allows the directory list to be cleared.  

2008-04-18  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating Krazy2 checks  

2008-04-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp: Add support for
  always giving a transparent background. We can make this a configuration
  option (e.g., amount of transparency), but it's currently great for exporting
  graphics.  

  * ChangeLog, libavogadro/include/avogadro/treeitem.h,
  libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/directorytreemodel.cpp,
  libavogadro/src/tools/directorytreemodel.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/insertfragmentdialog.cpp,
  libavogadro/src/tools/insertfragmentdialog.h,
  libavogadro/src/tools/insertfragmentdialog.ui, libavogadro/src/treeitem.cpp,
  libavogadro/src/treeitem.h: * libavogadro/src/treeitem.*: New class for
  handling filenames in model/view context, particularly a tree browser.  *
  libavogadro/src/tools/directorytreemodel.*: New class for handling directory
  trees with multiple paths. (Basic Qt class QDirModel gives too much file info
  and doesn't handle multiple top-level directories.)  *
  libavogadro/src/tools/insertfragmentdialog.*: New class to combine the SMILES
  generation and reading in fragment files. Still needs a bit of polish.  *
  libavogadro/src/tools/drawtool.*: Use above.  *
  libavogadro/src/tools/drawcommand.*: Change InsertSMILES class to
  InsertFragment (now that we have a general fragment browser).   

  * ChangeLog, libavogadro/src/navigate.cpp, libavogadro/src/navigate.h: *
  libavogadro/src/navigate.*: Add general rotate(x, y, z) method (for
  scripting).   

2008-04-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Use the shift key rather than alt key
  as the second modifier.  

2008-04-16  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some translations (axes and python for instance) added

2008-04-15  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/config.h.in, avogadro/src/mainwindow.cpp,
  libavogadro/src/config.h.in, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/toolgroup.cpp: Added
  INSTALL_LIBDIR define in order to more reliably load plugins. Adapted the
  loading scheme for tools, engines and extensions to use INSTALL_LIBDIR.  

2008-04-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  avogadro/src/settingsdialog.ui: Removed the axes and debug display options
  from the global config - to be relocated to the view menu. Also (hopefully)
  improved the display quality feedback.  

  * ChangeLog, libavogadro/include/avogadro/navigate.h,
  libavogadro/src/navigate.cpp, libavogadro/src/navigate.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/aligntool.cpp,
  libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigate.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Moved the navigate functions from
  the tools directory into the library. They should be exposed as part of our
  API and would be useful in scripting.  

  * ChangeLog, libavogadro/src/tools/CMakeLists.txt: Removed the duplicate
  definition of bondcentrictool.  

  * CMakeLists.txt: Enable symbol hiding - currently needs OB trunk as of one
  minute ago built using cmake (not sure how to fix auto* - shouldn't be too
  hard).  

  * CMakeLists.txt, libavogadro/src/global.h: Disabled the visibility flags
  again (for now) while I work on getting it working in OpenBabel - still
  having issues with the formats and visibility.  

2008-04-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfacesettingswidget.ui: *
  libavogadro/src/engines/surfaceengine.*,
  libavogadro/src/engines/surfacesettingswidget.ui: Clipping now works for any
  specified plane.   

2008-04-12  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, libavogadro/src/global.h: Only do the GCC visibility stuff
  when we have a supported compiler.  

2008-04-12  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating the Krazy files  

  * libavogadro/src/engines/axesengine.cpp: Include own header first  

  * libavogadro/src/tools/navigatetool.cpp: Typo--  

2008-04-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui: *
  libavogadro/src/engines/surfaceengine.*,
  libavogadro/src/engines/surfacesettingswidget.ui: Added clipping plane. This
  feature could later be moved to glwidget to clip any engine... This would
  probably require engines to have a clipped and solid property (like they
  currently have radius)   

2008-04-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * scripts/distclean.sh: Minor fix to clean out other misc files (e.g. dylibs)
  which can build up if srcdir == builddir  

2008-04-10  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.cpp, libavogadro/src/glwidget.cpp:
  Parts of the patch from Benoit Jacob - fix handling of quality change.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed bug where display lists were
  not being invalidated when the display quality was adjusted.  

  * ChangeLog, libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp: Fixed some compiler warnings.  

2008-04-09  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/camera.h, libavogadro/src/textrenderer.h,
  libavogadro/src/tools/drawtool.cpp: Fixed a few compiler warnings.  

2008-04-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/boost.h, libavogadro/src/extensions/pythonextension.cpp:
  Add some preliminary auto-complete features for the Python terminal and
  several new Open Babel features in the scripting support.  

  * libavogadro/src/extensions/forcefieldextension.cpp: Add indications of
  warnings for problems when molecules cannot be configured by a force field.  

2008-04-08  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/CMakeLists.txt: Removed duplicate call to
  automoc.  

2008-04-07  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog: Only set the linker flag on Linux systems.  

  * CMakeLists.txt, ChangeLog,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h: Disabled the visibility
  flags for now as the seem to break forcefield support.  

  * ChangeLog, avogadro/src/mainwindow.cpp: Added a warning dialog when no
  engines and/or tools were loaded.  

  * ChangeLog, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/glwidget.cpp:
  Statically linked the ball and stick engine to libavogadro. This guarantees
  the minimal ability to display a molecule.  

  * CMakeLists.txt, ChangeLog: Added the pedantic compiler flag to spot many
  issues with C++ code such as those picked up by KDE developers. Also
  introduce symbol hiding if a recent GCC is installed. We need to explicitly
  export all symbols on Linux/Apple systems.  

  * ChangeLog, cmake/modules/FindBoostPython.cmake,
  cmake/modules/MacroEnsureVersion.cmake, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extensions/CMakeLists.txt: Added extra cmake modules from KDE
  4.1 (trunk) to improve Boost Python detection and check versions. Improved
  the Boost Python detection and linked to the dynamic Python library.  

  * ChangeLog, avogadro/src/application.h, avogadro/src/enginelistview.h,
  avogadro/src/engineprimitiveswidget.h, avogadro/src/enginesetupwidget.h,
  avogadro/src/mainwindow.h, libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/surfaceengine.h, libavogadro/src/extension.h,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessefpmatchdialog.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/tools/autoopttool.h: Fixed errors pointed out by the pedantic
  compiler flag - mainly extra ;s and ,s.  

  * ChangeLog, libavogadro/src/pythoninterpreter.h: Ensure the Python
  interpreter exports its symbols.  

2008-04-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/primitive.h, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/tool.h: Changes made by Pino Toscano in KDE upstream.  

  * ChangeLog, libavogadro/src/periodictableview.h: Only export the
  PeriodicTableView class.  

  * ChangeLog, libavogadro/src/tools/navigatetool.cpp: Remember to account for
  the situation where no molecule is loaded.  

  * ChangeLog, libavogadro/src/global.h: Added visibility attributes to the
  A_EXPORT definitions so that our symbols are correctly exported when the
  default visibility is changed to hidden (as in KDE 4.1 trunk).  

2008-04-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/CMakeLists.txt: Forgot to link to the navigate code -
  worked on Linux somehow but now on Mac.  

  * ChangeLog, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/aligntool.cpp, libavogadro/src/tools/aligntool.h,
  libavogadro/src/tools/aligntool.qrc: Added new align tool. Currently it just
  aligns the selected atom to the origin, if there are two selected atoms they
  will be aligned along the chosen axis.  

2008-04-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h:
  Added new axes engine to display the x, y, z axes in the scene. More options
  soon.  

2008-04-01  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/extensions/gamessinputdialog.cpp: Correct bug
  where nd was also being used to set np in the basic tab.  

2008-03-31  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, libavogadro/src/CMakeLists.txt: Updated CMake
  files to properly link with Python and Boost.  Thanks to Jens Thomas for
  reporting and helping me debug.  

2008-03-24  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating to latest Krazy  

2008-03-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, libavogadro/src/boost.h,
  libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/python/deleteAll.py,
  libavogadro/src/extensions/python/test.py,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythoninterpreter.h:
  Python scripts are now available.  This means you can write a python script
  (including PyQt) and it will function along with the data loaded already.  We
  have not yet exposed all parts of the API but this should give us the basis
  of where to go.  To utilize this new stuff.  Place scripts in
  $HOME/.avogadro/scripts  Avogadro should automatically detect them on loadup.
   Also, if you modify a script while the application is running it will reload
  that script before executing it again.  See the example scripts provided. 
  They are installed to $PREFIX/libavogadro/scripts but they are not
  automatically enabled.  Until we get a "script manager" then we will keep it
  like this.  -- Donald  

  * libavogadro/src/CMakeLists.txt: Fix build hangup where system doesn't have
  boost installed.  Will automatically disable Python support.  

  * libavogadro/src/boost.h, libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/pythonterminalwidget.ui: Python Extension input
  line now remembers your command history.  

  * CMakeLists.txt, avogadro/src/mainwindow.cpp,
  libavogadro/include/avogadro/boost.h,
  libavogadro/include/avogadro/pythoninterpreter.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/boost.h,
  libavogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/extensions/pythonextension.cpp,
  libavogadro/src/extensions/pythonextension.h,
  libavogadro/src/extensions/pythonterminalwidget.ui,
  libavogadro/src/pythoninterpreter.cpp, libavogadro/src/pythoninterpreter.h:
  Added initial python support.  Python Extension includes an interactive
  interpreter.  

  * libavogadro/src/extensions/templateextension.cpp,
  libavogadro/src/extensions/templateextension.h: Added a set of extension
  template files.  

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/dockingextension.h,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h: Finalize moving extensions to
  the library and make a few patches.  See the updated ChangeLog for more
  details.  There is now an Extension::setMolecule function (which is a signal)
  that Extensions can reimplement and keep better tabs on the underlying data
  model.  

  * libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/dockingextension.h,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h: Move extensions to
  libavogadro  

2008-03-22  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-extensions.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/runkrazy.rb: Reran Krazy.  

  * krazy/avogadro-src-extensions.html: new directory (src/extensions moved)  

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating the Krazy files  

2008-03-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extension.h: Removing orphaned file.  

  * ChangeLog, avogadro/src/CMakeLists.txt,
  avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/conformersearchdialog.cpp,
  avogadro/src/extensions/conformersearchdialog.h,
  avogadro/src/extensions/conformersearchdialog.ui,
  avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsdialog.ui,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/dockingextension.cpp,
  avogadro/src/extensions/dockingextension.h,
  avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefielddialog.h,
  avogadro/src/extensions/forcefielddialog.ui,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessefpmatchdialog.ui,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/gamessinputdata.h,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/gamessinputdialog.h,
  avogadro/src/extensions/gamessinputdialog.ui,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/liganddialog.cpp,
  avogadro/src/extensions/liganddialog.h,
  avogadro/src/extensions/liganddialog.ui,
  avogadro/src/extensions/pocketdialog.cpp,
  avogadro/src/extensions/pocketdialog.h,
  avogadro/src/extensions/pocketdialog.ui,
  avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h,
  avogadro/src/extensions/selectextension.cpp,
  avogadro/src/extensions/selectextension.h,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/extensions/unitcellparamdialog.ui,
  avogadro/src/extensions/wiitrackextension.cpp,
  avogadro/src/extensions/wiitrackextension.h, avogadro/src/mainwindow.cpp,
  libavogadro/include/avogadro/extension.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/extension.cpp, libavogadro/src/extension.h,
  libavogadro/src/extensions/CMakeLists.txt,
  .../src/extensions/conformersearchdialog.cpp,
  libavogadro/src/extensions/conformersearchdialog.h,
  .../src/extensions/conformersearchdialog.ui,
  libavogadro/src/extensions/constraintsdialog.cpp,
  libavogadro/src/extensions/constraintsdialog.h,
  libavogadro/src/extensions/constraintsdialog.ui,
  libavogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/extensions/constraintsmodel.h,
  libavogadro/src/extensions/dockingextension.cpp,
  libavogadro/src/extensions/dockingextension.h,
  libavogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/extensions/forcefielddialog.h,
  libavogadro/src/extensions/forcefielddialog.ui,
  libavogadro/src/extensions/forcefieldextension.cpp,
  libavogadro/src/extensions/forcefieldextension.h,
  .../src/extensions/gamessefpmatchdialog.cpp,
  libavogadro/src/extensions/gamessefpmatchdialog.h,
  libavogadro/src/extensions/gamessefpmatchdialog.ui,
  libavogadro/src/extensions/gamessextension.cpp,
  libavogadro/src/extensions/gamessextension.h,
  libavogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/extensions/gamessinputdata.h,
  libavogadro/src/extensions/gamessinputdialog.cpp,
  libavogadro/src/extensions/gamessinputdialog.h,
  libavogadro/src/extensions/gamessinputdialog.ui,
  libavogadro/src/extensions/h2methylextension.cpp,
  libavogadro/src/extensions/h2methylextension.h,
  libavogadro/src/extensions/hydrogensextension.cpp,
  libavogadro/src/extensions/hydrogensextension.h,
  libavogadro/src/extensions/liganddialog.cpp,
  libavogadro/src/extensions/liganddialog.h,
  libavogadro/src/extensions/liganddialog.ui,
  libavogadro/src/extensions/pocketdialog.cpp,
  libavogadro/src/extensions/pocketdialog.h,
  libavogadro/src/extensions/pocketdialog.ui,
  libavogadro/src/extensions/propextension.cpp,
  libavogadro/src/extensions/propextension.h,
  libavogadro/src/extensions/propmodel.cpp,
  libavogadro/src/extensions/propmodel.h,
  libavogadro/src/extensions/selectextension.cpp,
  libavogadro/src/extensions/selectextension.h,
  libavogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/extensions/unitcellextension.h,
  libavogadro/src/extensions/unitcellparamdialog.cpp,
  libavogadro/src/extensions/unitcellparamdialog.h,
  libavogadro/src/extensions/unitcellparamdialog.ui,
  libavogadro/src/extensions/wiitrackextension.cpp,
  libavogadro/src/extensions/wiitrackextension.h, libavogadro/src/tool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Moved extensions to libavogadro. 
  Added Extension::setMolecule as a signal.  Updated previous engines to take
  advantage of this new ::setMolecule function. Gives more view on when the
  underlying data model changes.  

2008-03-21  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, testfiles/ch3cl.cube.gz, testfiles/multicubes.cube.gz: *
  testfiles/ch3cl.cube.gz: Deleted incorrect test file.  *
  testfiles/multicube.cubes.gz: Added new multi-cube test file supplied by
  Louis Ricard.   

2008-03-21  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: German translations added. 

2008-03-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h: POV-Ray export: the aspect-ratio input dialog
  belongs to avogadro not libavogadro. In lib, just make the POVPainterDevice
  constructor take an aspectRatio argument.   

2008-03-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp: Default to not displaying debug information. 

  * ChangeLog, libavogadro/src/tools/selectrotatetool.cpp: Modified the
  selection behaviour to be more consistent with other applications. Just the
  selected primitives are selected when clicking primitives or drawing
  selection boxes. Pressing shift causes them to be added to the existing
  selection.  

2008-03-15  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: German translations added. 

2008-03-15  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating Krazy. I fixed many issues and updated
  to the latest release of Krazy2  

  * avogadro/src/extensions/gamessinputdata.cpp,
  libavogadro/src/engines/iso.cpp, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/clickmeasuretool.cpp: Many Krazy fixes  

2008-03-14  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: new run of Krazy  

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Update Krazy  

2008-03-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp: Clean up and get rid of some
  debug statements.  

2008-03-12  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/wiitrackextension.cpp,
  avogadro/src/extensions/wiitrackextension.h: *
  avogadro/src/extensions/wiitrackextension.*: Wiimote head tracking extension.
   * avogadro/src/extensions/CMakeLists.txt: Do not compile Wiimote head
  tracking extension as default   

2008-03-12  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/CMakeLists.txt, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h: - pov-ray: fix lighting (add 2nd light, emulate
  lights at infinity even though pov-ray is too stupid to understand that
  notion, fix light position when cam moves, fix material properties) -
  #include "config.h" as suggested by Donald   

  * avogadro/src/extensions/hydrogensextension.cpp: fix a bug (discovered by a
  gcc-4.3 warning)   

  * libavogadro/src/povpainter.cpp: this time it really works -- the camera is
  correctly preserved by povray export.   

2008-03-11  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/povpainter.cpp: fix the camera in pov-ray export. remains
  todo: lighting, viewport settings i hate povray.   

  * libavogadro/src/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/povpainter.cpp: - fix bug #1911509 : missing bg color in
  povray export - #include<config.h> gave me headaches because another config.h
  file was getting included! I fixed that in glwidget.cpp which was enough for
  me, but potentially all the other #include<config.h> could give that problem.
  Not sure what the standard practice is. We have many include paths defined
  including OB's so it's not surprising that #include<config.h> can fail!   

2008-03-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/colorbutton.h,
  libavogadro/src/periodictableview.h: * libavogadro/src/colorbutton.h: Added
  A_EXPORT.  * libavogadro/src/periodictableview.h: Added A_EXPORT.   

2008-03-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glwidget.cpp: Remove some debug statements that are not
  needed any longer.  

2008-03-11  Jordan Mantha <jordan.mantha@gmail.com>

  * ChangeLog, doc/CMakeLists.txt: * fixed up doc CMakeLists.txt so that it
  detects docbook.{pdf,html} * added some install rule bits, but left them
  commented out for now as it's still a bit buggy  

2008-03-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/povpainter.cpp: *
  libavogadro/src/povpainter.cpp: Add } to camera {. Fixes #1911507   

2008-03-10  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/aboutdialog.cpp, avogadro/src/engineprimitiveswidget.h,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/dockingextension.h,
  avogadro/src/extensions/gamessinputdialog.h,
  avogadro/src/extensions/propmodel.h: Krazy fixes  

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating KRAZY files.  

2008-03-10  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/main.cpp, libavogadro/CMakeLists.txt,
  libavogadro/src/config.h.in, libavogadro/src/global.cpp,
  libavogadro/src/global.h, libavogadro/src/glwidget.cpp: With Marcus advising
  we updated the threading makeCurrent/doneCurrents in the GLWidget once again.
   It's getting better all the time.  

2008-03-10  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/CMakeLists.txt: aargh, and this one also   

  * CMakeLists.txt, avogadro/src/CMakeLists.txt, i18n/avogadro_de.ts,
  i18n/avogadro_en_GB.ts, i18n/avogadro_fr.ts, libavogadro/src/CMakeLists.txt,
  libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/painterengine.cpp,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h,
  libavogadro/src/textrenderer.cpp: -update french translation -CMakeLists: now
  do cmake -DRELEASE_MODE=ON to enable "release mode": defines NDEBUG, and adds
  -O3 flag if using gcc. -textrenderer: change gamma factor from 0.5 to 0.75
  for more moderate effect -painters: pass vectors by const reference, not by
  value. Even if the implementation needs to make a copy, this should not
  influence the API. Hope I didn't introduce bugs. -painterengine.cpp: minor
  readibility improvement. Hope I got it right. -camera: fix warning with gcc
  4.3.   

2008-03-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/iso.cpp: Remove some debug output. Correct a bug
  where all surface generation was stepping off the end of the cube by one
  unit.  

2008-03-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version numbers.
  I'm not sure what the next release will be, but for now trunk is 0.6.9.  

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/sticksettingswidget.ui: Add settings for sticks,
  fixes PR#1909099.  

2008-03-09  Jordan Mantha <jordan.mantha@gmail.com>

  * libavogadro/src/engines/ribbonsettingswidget.ui: More work on ribbon engine
  config ui * use "Include Nitrogens" rather than just "Nitrogens" in ribbon
  engine configuration * move checkbox to left side of label to be more
  consistent  

2008-03-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * testfiles/ch3cl.cube.gz: 

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: *
  libavogadro/src/engines/orbital*.*: Add support for multiple orbitals/cubes. 
  * testfiles/ch3cl.cube.gz: Example file for multiple cubes.   

2008-03-09  Jordan Mantha <jordan.mantha@gmail.com>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ribbonsettingswidget.ui: Added support for nitrogens
  in backbone for ribbon engine rendering  

2008-03-09  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.cpp: Patch from Jordan Mantha
  <jordan.mantha@gmail.com> fixes ribbon rendering - go right to the end of the
  protein backbone. Thanks for the patch Jordan.  

2008-03-08  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Reverted - locks up a lot...  

  * ChangeLog, libavogadro/src/glwidget.cpp: Added some read and write locks in
  the GLWidget. It should help but it may need to be finer grained... Should
  help to reduce race conditions in threads.  

  * ChangeLog, avogadro/src/main.cpp: Looks like some drivers have bad
  XInitThreads() functions, only enable for threaded GL builds.  

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Just return form the render function
  if the VdW thread is running, should fix the crashes observed.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Removed the doneCurrent() calls in
  the non-threaded GL code paths. These calls were breaking hits calls among
  other things.  

2008-03-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/primitiveitemmodel.cpp: replace assert(row > -1); by if
  (row < 0) return;  

2008-03-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/main.cpp, libavogadro/src/glwidget.cpp: Stepped through the
  rendering pipeline and makeCurrent / doneCurrent should now be in the correct
  spots.  

2008-03-07  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/main.cpp: Added extra GL initialisation debug
  output.  

2008-03-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp:
  Check that a window isn't moved off-screen on Mac or Windows (since we
  remember window positions on those platforms). PR#1903437. (saveFile) Add
  .cml extension to a filename if none is provided. PR#1817621.   

2008-03-06  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/eyecandy.cpp: Make the eye candy opaque.
  Still looks great in my opinion. This does get rid of potentially expensive
  blending operations in the quick render pipeline.  

  * ChangeLog, libavogadro/src/engine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: The engines now emit changed when their status is
  changed. Updated the GLWidget logic for invalidating its display lists and
  also added a new slot to do this.  

2008-03-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefieldextension.cpp: Change default force field
  to MMFF94, 500 iterations, steepest descent. (Good options, since typical
  structure is far from the minima.)  

  * avogadro/src/mainwindow.cpp: Fix PR# 1817621. Add a CML extension if no
  extension is supplied.  

2008-03-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/CMakeLists.txt: Forgot CMakeList.txt  

  * ChangeLog, libavogadro/src/engines/forceengine.cpp,
  libavogadro/src/engines/forceengine.h: *
  libavogadro/src/engines/forceengine.*: Render forces on atoms. Uses
  OBConformerData, needs latest OB SVN to work.   

2008-03-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Stop invalidating the cache on
  mouse release. I think we have all of the events that should invalidate the
  display cache covered now.  

2008-03-05  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/propextension.h, krazy/runkrazy.rb,
  libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/elementcolor.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/residuecolor.cpp, libavogadro/src/tool.cpp: Adding many fixes
  for Krazy issues  

2008-03-05  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * Doxyfile, Doxyfileext: Update documentation version numbers.  

2008-03-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/orbitalengine.cpp: Just draw GL_LINES.  

  * ChangeLog, libavogadro/src/tools/selectrotatetool.cpp: Change cursor types
  depending upon the action being performed - better visual cues.  

2008-03-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp: Added a second light source to the
  GLWidget - improved surfaces.  

2008-03-04  Carsten Niehaus <carsten.niehaus@gmail.com>

  * doc/CMakeLists.txt: Alex Neundorf wrote this  

  * doc/figures/screenshot1.png, doc/index.docbook, doc/pdf/index.pdf: A much
  improved handbook. This version shows how to do links and picutures  

  * doc/generate_handbook.sh, doc/handbook.html, doc/pdf/index.pdf: Now
  ./generate_handbook.sh is generating PDF in the 'pdf' subdir and HTML in the
  'html' subdir. As the html is generated in multiple files I will only add the
  PDF in SVN.  

2008-03-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp: Draw multiple bonds in
  the quick render function - no more flicking bonds.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Add back in some makeCurrent calls
  that really were necessary outside of the threaded GL #ifdefs. This fixes
  PR#1906403.  

2008-03-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix for PR#1901633.  

  * libavogadro/src/tools/drawcommand.cpp: Fix problems with h-addition
  breaking ring engine, PR#1897744. (There are probably still some problems
  with atom numbering. The ring engine probably needs to invalidate its list of
  rings whenever the molecule is update.)  

2008-03-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * doc/index.docbook: Remove KDE dependency from index.docbook  

2008-03-02  Carsten Niehaus <carsten.niehaus@gmail.com>

  * doc/CMakeLists.txt: Starting a real CMake file  

  * CMakeLists.txt, doc/index.docbook: First version of the new handbook  

2008-03-01  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: Added a renderQuick function to this
  engine. Selected atoms/bonds rendered as opaque objects using the selection
  colour. Multiple bonds are not displayed. No transparency used.  

  * ChangeLog, libavogadro/src/engine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/sphereengine.h, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp: API cleanup - remove the second unused argument
  from the quickRender function. Ported everything to use the new quickRender
  function.  

2008-02-29  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Correct a bug in the setSelected
  function which was causing it to toggle the selection rather than set it as
  the calling functions were expecting. Reverted the fix in mainwindow.cpp as
  setSelected now works as expected. The select molecule function in the select
  rotate tool also works as expected now.  

2008-02-29  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version numbers
  to 0.6  

  * avogadro/src/mainwindow.cpp, libavogadro/src/tools/selectrotatetool.cpp:
  Fix selection bugs: select all doesn't toggle (weird bug). Selecting molecule
  will now also select all connected bonds.  

2008-02-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Run as a single thread  

2008-02-29  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, avogadro/src/extensions/forcefieldextension.cpp: Disable the
  constraints menu item for now.  

  * ChangeLog, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Fixed the integer based
  eval function to actually use the m_iso value set. Defaulted the orbital
  engine to not use interpolation but added a check box that will force
  interpolation if desired.  

  * ChangeLog, libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp: Added a new marching cubes
  function that does not use interpolation. This should significantly reduce
  the resources needed to calculated many surfaces. Ported surface engine to
  use the non-interpolated functions - should never interpolate values we
  calculate at the resolution we choose. The orbital engine should optionally
  use interpolation but I need to hunt down a bug in the non-interpolated
  functions that is affecting the orbital cubes.  

2008-02-29  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: Updating the krazy files  

2008-02-29  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp: Remove debug output...  

  * ChangeLog, libavogadro/src/engines/surfaceengine.cpp: Update the surface
  engine to use the new features of the GridData class - requires fresh
  OpenBabel SVN...  

2008-02-28  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Provide more visual cues by changing
  the mouse cursor.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed up some of the makeCurrent
  and doneCurrent calls - this seems to improve things a little here. My ATI
  driver still hates Avogadro though...  

2008-02-27  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/orbitalengine.cpp: Add debugging output of the
  orbital title. (Needs bleeding-edge SVN trunk of Open Babel.)  

  * scripts/distclean.sh: Updated "dist clean" script for upcoming 0.6 release.
   

2008-02-26  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Make VDWSurface a thread  

2008-02-26  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/hbondengine.cpp: Add a minimum distance criteria.
  This appears to solve some crashing when copy/pasting with h-bond active.  

  * avogadro/src/mac/MacOSXBundleInfo.plist.in: Add support for Mac document
  icons and launching. (Double-clicking an XYZ or PDB file is now supported.)  

  * AUTHORS: Add Shahzad's email.  

2008-02-25  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some translations added 

2008-02-22  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog: ChangeLog entries for recent changes...  

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui: Removed the set step size
  and associated functions.  

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Removed the set step size
  spinner and functions.  

  * libavogadro/src/engines/surfaceengine.cpp: Fixed the opacity slider to
  change the opacity and ported to use the new IsoGen init function.  

  * libavogadro/src/engines/orbitalengine.cpp: Fixed the opacity slider to
  actually change the surface opacity. Ported to new style IsoGen init
  function.  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: Adapted the
  IsoGen class to use the global quality level to set the step size.  

  * libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: Added new virtual function - quality() so that
  IsoGen can use it.  

2008-02-21  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h, libavogadro/src/painterdevice.h:
  Tweaked include files a little so that IsoGen doesn't include the whole of
  GLWidget. Fixed others.  

2008-02-20  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawtool.cpp: Broke comile, fixed again  

  * libavogadro/src/tools/drawtool.cpp: Don't return an QUndoCommand when the
  element or the bond order did not change  

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  Small bug fixes  

  * libavogadro/src/tools/drawtool.cpp: Add m_beginAtom->update() to
  DrawTool::mousePress() so the element changes. (problem described by dcurtis
  on IRC)  

2008-02-20  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some translation updates 

2008-02-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h: readSettings and writeSettings for
  SphereEngine  

  * ChangeLog: ChangeLog for readSettings/writeSettings progress  

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h: readSettings and writeSettings for
  BSDYEngine  

  * libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/ringengine.h: readSettings and writeSettings for
  RingEngine  

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h: readSettings and writeSettings for
  HBondEngine  

  * libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h: readSettings and writeSettings for
  WireEngine  

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: readSettings and writeSettings for
  BondCentric tool.  

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  readSettings and writeSettings for AutoOpt tool.  

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Various
  bug fixes for draw tool (undo/redo) while adjust hydrogens is on. AutoOpt:
  drawText with some information when running  

2008-02-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h: Label Engine now saves settings.  

  * libavogadro/src/tools/drawtool.cpp: Tools and Engines reading/writing
  settings should call the base class functions too to save some code and also
  save the name / description (default information).  

  * avogadro/src/mainwindow.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/toolgroup.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Updated Tools to read/write settings.  The
  tools will need to be updated to take advantage of this but the mechanism is
  there.  Please see drawtool.cpp/h for an example of how to implement this
  functionality.  

2008-02-19  Carsten Niehaus <carsten.niehaus@gmail.com>

  * testfiles/2-aminoethanol.cml, testfiles/2-thioethanol.cml,
  testfiles/2_2_2-trifluoroethanol.cml, testfiles/but-2-yne-1_4-diol.cml,
  testfiles/butane.cml, testfiles/ethane-1_2-diol.cml, testfiles/ethane.cml,
  testfiles/ethanol.cml, testfiles/methane.cml, testfiles/methanol.cml,
  testfiles/propan-1-ol.cml, testfiles/propan-2-ol.cml, testfiles/propane.cml,
  testfiles/thiophene.cml: sync  

2008-02-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitiveitemmodel.cpp: Fixed the PrimitiveItemList  It's
  not a problem but the way that OpenBabel does deletions and additions is not
  quite as convenient for QAbstractItemModels and so for Molecules we need a
  cache to hold a list of the primitives so that we have access to them by
  index after they have been removed from the Molecule.  

  * avogadro/src/mainwindow.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h: Fixed auto-change of tools.  Tools are loaded
  during main window initialization.  Still delays showing the widget until
  later.  Removed some debugging code from the engine class and removed a
  function for setting primitives from a QList<Primitve *> which we don't need
  since PrimitiveList has a default constructor for QList<Primitive *>  

2008-02-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Change to navigate tool every time after
  loading a file.  

  * avogadro/src/extensions/forcefieldextension.cpp: Fix bug where undo of
  geometry optimization would not redraw window.  

2008-02-19  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp: Fixed some compiler warnings.
  Updating OpenBabel to latest trunk improves AutoOpt's stability alot.  

2008-02-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp: Drawing H-H now possible while
  adjust hydrogens is on.  

2008-02-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp: Fix up the conditional in
  renderQuick, remove surplus glEnd()s...  

2008-02-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawtool.cpp: Always allow deletion of non-bonded H  

  * libavogadro/src/tools/drawtool.cpp: Same for atoms: Don't delete H when
  adjust hydrogens is on  

  * libavogadro/src/tools/drawtool.cpp: Don't delete ?-H bonds when adjust
  hydrogens is on.  

2008-02-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/surfaceengine.cpp: Switch colors around: chemistry
  convention: red = negative, blue = positive.  

  * libavogadro/src/engines/iso.h: Fix crash when closing multiple views.  

2008-02-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp: Fixed error where I moved the
  mol to the wrong place - sorry.  

  * libavogadro/src/engines/surfaceengine.cpp: Adapted the surface engine to
  use the modified IsoGen class. Still needs more work to add renderTransparent
  and renderQuick as in the orbital engine.  

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Added renderTransparent and
  renderQuick functions to ensure proper rendering of the surfaces. Also
  modified tbe criteria for surface invalidation and cleaned up other parts of
  the code.  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: Several
  changes made to make the IsoGen class more general. It now gets the minimum
  and maximum points of the cube directly from the grid and then uses the step
  size more intelligently.  

2008-02-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Insert Smiles is now undo-able  

2008-02-18  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Tweaked the surface engine to use
  the standard functions to invalidate the surface. Still needs more tweaking I
  think.  

  * ChangeLog: Added ChangeLog entry...  

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Used Geoff's new colour
  widget in the configuration dialog. Added support for drawing both the
  positive and negative iso surfaces as well as ensuring the surfaces are only
  recalculated if the molecule was modified.  

2008-02-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/addenginedialog.cpp,
  avogadro/src/addenginedialog.h: * avogadro/src/addenginedialog.*: Set the
  default "name" when adding an engine to the engine type. (This saves some
  typing.)   

  * ChangeLog, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawtool.cpp: Auto-addition of hydrogens. Should work
  cleanly. Try it out and report bugs. (There are probably still some corner
  cases.)   

2008-02-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/drawcommand.cpp: Adjust valence of neighbouring atoms
  when deleting an atom.  

2008-02-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawcommand.cpp: Fixed most bugs with auto-adjusting
  hydrogens. Give it a try!  

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp:
  More progress to auto-add hydrogens. (Currently defaults to off -- still some
  weird bugs with interactive drawing.)   

2008-02-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp: Mac fix: gotta save the position too.   

2008-02-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalsettingswidget.ui: Modified the default value
  for the iso surface - still needs a little more work to show the orbitals
  correctly but the big stuff is now working.  

  * libavogadro/src/engines/iso.h: Actually use the iso value that is set -
  orbitals can now be visualised!  

2008-02-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Fix PR#1849616
  with "flash of reorganizing tools".  

  * ChangeLog, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: * libavogadro/src/tools/drawtool.*,
  libavogadro/src/tools/drawcommand.*: Indentation and comment cleanup in draw
  tool. Added initial support for adjusting hydrogens while drawing. Still
  needs interactive drawing changes for hydrogens, but changing elements,
  delete, etc. work.   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Mac fixes --
  unified toolbar and saving window position.  

2008-02-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Add "Change Bond Order" to drawtool. Make
  this feature and "Change Element" undo-able.  

2008-02-16  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h, avogadro/src/mainwindow.cpp:
  DockWidget and Toolbar state are now saved in the settings.  

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui: Cleaned up the
  openFile and loadFile functions.  loadFile is now private. MainWindow now
  handles all opening of files.  Please check the updated main.cpp to see how
  this works.  This solves a problem where if you specified a file more than
  once on the command line you would get multiple windows with the same file. 
  Also, this makes opening files look nicer, one window pops up at a time.
  Unfortunatly this means we have to push events through.  MainWindow::show()
  simply does a ::setVisible and draws the preliminary outline of the window
  but doesn't do a "Polish" which means that the window looks like it's stuck
  loading.  I made loadFile private because I believe that openFile will
  eventually call loadFile but it also handles checking that the file is not
  already loaded in another window.  The other change I made is that I stopped
  read/write of settings for the window position.  In linux the window
  positioning should really be handled by the window manager.  The other reason
  is that because of our settings being saved we weren't getting any benefit. 
  If this needs to be implemented in mac (which I think mac can do it's own
  smart window placement) then we can add it back in for mac only.   Dimensions
  are still saved.  

2008-02-16  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/mainwindow.cpp: Added Primitives Dock to menuDock  

2008-02-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Moved VDWSurface to IsoGen thread to
  make surface engine more interactive  

2008-02-15  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some translations corrected 

2008-02-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/include/avogadro/colorbutton.h: Add colorbutton.h template.
  Marcus can't find the include file.  

  * ChangeLog, libavogadro/src/tools/skeletontree.cpp: *
  libavogadro/src/tools/skeletontree.cpp: Fix bug with bond-centric manipulate
  tool. Translations and rotations were not telling atoms that they were
  updated. Fixes PR#1854343.   

  * libavogadro/src/tools/autorotatetool.cpp: *
  libavogadro/src/tools/autorotatetool.cpp: Quick fix for PR#1891101. Will not
  do rotations if no molecule is loaded.   

  * libavogadro/src/glwidget.h: Fixed documentation with debug info panel.  

  * ChangeLog, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/colorbutton.cpp, libavogadro/src/colorbutton.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfacesettingswidget.ui: *
  libavogadro/src/colorbutton.*: New widget to show the current color and bring
  up a color picker when clicked.  *
  libavogadro/src/engines/surfacesettingswidget.ui: Use it.  *
  libavogadro/src/engines/surfaceengine.*: Ditto.   

  * avogadro/src/mainwindow.ui: Fix Mac unified toolbar and select items in
  Edit menu. (Duplicate "Select all" is intentional. People expect them in Edit
  menu too.)  

2008-02-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/orbitalengine.cpp: Some improvements to the orbital
  engine code but still no sight of the orbitals!  

2008-02-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/engineprimitiveswidget.cpp, avogadro/src/enginesetupwidget.cpp,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/engine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/manipulatetool.cpp: PrimitiveList now acts exactly as a
  QList<Primitive *> and with benefits.  This means you should always pass
  around a PrimitiveList and not a QList<Primitive *>.  I have updated all the
  function calls etc.  

  * avogadro/src/engineprimitiveswidget.cpp: The "set engine to selection"
  button was enabled when there wasn't an engine selected.  

  * avogadro/src/engineprimitiveswidget.cpp,
  avogadro/src/engineprimitiveswidget.h,
  avogadro/src/engineprimitiveswidget.ui,
  avogadro/src/extensions/selectextension.cpp,
  libavogadro/include/avogadro/periodictableview.h, libavogadro/src/glwidget.h,
  libavogadro/src/periodictableview.h: Added a button to set the engine
  primitives to the current selection.  

  * avogadro/src/avogadro.qrc, avogadro/src/engineprimitiveswidget.ui,
  avogadro/src/icons/copy.png, avogadro/src/icons/cut.png,
  avogadro/src/icons/paste.png, avogadro/src/icons/rebuild.png,
  avogadro/src/icons/selecttable.png, avogadro/src/icons/tab_new.png,
  avogadro/src/icons/tab_remove.png, avogadro/src/mainwindow.ui: Added some new
  icons, updated the mainwindow and added a new button for setting engine
  primitives to the selection.  

2008-02-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h,
  libavogadro/src/engines/orbitalsettingswidget.ui: Fixed the orbitals engine
  to the point that it now compiles. Still not showing any actual molecular
  orbitals yet though...  

2008-02-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/surfaceengine.cpp: Small changes to make sure the
  surface is invalidated when you select a new step size or padding. The check
  for the MoleculeType in invalidateSurface(), makes sure the surface is
  invalidated while auoopt is running.  

2008-02-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/orbitalengine.cpp,
  libavogadro/src/engines/orbitalengine.h: Added initial (broken compile)
  orbital engine for Marcus.  

2008-02-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Added m_surfaceValid boolean to hold
  the state (valid or not) of the surface. For large molecules, the
  VDWSurface() function should also be in a thread. Do we create a seperate
  thread for this?  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Make IsoGen run as a real thread  

2008-02-10  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some surface translations and other things added. Does
  someone know a sane translation for dock & pocket? 

2008-02-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/iso.cpp, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/surfaceengine2.cpp,
  libavogadro/src/engines/surfaceengine2.h,
  libavogadro/src/engines/surfacesettingswidget.ui: Added settings widget for
  the surface engine  

  * libavogadro/src/engines/surfaceengine.cpp: Slightly improved espColor
  function  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Make sure the surface center is the
  same as the molecule center. Added espColor function to handle ESP surface
  coloring. The cut-off energy is still too rough, it should be more smouth... 

2008-02-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: I couldn't resist playing and so now
  we have a semi-transparent surface engine rendering in red right now using
  triangles... It is looking pretty good already. It still needs more work in
  order to get the colours right and make it more useful. The algorithm seems
  to be working quite well with small molecules at the very least.  

2008-02-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/surfaceengine.cpp:
  Removed lots of qDebug statements. Thanks lots to Tim for spotting the bug!  

2008-02-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/surfaceengine.cpp: rremoved line98: first resizing
  the vector and then push_back items will cause the vector to contain twice
  the number of items...  

2008-02-08  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: It compiles, but completely fails to
  find any triangles! Obviously more work is required and I can't spot where it
  is failing. Comparing it to the work done in surfaceengine2.* may help but I
  think it is close...  

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: It
  compiles! Still need to verify it is doing useful things though...  

2008-02-08  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/surfaceengine2.cpp,
  libavogadro/src/engines/surfaceengine2.h: Surface engine, able to draw the
  dots of the surface. Still needs some work...  

2008-02-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: Tweaked
  formatting to fit with ours, removed some application specific elements and
  tried to get it working in the Avogadro framework. More work still required
  as there are several application specific elements remaining before this
  class is self contained and able to generate isofurfaces.  

2008-02-05  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/glwidget.cpp: Fixed a small startup bug.  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp: The "duplicate" button on the engine
  list now works properly.  It required adding a Engine::clone function that is
  purely virutal (there is no way around this).  Did some minor testing but
  seemed to work fine.   

2008-02-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h:
  Engine *clone const; instead of XXXEngine *clone const;  

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h:
  Added ::clone() functions  

2008-02-04  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: Added support for measuring the
  dihedral angle. Also made the tool update dynamically as the molecule is
  changed, optimised the label placement and ported it to use the OpenBabel
  functions to find the angles concerned.  

2008-02-03  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp: Fix a bug where the
  angle between bonds was miscalculated. Thanks to Albert DeFusco for reporting
  the bug and providing a test case.  

2008-01-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/polygonizer.cpp,
  libavogadro/src/engines/polygonizer.h: Remove old polygonizer code (since
  we'll use the iso.cpp code instead.)  

2008-01-17  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/CMakeLists.txt: Comment out docking extension in
  CMakeList.txt, it's removed from OpenBabel for the moment. You might need to
  remove /usr/(local/)lib/avogadro/libdockingextension.so to make sure avogadro
  doesn't load the extension.  

2008-01-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessinputdata.cpp: Fixed bug with GAMESS dialog
  remaining present even after the main application window had closed.  Also
  fixed a problem with the generated GAMESS input file being incorrect.   

2008-01-12  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Ligand translations added. Does someone know a sane
  translation for pocket? 

  * i18n/avogadro_de.ts: Conformer translations added. Thanks especially to
  Jerome Pansanel\! 

2008-01-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/iso.cpp, libavogadro/src/engines/iso.h: Importing
  iso.h and iso.cpp from the Zhu3D project (3.4.0). These can be adapted and
  used to provide surface support in Avogadro. These files are not yet modified
  for use in Avogadro and so are not currently compiled/linked to. They are
  thread safe and I think this algorithm is the best choice. I will make
  modifications to these files in the near future.  

2008-01-09  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/conformersearchdialog.cpp,
  avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.ui,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h: Use OpenBabel::OBRotorKeys  

2007-12-28  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Some translations added. Don't really know how to
  translate 'conformer', help appreciated\! 

2007-12-20  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts: update french translation   

2007-12-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.h: * libavogadro/src/tools/autoopt.[h,cpp]:
  Use new HasAnalyticalGradients() method from Open Babel SVN trunk.   

2007-12-20  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/camera.cpp, libavogadro/src/camera.h: Added a
  copy constructor.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed the race condition in the
  render quick code.  

2007-12-19  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Translation updated a bit, obsolete ones removed. 

2007-12-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: New function to
  render unit cell axes for crystal cells. Needs a config option to turn on and
  off display.  

2007-12-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/constraintsmodel.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  AutoOpt: removed conjugated gradients, added molecular dynamics  

2007-12-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdysettingswidget.ui: Add in more bond granularity
  -- more steps, and a thin bond at the smallest size. Suggested by Andrew
  Dalke.  

  * ChangeLog, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: * libavogadro/src/tools/*.cpp:
  Add Navigate::zoom() to wheel operations for all tools.   

2007-12-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp: * libavogadro/src/color.[h, cpp]: New
  method setToSelectionColor to allow overloading and customization of the
  selection color in render engines.  * libavogadro/src/engines/*.cpp: Use it. 
   

2007-12-16  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: fix mousewheel action which hadn't got
  updated in the last round; and by the way make it much faster by always
  assuming that no atom is clicked (instead of performing an expensive gl
  selection) and instead using the m_referencePoint which is already quite
  precisely what the user sees. Also, fine-tune a constant in the
  m_referencePoint computation.   

  * libavogadro/src/glwidget.cpp: Revert the change causing the quicklist to be
  recompiled on mouseRelease. So now we're back to recompiling on mousePress.
  This fixes the bug with the quicklist not getting properly recompiled. One of
  the causes of this bug was that I forgot to call makeCurrent. This could of
  course easily be added. But then, there's another big issue: if we went on
  with updating quicklist on mouseRelease, then the engines themselves should
  make sure to notify the glwidget whenever the quicklist needs to be updated
  (e.g. some engine parameter changed, or some engine got enabled/disabled).
  This is much hassle and error-prone. What is the benefit? On my
  hw-accelerated system, updating on mouseRelease made the latency on the next
  mousepress shrink by 20% (from 390 to 310 ms). Not enough IMO to justify the
  hassle. This is why I reverted. I leave as is the other changes I made,
  moving pd into d->, introducing updateListQuick, etc, feel free to change
  that at your convenience.   

2007-12-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Draw cylinders between backbone
  points when using quickRender.  

  * ChangeLog, libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/ringengine.h: Added support for colouring rings based
  upon the number of ring members.  

2007-12-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extensions/forcefielddialog.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h: *
  libavogadro/src/tools/autoopttool.[h,cpp] Add support for OBPluginList to
  dynamically get list of force field types.  *
  avogadro/src/extensions/forcefieldextension*: As above.   

  * libavogadro/src/engines/hbondengine.cpp: *
  libavogadro/src/engines/hbondengine.cpp: Add support for stippled lines.   

  * avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefielddialog.ui,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h: Added OBPluginList support to
  add force fields to the menu. Now auto-discovers any force fields added to
  Open Babel.  

  * libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glpainter.cpp: Fix
  incomplete implementation of line stipple to be used for hydrogen-bonding.
  Now shows nice dashed lines for the hbond engine.  

2007-12-15  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/engines/CMakeLists.txt: forgot CMakeList.txt  

2007-12-14  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/engines/hbondengine.cpp,
  libavogadro/src/engines/hbondengine.h,
  libavogadro/src/engines/hbondsettingswidget.ui: Added HBond engine  

2007-12-14  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: the updating of
  the quicklist now occurs on mouseRelease, not on mousePress. The rational is
  that we want a very low latency on mousePress. With this change, on
  mousePress, we already have a quick-list ready for use. This further reduces
  latency when handling very large molecules. This prompted some deeped changes
  in GLWidget/GLWidgetPrivate, I hope they are OK, for instance pd is now in
  GLWidgetPrivate, I hope I got it right, as I didn't see any reason not to
  have it here (though it has to be constructed in GLWidget::constructor(), not
  in GLWidgetPrivate, because we need the this pointer of the GLWidget).   

  * libavogadro/src/glwidget.cpp: use "quickrender" mode for opengl selection
  (GLWidget::hits) This reduces latency when clicking in a very large molecule.
    

  * libavogadro/src/glpainter.cpp: optimization: remove all frustum-culling
  code! Indeed, since we have the "quick display lists", this code has become
  useless! GLPainter is now more clear, and, had this change been made together
  with the introduction of the "quick display lists", we would not have the
  computeClickedAtoms() bug.   

  * libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: fix this bug: [ avogadro-Bugs-1849990
  ] movement shoud be relative to visible part of the molecule When no atom is
  clicked, the navigatetool is now moving relatively to a weighted barycenter
  of the atoms, where atoms have a higher weight when they are central in the
  view and a lower weight when they are outside the frustum. A decreasing
  exponential formula is used to compute the weights. This may sound intensive,
  but is only done once on mousePress, and turns out (according to some
  qDebugs) to be almost negligible and not the cause for the short lag occuring
  on mousePress with big molecules (tested with a mol with 7000 atoms). The
  complexity is linear.   

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/tools/navigatetool.h: fix the issue that I reported on the
  mailing list, about computeClickedAtom(). Will write an explanation on the
  list about that.   

2007-12-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/propextension.cpp: moved angles and torsions to
  correct sub-menu  

2007-12-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/dockingextension.cpp,
  avogadro/src/extensions/selectextension.cpp: Spelling fixes with action
  names.  

2007-12-13  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Added angles and torsions to PropertiesModel, added Numerical/Analytical
  gradients option to AutoOpt  

2007-12-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h: Disabled drawing of labels when moving
  the view, i.e. in quickRender().  

  * libavogadro/src/glwidget.cpp: Invalidate the display list cache after mouse
  release events - sorry not as pretty as it should be. Probably want to use
  signals and slots...  

2007-12-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: *
  libavogadro/src/glwidget.cpp (renderCrystal): Clean up main render() function
  with additional function to handle translations of crystal cells via display
  lists. Much cleaner code and should be faster on larger crystals.   

2007-12-13  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts, libavogadro/src/textrenderer.cpp: - improve text
  rendering: -- apply a gamma (0.5) correction to the rawbitmap to get rid of
  dim legs in "n" and "m" letters; this also makes all the text look a bit
  bolder, I hope you like it and agree it's more suitable for outlining --
  fine-tune the 7x7 outlining brush - improve french translation   

  * libavogadro/src/glpainter.cpp: make drawCone properly work. Thanks for the
  person (Marcus is it you?) who made the initial implementation, and sorry for
  stealing the fun part of the job. Things fixed: - after all a GL_TRIANGLE_FAN
  was not appropriate since we want to specify different normal vectors at the
  tip. Sorry Marcus for having given wrong advice on IRC. GL_TRIANGLE_FAN
  remains appropriate for the base, though. - the first vertex had no normal
  specified - the formulas for normal vectors were wrong - the order of the
  vertices was wrong, leading to problems with backface culling. This code is
  now doing more calculations, which would benefit from being cached in a
  display list like we do for cylinder and sphere.   

  * avogadro/src/extensions/dockingextension.cpp, i18n/avogadro_fr.ts: - update
  french translation, make it more complete (I used google/online chemistry
  dictionaries/wikipedia for some chemistry terms) - fix typos in
  dockingextension.cpp   

2007-12-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/icons/Aspirin.png,
  avogadro/src/icons/AvoDocument.png, avogadro/src/mac/AvogadroDocument.icns,
  avogadro/src/mac/MacOSXBundleInfo.plist.in: Updated Mac OS document icons.  

2007-12-13  Marcus D. Hanwell <marcus@cryos.org>

  * i18n/avogadro_en_GB.ts: Correct dodgy spelling of aluminium...  

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h: Removed the debug engine - moved to
  the GLWidget now.  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.ui,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added debug
  information to the GLWidget along with config options etc.  

  * libavogadro/src/glwidget.cpp: Fixed some bugs in the new quick rendering
  framework - drawing works again!  

2007-12-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/textrenderer.cpp: Fix GCC-4.2 warning about an empty for
  loop.  

  * libavogadro/src/elementtranslate.cpp: *
  libavogadro/src/elementtranslate.cpp: Fix US spelling of aluminum. Marcus can
  adjust accordingly in GB translation.   

  * libavogadro/src/glwidget.cpp: * libavogadro/src/glwidget.cpp: Add in
  display lists for renderQuick. Wraps all engines into one list for maximum
  speed.  * libavogadro/src/engines/wireengine.[h,cpp]: Skip display lists, as
  glWidget now handles this for us.   

  * ChangeLog, libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h: * libavogadro/src/glwidget.cpp: Add in
  display lists for renderQuick. Wraps all engines into one list for maximum
  speed.  * libavogadro/src/engines/wireengine.[h,cpp]: Skip display lists, as
  glWidget now handles this for us.   

  * avogadro/src/mainwindow.cpp: Fix window position on Mac. (Somehow this was
  commented out!?) Call move() based on the "pos" QSettings result.  

2007-12-12  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engine.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp: Added more logic to implement renderQuick in
  the engines, GLPainter and the GLWidget. The renderQuick function.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Don't use dynamic scaling to
  render the axes - cylinders were reduced to lines before.  

  * ChangeLog, libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h:
  Added a dynamic scaling variable to the clas and a setter. This turns dynamic
  scaling on (default) and off.  

  * avogadro/src/CMakeLists.txt, i18n/avogadro_en_GB.ts,
  libavogadro/src/CMakeLists.txt: Added a British English translation (you know
  - the original one that uses all the extra letters).  

2007-12-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propmodel.cpp: *
  avogadro/src/extensions/propmodel.cpp,
  avogadro/src/extensions/propextension.cpp: Minor fixes to get compilation
  working again.   

  * libavogadro/src/primitive.h: * libavogadro/src/primitive.h: New primitive
  types defined for "future expansion."   

  * avogadro/src/extensions/gamessinputdialog.ui: *
  avogadro/src/extensions/gamessinputdialog.ui: Fix typos mentioned by Benoit. 
   

2007-12-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/forcefieldextension.cpp: removed #include
  <avogadro/forcefield.h> (not needed)  

  * libavogadro/src/tools/autoopttool.cpp: Small bugfix  

  * avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/dockingextension.cpp,
  avogadro/src/extensions/liganddialog.cpp,
  avogadro/src/extensions/liganddialog.ui,
  avogadro/src/extensions/pocketdialog.cpp,
  avogadro/src/extensions/pocketdialog.ui,
  libavogadro/src/tools/autoopttool.cpp: *
  libavogadro/src/tools/autoopttool.[h,cpp]: Added "Ignored atoms are movable"
  and "Fixed atoms are movable". Small changes to ::redo() and ::undo(), undo
  still seems to work. I had to change it to makje sure the passed molecule
  pointer would not point to a molecule that would be deleted. This caused the
  constraints in the model to be lossed. (note: OB does not support angle and
  torsion constraints yet, ignoring atoms only works for MMFF94 at the moment.)
   * avogadro/src/extentions/constraintsmodel.[h,cpp]: now connects to
  primitiveRemoved signal from a Molecule to delete invalid constraints as you
  remove atoms.  * avogadro/src/extentions/constraintsdialog.[h,cpp]: You can
  now only add valid constraints.  *
  avogadro/src/extentions/forcefieldextension.cpp: Added "Ignore selected
  atoms" and "Fix selected atoms" + changes to make sure constraints are
  consistent for both the forcefield extension and the AutoOpt tool. Undo
  doesn't work for conformersearch yet, I'll probably fix this by moving the
  ConformerSearchDialog to the ForceFieldCommand itself.  *
  avogadro/src/extentions/liganddialog.[ui,h,cpp]: Dialog to create a ligand.
  (dockingextension)  * avogadro/src/extentions/pocketdialog.[ui,h,cpp]: Dialog
  to create a pocket. (dockingextension)  *
  avogadro/src/extentions/dockingextension.[h,cpp]: Avogadro class to handle
  docking.  * avogadro/src/extensions/propmodel.cpp: Small  change to the way
  rows are added and deleted.   

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/dockingextension.h,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/liganddialog.h,
  avogadro/src/extensions/pocketdialog.h,
  avogadro/src/extensions/propmodel.cpp, libavogadro/src/tools/autoopttool.h:
  see ChangeLog...  

2007-12-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h: Initial wireframe optimization.  

2007-12-11  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/conformersearchdialog.cpp: added tr()  

2007-12-10  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Ported
  the renderAxesOverlay function to use the new renderCone function.  

  * ChangeLog, libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: Added a drawCone function to draw 3D cones that
  can be used for arrows etc.  

  * libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: Added new drawCone function to the painters.  

2007-12-10  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts: updated french translation   

2007-12-10  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/selectextension.cpp,
  avogadro/src/extensions/selectextension.h: Added select by element, residue
  and solvent  

2007-12-09  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/drawtool.h: Small fix to the include directive for
  PeriodicTableView.  

  * libavogadro/include/avogadro/periodictableview.h,
  libavogadro/src/periodictableview.cpp, libavogadro/src/periodictableview.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/periodictablegv.cpp,
  libavogadro/src/tools/periodictablegv.h: Moved the PeriodicTableGV from the
  tools directory to the library directory. Also renamed it to
  PeriodicTableView and added an include file in the includes directory. Some
  small enhancements to the layout too.  

2007-12-09  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/propmodel.cpp: Updated properties model so that
  bond ordering begins at 0 rather than 1 to correspond to the information
  given by the labels engine 

  * avogadro/src/mainwindow.cpp, cmake/modules/FindOpenBabel2.cmake: Updated
  the CMake script to use OPENBABEL2_VERSION_MET keyword and fixed a bug I was
  having with a slow GLWidget when first starting up.  PR#1847479   

2007-12-08  Benoit Jacob <jacob.benoit.1@gmail.com>

  * i18n/avogadro_fr.ts: had forgotten to "make update-translations" the last
  time. Now there are the really complete and uptodate french translations   

  * i18n/avogadro_fr.ts: almost full french translation   

  * avogadro/src/extensions/propmodel.cpp: compilation fix. I hope someone
  knowing OB well can check I got it right.   

2007-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/conformersearchdialog.cpp,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h: setting the number of
  conformers to be generated is now connected  

  * avogadro/src/extensions/propextension.cpp: forgot one file  

2007-12-07  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Translation updated, obsolete ones removed. 

2007-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/conformersearchdialog.cpp,
  avogadro/src/extensions/conformersearchdialog.h,
  avogadro/src/extensions/conformersearchdialog.ui,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp: Added Conformer Search dialog  

2007-12-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp: Don't create duplicate element names --
  use the translator for the combo menu.  

2007-12-07  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/glpainter.h,
  libavogadro/include/avogadro/sphere.h,
  libavogadro/include/avogadro/textrenderer.h: re-add four mini-headers that
  somehow were missing, making the compilation fail.   

2007-12-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp: Fixed compilation with threaded OpenGL.x  

2007-12-07  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: Slighty over 150 translations added, for the rest I
  have to ask carsten or look up further in books. One writing mistake:
  'propertiesd' should probably be 'properties' 

2007-12-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/propextension.cpp: Minor fix for menu names
  (capitalize and add "..." since we open new windows.)  

  * ChangeLog, libavogadro/src/engines/labelengine.cpp: Use new element
  translation feature.  

  * ChangeLog, libavogadro/include/avogadro/elementtranslate.h,
  libavogadro/src/elementtranslate.cpp, libavogadro/src/elementtranslate.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/periodictablegv.cpp: *
  libavogadro/src/elementtranslate.[h,cpp]: New class to handle
  translation/i18n of element names.  * libavogadro/src/tools/drawtool.cpp: Use
  the new translation feature. Also add in custom elements (from Periodic Table
  widget) into an ordered list.  * libavogadro/src/tools/periodictablegv.cpp:
  Use the new translation feature.   

2007-12-07  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/periodictablegv.cpp,
  libavogadro/src/tools/periodictablegv.h: Added a double click event to the
  periodic table - choose the element and close.  

2007-12-07  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h:
  Added PropertiesModel and PropertiesView to handle the represenwtation of
  properties in QTableViews  

2007-12-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix multi-molecule warning -- don't attempt to
  read another molecule. Instead, just peek at the file stream. (On big files,
  this saves us a lot.)  

2007-12-06  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt,
  scripts/distclean.sh: * scripts/distclean.sh: An enhanced "distclean" script
  for preparing source releases.  * avogadro/CMakeLists.txt,
  libavogadro/CMakeLists.txt: Bumped version number to 0.3.0b2.   

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: *
  libavogadro/src/tools/drawtool.cpp: Enhanced custom element support. Picking
  elements from the table will add a new entry and select it. Picking elements
  form the table *already* in the list will simply select that element again.  

2007-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h:
  Improved atom, bond cartesian editor + added conformer table, selecting an
  item in the table will also select the item in the 3D widget, or change the
  conformer.  

2007-12-06  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/periodictablegv.cpp: Spotted where I got a couple of
  the numbers wrong. Fixed now.  

  * libavogadro/src/tools/periodictablegv.cpp,
  libavogadro/src/tools/periodictablegv.h: More tweaking of the ElementDetail
  painting.  

  * libavogadro/src/tools/periodictablegv.cpp: This should hopefully make the
  ElementDetail render more consistently.  

  * ChangeLog: Updated the ChangeLog to reflect new changes.  

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/periodictabledialog.h,
  libavogadro/src/tools/periodictabledialog.ui,
  libavogadro/src/tools/periodictablegv.cpp: Removed the old perdiodic table
  dialog as it has now been replaced. Few tweaks to build files and stuff.  

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/periodictablegv.cpp,
  libavogadro/src/tools/periodictablegv.h: After much work I think my super
  QGraphicsView based periodic table is ready for the world to see. It still
  has some rough edges that will need taking care of but it is already very
  functional and I think in many ways surpasses what we already have in place.
  Feel free to make suggestions or buy me beer ;-)  

2007-12-06  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h:
  Added Conformer dialog, still needs selection handling  

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/propextension.cpp,
  avogadro/src/extensions/propextension.h,
  avogadro/src/extensions/propmodel.cpp, avogadro/src/extensions/propmodel.h,
  libavogadro/src/tools/autoopttool.cpp: Added editable atom and bond
  properties tables + cartesian coordinates editor  

2007-12-05  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h: Added emitData()  

  * libavogadro/src/tools/autoopttool.cpp: removed calls to OBAtom::SetFixed
  and OBAtom::UnsetFixed  

  * ChangeLog, avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsdialog.ui,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  You can now fix the position for an atom :D more constraints comming soon... 

2007-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * CMakeLists.txt, ChangeLog, Doxyfile, Doxyfileext, INSTALL,
  avogadro/Doxyfile, avogadro/README, avogadro/src/CMakeLists.txt,
  avogadro/src/addenginedialog.cpp, avogadro/src/addenginedialog.h,
  avogadro/src/application.cpp, avogadro/src/editcommands.cpp,
  avogadro/src/editcommands.h, avogadro/src/elementcombobox.h,
  avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.cpp,
  avogadro/src/enginelistview.h, avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  avogadro/src/extensions/selectextension.h,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/flattabwidget.cpp, avogadro/src/flattabwidget.h,
  avogadro/src/flowlayout.cpp, avogadro/src/icontabwidget.cpp,
  avogadro/src/icontabwidget.h, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/primitivetreeview.cpp, avogadro/src/primitivetreeview.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  cmake/modules/COPYING-CMAKE-SCRIPTS, cmake/modules/FindAvogadro.cmake,
  cmake/modules/FindLinguist.cmake, gpltemplate,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h, libavogadro/src/elementcolor.cpp,
  libavogadro/src/elementcolor.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/polygonizer.cpp,
  libavogadro/src/engines/polygonizer.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/global.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/glpicker.cpp.disabled,
  libavogadro/src/glpicker.h.disabled, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp.disabled,
  libavogadro/src/moleculetreeview.h.disabled, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h, libavogadro/src/painterengine.cpp,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/residuecolor.cpp,
  libavogadro/src/residuecolor.h, libavogadro/src/sphere.cpp,
  libavogadro/src/sphere.h, libavogadro/src/textrenderer.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/eyecandy.h, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigate.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/periodictabledialog.h,
  libavogadro/src/tools/quaternion.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/undosequence.cpp,
  libavogadro/src/undosequence.h: Removed trailing white space as discussed on
  the mailing list.  

2007-12-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/application.h, avogadro/src/editcommands.h,
  avogadro/src/elementcombobox.h, avogadro/src/engineitemmodel.cpp,
  avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.h,
  avogadro/src/engineprimitiveswidget.h, avogadro/src/extension.h,
  avogadro/src/extensions/forcefieldextension.h, avogadro/src/mainwindow.cpp,
  libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/elementcolor.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/global.cpp, libavogadro/src/global.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.h, libavogadro/src/painterengine.cpp,
  libavogadro/src/painterengine.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/primitiveitemmodel.h, libavogadro/src/primitivelist.cpp,
  libavogadro/src/primitivelist.h, libavogadro/src/residuecolor.cpp,
  libavogadro/src/sphere.h, libavogadro/src/textrenderer.cpp,
  libavogadro/src/textrenderer.h, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/undosequence.cpp: *
  libavogadro/*, avogadro/*: Update headers using script based on
  fixkdeincludes. Removes a *huge* pile of un-needed #include statments in both
  *.h and *.cpp files. Should improve compilation time.   

2007-12-04  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/forcefieldextension.cpp: Small fix to fix compilation
  - include the .moc file.  

  * libavogadro/src/povpainter.h: Small fix to function definitions to fix
  compiler warnings for unused vars.  

2007-12-04  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/constraintsmodel.h: compile error fixed  

  * avogadro/src/extensions/forcefieldextension.h: removed wrong include  

  * avogadro/src/extensions/CMakeLists.txt: forgot make file  

  * ChangeLog, avogadro/src/extensions/constraintsdialog.cpp,
  avogadro/src/extensions/constraintsdialog.h,
  avogadro/src/extensions/constraintsdialog.ui,
  avogadro/src/extensions/constraintsmodel.cpp,
  avogadro/src/extensions/constraintsmodel.h,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h: Added constraints dialog  

2007-12-04  Carsten Niehaus <carsten.niehaus@gmail.com>

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/tools/bondcentrictool.h: use const& QString and explicit
  ctors if possible 

2007-12-03  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html: updated the Krazy files. 

2007-12-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.cpp.disabled,
  libavogadro/src/moleculetreeview.h,
  libavogadro/src/moleculetreeview.h.disabled: Disabled moleculetreeview --
  unused, deprecated. Use primitiveitemmodel.cpp and others.  

2007-12-03  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp: Added IsSetupNeeded to
  AutoOpt to increase performance  

2007-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp: Small bugfix  

2007-12-02  Carsten Niehaus <carsten.niehaus@gmail.com>

  * cmake/modules/FindOpenBabel2.cmake: Making everything depend on OB 2.2  

  * cmake/modules/FindOpenBabel2.cmake: Syncing this file with the one in KDE  

2007-12-02  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: German translation completed (without GAMESS input,
  44/288 completed there); all obsolete translations dropped, greetings to
  Paris\! 

2007-12-02  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/navigate.h: Improved the layout of the function
  prototypes.  

  * libavogadro/src/tools/navigate.h: Small improvements to the Navigate class
  documentation.  

  * libavogadro/src/tools/navigatetool.h: Improvements to the NavigateTool and
  NavigateToolFactory class documentation.  

  * ChangeLog, libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h: More
  documentation improvements. Also moved some empty function implementations in
  POVPainter to the header to make it clearer that they do not do anything.  

  * ChangeLog, libavogadro/src/glpainter.h: Improvements to the GLPainter
  documentation.  

  * ChangeLog, libavogadro/src/glwidget.h: Updated the documentation of the
  GLWidget and GLHits classes.  

2007-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * avogadro/src/extensions/forcefieldextension.cpp: same for RandomRotorSearch
   

2007-12-02  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog: Updated the ChangeLog.  

  * libavogadro/src/tool.h: Improvements to the documentation for the Tool and
  ToolFactory classes.  

  * libavogadro/src/engine.h: Small fixes to the EngineFactory documentation.  

2007-12-02  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h: Added progress bar to
  Systematic Rotor Search  

2007-12-01  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.h: Added some examples to the engine documentation. 

  * ChangeLog, libavogadro/src/engines/debugengine.cpp: Small fix to use the
  painter.  

  * ChangeLog: Add a ChangeLog entry for my move of the axes engine to the
  GLWidget.  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.ui,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Moved the axes
  engine into the GLWidget where it belongs. Added a global configuration
  option for it.  

2007-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engine.h: Fixed up the documentation a little. 

  * ChangeLog, libavogadro/src/color.h: Fixed up the documentation a little. 

  * ChangeLog, libavogadro/src/camera.h: Fixed up the documentation a little. 

  * ChangeLog, avogadro/src/mainwindow.h: Fix the API documentation title. 

2007-11-30  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/tools/autoopttool.cpp: *
  libavogadro/src/tools/autoopttool.cpp: Remove "OBPatched" ifdefs. These are
  now all supported in OB-2.2.   

2007-11-30  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/ringsettingswidget.ui: Made the ring engine default
  to being opaque... 

2007-11-30  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/primitiveitemmodel.cpp: *
  libavogadro/src/primitiveitemmodel.cpp: Add back missing functionality from
  MoleculeTreeView. Atoms now have elements, residues have names and numbers,
  etc. May need further tinkering.   

  * libavogadro/src/tools/drawtool.cpp: * libavogadro/src/tools/drawtool.cpp:
  Minor changes to SMILES text.   

  * ChangeLog, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/elementcolor.cpp, libavogadro/src/elementcolor.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/painterdevice.h,
  libavogadro/src/povpainter.h: Initial color map support, including default
  base class (i.e., color by element)  

2007-11-29  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp: Added UFF & MMFF94 to AutoOpt  

  * ChangeLog, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: smiles to 3D added to DrawTool  

  * ChangeLog, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Added widgets for OBBuilder class, see
  Changelog for details  

  * ChangeLog, avogadro/src/extensions/forcefieldextension.cpp: Corrected
  important typo: MMF94 -> MMFF94 (ffID)  

2007-11-28  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ribbonsettingswidget.ui: Removed the opacity slider
  for now. Also added in a new display type - lines. Renders cylinders between
  points and spheres at each point. 

2007-11-28  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt: fixed CMake file to install binary on linux 

2007-11-28  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp: Optimisation for the ball and stick
  engine when drawing single bonds.  

2007-11-28  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: German translation: some more updates #4 

  * i18n/avogadro_de.ts: German translation: some more updates #3 

  * i18n/avogadro_de.ts: German translation: some more updates #2 

  * i18n/avogadro_de.ts: German translation: some more updates 

  * i18n/avogadro_de.ts: German translation updated to reflect recent additions
   and completed again (without GAMESS input, 44/288 completed there); all
  obsolete translations dropped. Reworked the tools ... translations should be
  more homogenous now. 

2007-11-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/h2methylextension.cpp: Remove unused parameters to
  prevent compiler warning.  

2007-11-28  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/wireengine.cpp: Optimised the bond
  drawing, only use multiLines when the bond order is greater than one.  

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h: Added my name
  to the copyright headers.  

  * libavogadro/src/glpainter.cpp: Optmisations to some of the drawing
  routines.  

2007-11-27  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Changed unified
  toolbar (on Mac) to use Designer flag.  

  * avogadro/src/mainwindow.cpp: Fixed weird "cancel" bug on Mac -- canceling a
  save now leaves the molecule intact.  

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/clickmeasuretool.h: Fix a few names to be more
  readable. (Should also improve translation?)  

  * avogadro/src/extensions/hydrogensextension.cpp: Fix minor compilation
  warning with unused parameters.  

  * avogadro/src/mainwindow.cpp: Add back tooltips for tabbed tools.  

  * Doxyfile, Doxyfileext: Update for 0.3.0b2 version number.  

2007-11-27  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/addenginedialog.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp: engine.h:  New macros AVOGADRO_ENGINE and
  AVOGADRO_ENGINE_FACTORY can help people with their engine headers so they
  don't have to include redundant functions.  These are things we can generate
  automatically at the moment.  Updated all the engines.  Properly fixed the
  addenginedialog.cpp hack.   

2007-11-26  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.h: Added new
  drawTriangle function that takes a normal as the fourth argument. Calculate a
  normal and use it for the whole ring - improved lighting with no artifacts in
  each ring, still issues around turning points. 

2007-11-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/addenginedialog.cpp: fixed memory leak in *hack* 

2007-11-26  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: German translation completed (without GAMESS input,
  44/288 completed there); all obsolete translations dropped. if something got
  lost, complain\! 

2007-11-26  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ringengine.cpp: Add back in
  optimisations for the ring engine. 

2007-11-26  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/addenginedialog.cpp, avogadro/src/addenginedialog.ui,
  avogadro/src/settingsdialog.ui: User Interface fixes.  

  * libavogadro/src/glwidget.cpp: Add back 2 as the default quality level. 0 ==
  Yuck.  

2007-11-26  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/povpainter.cpp, libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigate.cpp: Fixed the case of the back transformed
  axis functions and ported the existing code. 

2007-11-26  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: german translation updated 

  * i18n/avogadro_de.ts: german translation updated 

2007-11-26  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Change anonymous checkbox to a fixed title
  label with the name of the tool.  

2007-11-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/engineprimitiveswidget.cpp,
  avogadro/src/engineprimitiveswidget.h,
  avogadro/src/engineprimitiveswidget.ui, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui: Separated the Engine
  Configuration dialog into two separate dialogs.  The titles need some
  changing and/or they need to become icons.  This is what we should actually
  do.  Unfortunatly I believe this is deeply embeded in the MainWindow widget
  and far be it for me to want to dig into it.   

2007-11-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/glpainter.cpp: problem with re-creating objects 

2007-11-25  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: german translation, 1 fix 

  * i18n/avogadro_de.ts: german translation, some corrected shortcurts ... this
  time i'll get it right :-)... really \! 

  * i18n/avogadro_de.ts: german translation, some corrected shortcurts ... this
  time i'll get it right :-) 

  * i18n/avogadro_de.ts: german translation, some corrected shortcurts 

  * i18n/avogadro_de.ts: german translation, some corrected shortcurts 

  * i18n/avogadro_de.ts: german translation, some corrected shortcurts 

  * i18n/avogadro_de.ts: german translation, some fixes 

  * i18n/avogadro_de.ts: german translation, some fixes 

  * i18n/avogadro_de.ts: german translation, 1 fix 

  * i18n/avogadro_de.ts: german translation, 1 fix 

  * i18n/avogadro_de.ts: german translations (except GAMESSInputDialog) almost
  complete, thanks to carsten. 

  * i18n/avogadro_de.ts: some more german translations. many corrections thanks
  to carsten. #3 

  * i18n/avogadro_de.ts: some more german translations. many corrections thanks
  to carsten. #2 

  * i18n/avogadro_de.ts: some more german translations. many corrections thanks
  to carsten. 

2007-11-25  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/extensions/gamessinputdata.cpp,
  krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/runkrazy.rb, libavogadro/src/toolgroup.cpp,
  libavogadro/src/toolgroup.h: * Updated the krazy results and fix two of the
  issues  

2007-11-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glpainter.cpp: Removed some verbose debugging output. 

2007-11-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/selectextension.cpp,
  avogadro/src/extensions/selectextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h, avogadro/src/mainwindow.cpp: *
  avogadro/src/extensions/selectextension.cpp: Renamed extension for SMARTS
  selection. Added support for new options, such as invert selection. (More to
  come later, e.g., atom selection by name, residue by name, etc.)   

  * libavogadro/src/engines/surfaceengine.cpp: Slightly improved version. Now
  with less crashing.  

  * libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: Some test code for surfaces.  

2007-11-20  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/polygonengine.cpp,
  libavogadro/src/engines/polygonengine.h, libavogadro/src/glpainter.cpp: More
  tweaks to the drawTriangle function. Added a new polygon engine. Render
  certain structures as polygons. 

  * libavogadro/src/glpainter.cpp: Calculate the normal and correct the winding
  order in drawTriangle. 

2007-11-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/glpainter.cpp: * libavogadro/src/glpainter.cpp:
  Refinement of multiple bonds in wireframe view.   

  * ChangeLog, libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wireengine.h,
  libavogadro/src/engines/wiresettingswidget.ui, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: * libavogadro/src/painter.h,
  libavogadro/src/glpainter.h, libavogadro/src/povpainter.h,
  libavogadro/src/glpainter.cpp: Add drawMultiLine method for wireframe
  multiple bonds.  * libavogadro/src/engines/wireengine.h,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/engines/wiresettingswidget.ui: Add multiple bond indications
  for wireframe render engine. (Still needs some refinement, particularly
  triple bonds.)   

2007-11-17  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/engines/ribbonsettingswidget.ui,
  libavogadro/src/engines/ringsettingswidget.ui,
  libavogadro/src/engines/spheresettingswidget.ui: Added spacers to the engine
  configuration dialogs. 

2007-11-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.ui: Revised menu structure, adding "Build" and
  "Select" menus. Changed extensions to build menu paths by catenation of
  strings. This facilitates translation.  

2007-11-17  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdysettingswidget.ui: Added check box to show higher
  order bonds or not. 

  * ChangeLog, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/glpainter.cpp: Added a new OpenGL material that should work
  better with the ring engine. 

2007-11-16  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/engines/wiresettingswidget.ui: Added new settings for the
  wireframe engine -- turn off the dots for atoms. Provides a really nice view
  for proteins.  

  * avogadro/src/mainwindow.cpp: Added warning when non-3D data is opened.  

  * testfiles/Fe.sdf, testfiles/icsd_83086.cif, testfiles/icsd_83086.res,
  testfiles/tpy-Ru.sdf: Added a few test files for a polygon engine.  

2007-11-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Bump version number
  for 2007-11-14 snapshot.  

  * testfiles/nanotube.xyz: Added nanotube for ringengine testing.  

  * libavogadro/src/engines/CMakeLists.txt: Remove surface engine until it's
  more stable.  

2007-11-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.h: Fixed a small bug in
  the drawTriangle function. 

2007-11-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/untitled01.gpr, testfiles/benzene-homo.cube.gz,
  testfiles/ch3cl-density.cub.gz, testfiles/ch3cl-esp.cub.gz,
  testfiles/untitled01.gpr: Added some test files, including cube/surface
  tests.  

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/polygonizer.cpp,
  libavogadro/src/engines/polygonizer.h,
  libavogadro/src/engines/surfaceengine.cpp,
  libavogadro/src/engines/surfaceengine.h: First pass at a surface engine,
  using OB-2.2 SVN trunk. Definitely needs some work, but it does compile and
  show some surfaces.  

  * libavogadro/src/engines/wireengine.cpp: Minor typo in engine factory plugin
  declaration.  

2007-11-14  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/ringengine.cpp,
  libavogadro/src/engines/ringengine.h: Correct file headers.  

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h,
  libavogadro/src/engines/ringsettingswidget.ui: Added opactiy slider,
  transparency now working.  

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ringengine.cpp, libavogadro/src/engines/ringengine.h:
  Added new ring engine, renders ring structures. Transparency is not working
  yet.  

2007-11-13  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Updated the ribbon engine so that we
  now have multiple chain colours! 

2007-11-12  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: some more german translations. as always: file bugs,
  fix it or tell us if some translations are inaccurate. #2 

  * i18n/avogadro_de.ts: some more german translations. as always: file bugs,
  fix it or tell us if some translations are inaccurate. 

2007-11-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * gpltemplate: reverting back, leaving gplv2+ for now til we resolve this 

  * gpltemplate: updated license for GPLv2 

2007-11-12  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.cpp: And the glpainter...  

  * libavogadro/src/glpainter.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/painter.h, libavogadro/src/painterdevice.h: Exposed the
  loaded Molecule to the PainterDevice. Added the drawTriangle function.  

2007-11-11  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts, libavogadro/src/glwidget.cpp:
  Missing tr() in glwidget to set the default engine.  This will be obsolete
  soon as we can save settings.  Fixed some translations.    

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts: reverted some of Benoits original
  french translations that somehow got lost in the transfer 

  * avogadro/src/aboutdialog.cpp, avogadro/src/engineitemmodel.cpp,
  avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/flattabwidget.cpp, i18n/avogadro_de.ts, i18n/avogadro_fr.ts,
  libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/sphere.cpp,
  libavogadro/src/textrenderer.cpp, libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/quaternion.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/skeletontree.cpp: Big i18n fix.  Class implementations
  (.cpp) need to be surrounded by namespace Avogadro {} if the class is defined
  in that namespace.  Causes inconsistencies between linguist and lupdate   

2007-11-11  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: some more additions. tey are more visible and some
  will need furter a look and a decision ow we translate certain words in a
  consistent way. FIXME: can't find te rigt word for 'residue'. if somebody
  knows it, go troug te translation wit ctrl+f and fix it. (or tell me to do it
  :-P) 

2007-11-11  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp, libavogadro/src/tool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h: tool.h: the Tool class now has a
  signal for emitting messages.  main.cpp: fixed some translation loading
  issues. (MORE TO COME).  mainwindow.cpp: tools that emit messages now get
  sent to the message box.  clickmeasuretool.*: now emit distances and angles. 
  fixes PR #1807092   

2007-11-11  Simon Ochsenreither <simon@ochsenreither.de>

  * i18n/avogadro_de.ts: added some german translations, some tings need to be
  discussed, so please bug me if you feel anyting sounds funny :-) 

2007-11-11  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts, libavogadro/src/glpainter.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/eyecandy.h, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  Updated translation files.  libavogadro/src/tools/eyecandy.*: Added some
  functions to allow specifying your own parameters for eyecandy.  Can still
  pass a pointer to an atom and have the parameters specified for you.  Added
  eyecandy for zooming.  libavogadro/src/tools/manipulatetool.*: Added eyecandy
  to manipulate tool. This resolves PR #1823559. 
  libavogadro/src/tools/navigatetool.cpp: Optimized some code that was repeated
  in all if/else statements.  libavogadro/src/glpainter.cpp: Removed unused
  variable.   

2007-11-10  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp
  (copy, exportGraphics): Embed MDL molfile and SMILES data in exported
  graphics. Should allow PNG files to be read back in via Open Babel 2.2.   

2007-11-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * i18n/avogadro_de.ts: updated translations 

2007-11-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/forcefieldextension.cpp: Changed to use
  WeightedRotorSearch from OB-2.2 SVN trunk for testing.gg  

2007-11-06  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/glpainter.cpp: More tuning has really improved
  the render speed - thanks to Thomas Margraf for providing an example which
  inspired what I did here. 

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ribbonsettingswidget.ui,
  libavogadro/src/glpainter.cpp: Added ability to set the ribbon radius, also
  tried to add transparency but that is not working for me here. Added some
  extra calculations to the drawSpline function so the tube should not be
  flattened and has a defined radius. 

2007-11-05  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/glpainter.cpp: Now filled with NURBS goodness. Still needs
  quite a bit of tuning and testing but visually improved. 

2007-11-05  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefielddialog.h,
  avogadro/src/extensions/forcefielddialog.ui,
  avogadro/src/extensions/forcefieldextension.cpp,
  avogadro/src/extensions/forcefieldextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h: General force field extension,
  allowing UFF and MMFF94. We still need to use OBPlugin to get a list of the
  active forcefields, rather than a hard-coded list.  

2007-11-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/eyecandy.cpp: much fine-tuning in the eyecandy;
  almost everything is now controlled by #defines at the top of eyecandy.cpp
  and can be fine-tuned by just changing their values.   

  * libavogadro/src/tools/eyecandy.cpp, libavogadro/src/tools/eyecandy.h,
  libavogadro/src/tools/navigatetool.cpp: Improvements in the eye-candy: - move
  the zoom-eyecandy from navigatetool.cpp to eyecandy.cpp, and let it honor the
  MINIMUM_APPARENT_SIZE constant - don't draw anything for the
  zoom-to-molecule-center as I can't think of any useful visual cue in that
  case. zoom-to-atom remains a sphere, but with minimum size scaled by a factor
  of 0.3 - reduce the value of the MINIMUM_APPARENT_SIZE constant. - introduce
  m_color member in Eyecandy to centralize the color.  This should close Bug
  #1825419   

2007-11-02  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Reimplemented the setPrimitives
  function due to changes in molecule loading. 

  * ChangeLog, libavogadro/src/glwidget.cpp: Updated the setMolecule function
  to call setPrimitives for each engine at the end of molecule loading, should
  make our molecule loading more efficient. 

  * ChangeLog, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Also added partial charge
  labelling for atoms, feature request 1824337.  

  * ChangeLog, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelsettingswidget.ui: Updated the label engineto
  label atoms by residue name and number and bonds by their order. Feature
  request 1820686 and 1824338.  

2007-10-31  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h: Improvements to the ribbon code so
  that it caches the chain and updates it if the molecule is changed. 

2007-10-31  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Now gives warning for multi-molecule files.
  Fixes PR#1819005.  

  * avogadro/src/mainwindow.cpp: Add support for changing tools. Change to the
  navigate tool when opening an existing file. Change to the manipulate tool
  after pasting.  

  * avogadro/src/mainwindow.ui: Add shortcut Control-Backspace for
  delete/clear. Should prevent inadvertant deletion, but still make it more
  convenient.  

  * libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h: ToolGroup now
  supports changing tool by name. When changing groups, the buttons should now
  enable/disable properly.  

  * libavogadro/src/engines/wireengine.cpp: Add some dynamic depth-of-field
  scaling to dots and lines. Looks better already.  

2007-10-29  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro.nsi, scripts/avogadro.nsi: Moved avogadro.nsi script to the
  scripts directory. 

  * avogadro.nsi, scripts/cmake-vs2005.bat: Added cmake bat file for easier
  generation in Windows Updated Windows installer Script 

2007-10-27  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts: updated translations 

2007-10-25  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp: Improve the ribbon
  engine to render multiple chains correctly and not crash when there is no
  chain. 

2007-10-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/1CRN.pdb, testfiles/1CRN.pdb: moved test file to the 'testfiles'
  directory 

2007-10-25  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/1CRN.pdb: Added example PDB for ribbon view.  

  * avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/unitcellextension.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/CMakeLists.txt, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/sphereengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Updates to translate more
  strings. Also fix version numbers of libavo and avo.  

  * avogadro/src/CMakeLists.txt: Fix for Mac installs -- change library to load
  from installed directory (i.e., /usr/local/lib rather than ~/Devel/avogadro
  etc.) Also now always installs into /Applications/Avogadro.app rather than
  /usr/local/bin  

2007-10-25  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ribbonengine.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/glpainter.h, libavogadro/src/painter.h,
  libavogadro/src/povpainter.h: Added what I have for the ribbon drawing so
  far. I have added a function to draw a cubic spline through a set of control
  points. The ribbon engine uses this with the CA atoms to draw secondary
  structure. This is still far from perfect and I am working on it. Feedback is
  welcome.  

2007-10-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Added stretch to layout, improves
  look.  

  * libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autorotatetool.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Added labels for tool options,
  and translation support.  

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autoopttool.ui, libavogadro/src/tools/drawtool.cpp:
  Updated auto-optimization tool. Removed Designer interface (using code makes
  it look better on Mac) and eliminated less-used options.  

2007-10-18  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/ribbonengine.cpp: Updated to use
  renderOpaque() and to draw cylinders between the CA atoms. The next step is
  to draw a smoothed curve between the points but the current code picks out
  the CA atoms of a molecule and connects the dots... Still disabled.  

2007-10-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/ribbonengine.cpp: Initial testing code - pick out
  the CA atoms and draw lines between them. This gives the control points
  between which b-splines should be rendered.  

2007-10-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * cmake/modules/FindLinguist.cmake: should look for lrelease-qt4 and
  lupdate-qt4 before the short-hand version 

2007-10-13  Carsten Niehaus <carsten.niehaus@gmail.com>

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts: regenerate after my fixuifiles
  script 

  * avogadro/src/enginesetupwidget.ui,
  libavogadro/src/engines/bsdysettingswidget.ui,
  libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/engines/ribbonsettingswidget.ui,
  libavogadro/src/engines/spheresettingswidget.ui: Using KDEs "fixuifiles" so
  that the "Form" string no longer appears in the .ts-files!  find . -name *.ui
  | xargs ~/svn/kdesdk/scripts/fixuifiles  

  * i18n/avogadro_de.ts, i18n/avogadro_fr.ts: * Updating the .ts-files after my
  string-changes. Also adding some * translation for testing  

  * avogadro/src/extensions/smartsextension.cpp, avogadro/src/mainwindow.cpp: *
  Fixing a couple of i18n issues  

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp: adding a couple of comments for
  translators 

2007-10-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt, i18n/avogadro_de.ts, i18n/avogadro_fr.ts,
  scripts/release_translations.sh, scripts/update_ts_files.sh: No longer need
  the translation scripts.  To update translations do 'make
  update-translations' 

  * libavogadro/include/avogadro/library.h: leftover files 

  * cmake/modules/FindLinguist.cmake, i18n/avogadro_de.ts, i18n/avogadro_fr.ts,
  libavogadro/include/avogadro/library.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/tools/bondcentrictool.cpp: Update French Translations and
  cleaned some bad uses of tr() 

  * avogadro/src/aboutdialog.cpp, avogadro/src/main.cpp,
  libavogadro/CMakeLists.txt, libavogadro/src/global.cpp,
  libavogadro/src/global.h: Added translation information and put the library
  functions (for version / svnrevision) in a file and put a function for the
  Library that does a ::createTranslator() 

2007-10-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * cmake/modules/FindLinguist.cmake: Forgot to add FindLinguist.cmake 

  * CMakeLists.txt, avogadro/CMakeLists.txt, avogadro/i18n/CMakeLists.txt,
  avogadro/i18n/avogadro_de.ts, avogadro/i18n/avogadro_fr.ts,
  avogadro/src/CMakeLists.txt, avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/gamessextension.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, i18n/avogadro_de.ts, i18n/avogadro_fr.ts,
  libavogadro/CMakeLists.txt, libavogadro/i18n/CMakeLists.txt,
  libavogadro/i18n/libavogadro_de.ts, libavogadro/i18n/libavogadro_fr.ts,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/drawtool.cpp: Updated Translation Stuff (common
  directory) and fixed up the CMakeLists to auto-generate the translation files
  (.qm) 

  * avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h: Attempt to fix the non-hiding
  geometric optimization dialog.  It works much better.  It's something to do
  with the way signals are getting passed to the thread and dialog. 

  * avogadro/src/main.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/glwidget.cpp: made a branch for
  the splash screen and disabled it.  for normal loading there is hardly any
  load time so the splash screen doesn't really do anything.  in the future
  this may be worth loading up depending on how costly plugin loading is (or
  startup time for that matter). 

  * avogadro/src/application.cpp,
  avogadro/src/extensions/ghemicalextension.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Added delayed initialization so that
  the mainwindow constructor creates all the objects but doesn't do any loading
  of plugins until the GUI is already up and running.  Once I did this, I
  realized it might be cool to have a splash screen because we do load a
  relatively large ammount of plugins and stuff.  Anyways, this is the result.
  We can revert it if it's too gaudy (too much). 

  * avogadro/src/enginesetupwidget.cpp: Fix for PR #1796189 - Make sure the
  reset button is disabled until the user selects an engine. 

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp: Fix for PR
  #1805401  We weren't properly setting background color.  Needed a call to
  qglClearColor before calling the renderGL function. 

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Only ever copy to the
  clipboard.  In Linux we don't currently copy to the selection buffer. 
  However, this should change in the future.  Fixed a bug where trying to undo
  the copy / cut commands was trying to restore the clipboard contents but this
  ends up causing crashes because the data gets deleted.   

2007-10-06  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/tools/bondcentrictool.cpp: Reworded the snap-to feature's
  interface to remove some of the ambiguity regarding what its actual function
  is.  

2007-10-05  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp: Forgot to comment out the #define  

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/bondcentrictool.cpp: Fixed a bug that caused avo to
  crash when you switched to our tool, did nothing then switched to another
  tool.  Also threaded the Geometry Optimisation in the AutoOpt tool  

2007-10-05  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Added some documentation and fixed a
  few cases during dihedral manipulation where mishapen or small rectangles
  were drawn.  

2007-10-04  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h, libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Added the ability to draw obtuse
  angle-sectors (defaults to acute)  

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Improved the math for calculating
  the rotation of bond angles and dihedral angles.  Interaction should be a lot
  smoother in the case where the bond being modified is almost perpindicular to
  the screen.  

  * libavogadro/src/tools/bondcentrictool.cpp: Changed the algorithm for
  dihedral rotation, now similar to the bond angle rotation algorithm.  

2007-10-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Revert "sheet" patch until I can get the logic
  right for quitting.  

2007-10-04  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Initial implementation of dihedral
  angle manipulation.  Still a little buggy and a few special cases that it
  doesn't work on but the basic concept is there.  

2007-10-04  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  The current status of AutoOpt tool, has #define that can be uncommented if
  you have a patched version of OpenBabel  

2007-10-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Initial maybeSave() support for Mac sheets.
  Needs work -- clicking "cancel" doesn't work right.  

2007-10-03  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/autoopttool.cpp,
  libavogadro/src/tools/autoopttool.ui,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Cleanups for Mac mouse buttons. Fixes
  PR#1720875.  

  * avogadro/src/extensions/gamessextension.cpp: Fix signal connection error.  

2007-10-03  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Fixed a bug with undo in the bond
  centric tool. Added the ability to view the dihedral/torsional angles of a
  given atom in relation to the selected bond by clicking on it.  This is in
  preparation for dihedral angle editing.  

2007-10-02  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Some documentation and improved undo
  functionality.  

  * libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Added a new procedure that checks if
  two atoms are bonded together in preparation for Dihedral angle manipulation.
   

2007-10-02  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h: Removed toolgroup signal hack  

2007-10-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/selectrotatetool.cpp: Re-added selectrotatetool to the
  CMakeLists.txt and fixed a selection bug. 

2007-10-02  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Changed it back as the thread was not working properly in linux  

2007-10-01  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h:
  Added a thread class to the autoopt tool for running the optimizer in  

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/autoopttool.cpp, libavogadro/src/tools/autoopttool.h,
  libavogadro/src/tools/autoopttool.png, libavogadro/src/tools/autoopttool.qrc,
  libavogadro/src/tools/autoopttool.ui: My research project for my Honors, an
  interactive Automatic Optimisation tool  

2007-09-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * cmake/modules/FindOpenBabel2.cmake: Update to give better error/warning
  messages about Open Babel >= 2.1.  

  * libavogadro/include/avogadro/painterdevice.h: Added stub header for
  painterdevice.h  

  * libavogadro/src/engines/CMakeLists.txt: Skip building ribbon engine -- not
  ready for release, according to Marcus.  

2007-09-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro.nsi, libavogadro/src/global.h, libavogadro/src/povpainter.h,
  libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/tools/bondcentrictool.cpp: Windows compile fixes.  Needed
  exports to library functions. 

2007-09-23  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/gamessextension.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/periodictabledialog.cpp: Mac interface fixes, including
  for PR#1723768 -- quit now prompts for save and closes each window.  

2007-09-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: woops.  the resizeGL call, which calls
  glViewport, must occur _before_ the glClear call! Otherwise only the old
  viewport is cleared. So there was a bug in the previous bugfix, and the
  reason why it worked nevertheless for Geoff is probably that the GL buffer
  just happened to have the correct initial state, but that was just luck. 
  Geoff: please test and tell me if it doesn't work!   

  * libavogadro/src/glwidget.cpp: Add a comment so that the bug fix won't be
  inadvertently removed. Indeed, this resizeGL() call seems redundant there and
  without an explanatory comment there's a high risk that a future maintainer
  will remove it, thinking that it was useless.   

  * libavogadro/src/glwidget.cpp: Fix this bug: [ 1797069 ] Initial painting
  yields "stretched" look   

2007-09-19  Carsten Niehaus <carsten.niehaus@gmail.com>

  * libavogadro/CMakeLists.txt: well, I also need to add the subdir. 

  * avogadro/src/main.cpp: make use of the new positiion 

  * avogadro/CMakeLists.txt, avogadro/i18n/CMakeLists.txt,
  libavogadro/i18n/CMakeLists.txt: Hey, now the .qm files even install in the
  correct directory ($PREFIX/i18n/)  

2007-09-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/i18n/avogadro_fr.ts: Quite complete french translation of the app,
  I only left out GAMESS and some chemical stuff I don't understand.  I don't
  translate libavogadro because there is so much redundancy between
  libavogadro*.ts and avogadro*.ts that it amounts to doing twice the same
  work. Quite frustrating, a solution must be found at the level of the source
  code.   

2007-09-18  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/eyecandy.cpp: some tweaking (smaller sizes) and
  cleanup (introduce a new define)   

2007-09-18  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/main.cpp: Ok, translations are now BASICALLY working. Now I
  need to fix the make install stuff and all that...  

  * avogadro/src/main.cpp: I *think* this is a better approch until translation
  works. The point is: qt_de_DE (which is what I get on my PC) cannot work as
  the file is called qt_de.qm ... No clue what is next 

  * scripts/release_translations.sh: This script creates the .qm files  

  * avogadro/i18n/avogadro_de.ts, avogadro/i18n/avogadro_fr.ts,
  libavogadro/i18n/libavogadro_de.ts, libavogadro/i18n/libavogadro_fr.ts: I
  hope this was correct. I ran lupdate on the files and started a basic
  translation. 

  * scripts/update_ts_files.sh: let us at least use the name avogadro... 

  * avogadro/src/main.cpp: I wonder how Donald was able to compile Avogadro
  without this line... 

2007-09-17  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/i18n/avogadro_fr.ts: add initial french translation. Note: I
  noticed many strings that should not be i18n'd, such as "Ctrl+S" or "alpha:".
  This should be fixed in the source code, as it's a waste of translators'
  efforts.   

2007-09-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/avogadro.pro, avogadro/i18n/avogadro_de.ts,
  avogadro/i18n/avogadro_fr.ts, avogadro/src/elementcombobox.cpp.disabled,
  avogadro/src/main.cpp, libavogadro/i18n/libavogadro_de.ts,
  libavogadro/i18n/libavogadro_fr.ts, testfiles/acid_chlorides.smi,
  testfiles/amines.smi: Added french and german (de?) translations to avogadro.
   To add a new translation, find out the code (fr) and then do  touch
  libavogadro/i18n/libavogadro_(code).ts touch avogadro/i18n/avogadro_(code).ts
   I know i know.  It's somewhat a pain to think of libavogadro and avogadro as
  separate but I reallly prefer them this way so we save having to split up
  translations later.  Please start doing some translations and i'll figure out
  how the hell to incorporate them.   

2007-09-17  Benoit Jacob <jacob.benoit.1@gmail.com>

  * AUTHORS: Add Shahzad, Ross, James as AUTHORS. Can anyone add Shahzad's
  e-mail address?  CCMAIL:dark.nz@gmail.com CCMAIL:james.bunt@gmail.com   

  * avogadro/src/CMakeLists.txt, avogadro/src/elementcombobox.cpp,
  avogadro/src/elementcombobox.cpp.disabled, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glpicker.cpp, libavogadro/src/glpicker.cpp.disabled,
  libavogadro/src/glpicker.h, libavogadro/src/glpicker.h.disabled: Make use of
  GLOB in CMakeLists whenever applicable, e.g.: FILE(GLOB libavogadro_SRCS
  "*.cpp") I browsed our CMakeLists to see which files should be excluded, and
  found glpicker.* and elementcombobox.cpp. So I appended ".disabled" to their
  filenames, so that they don't get globbed.   

2007-09-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * scripts/update_ts_files.sh: added update_ts_files.sh 

2007-09-17  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/eyecandy.cpp,
  libavogadro/src/tools/eyecandy.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: make the translation-eyecandy share the
  same infrastructure as the rotation-eyecandy, which uniformizes looks, and
  move all that in a separate eyecandy.{h,cpp} file.   

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: tweaking and cleanup in the rotation
  eyecandy   

  * libavogadro/src/cylinder.cpp, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Big improvements in the eyecandy in
  navigatetool: -- move rotation-eyecandy code to a separate class (now we
  should go on and do the same for translation-eyecandy) -- now also do
  eyecandy for mol-based movement (not only atom-based movement) -- improve how
  sizes are computed, so that the eyecandy is visible from far away in big
  molecules -- take away redundant code between front-face and back-face
  drawing, using glCullFace() -- fix bugs in comments where front-face and
  back-face were mixed up -- fix rendering bug caused by that mixing up   

2007-09-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/textrenderer.cpp,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Fixed PR#1796030  Also some other
  minor bug fixes introduced when allowing GL Names of 0. 

2007-09-16  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/main.cpp: Fix for PR#1788666 (feature request) avogadro -h
  should provide some help 

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Fix for PR#1788659 
  Open file and save file dialogs now remember last directory.   

  * avogadro/src/main.cpp: Missed a define so that XInitThreads() isn't called 

  * libavogadro/CMakeLists.txt, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp: Updated GLPainter and GLWidget so that
  when doing pushName / popName / setName, 0 is an acceptable value for a name.
   ie. no longer offset bonds.  drawtool.cpp: as per PR#1717871 the draw tool
  now deletes bonds  glwidget.cpp: added define to enable threaded OpenGL
  widget.  Disabled by default so we can get a release out.  It's some bug
  caused by XCB on my system. If you want to compile with a thread-enabled
  GLWidget do 'cmake -DENABLE_THREADED_GL ..' that should do it.  patch for
  PR#1760151    

2007-09-09  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/sphere.cpp: fix indentation in sphere.cpp   

2007-09-06  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html, krazy/runkrazy.rb: I am
  now using Krazy2. Updated the html files 

2007-09-06  Benoit Jacob <jacob.benoit.1@gmail.com>

  * CMakeLists.txt, avogadro/src/main.cpp, cmake/svn.h.cmake: fix the svn
  revision thingy -- don't install svn.h, instead store it in the CMake
  builddir, and add that dir to the list include dirs. make avogadro output it
  (example of usage. feel free to remove)   

  * CMakeLists.txt, cmake/svn.h.cmake: Let CMake produce a special header file
  definining a string SVN_REVISION_STRING. The header is installed at
  $CMAKE_INSTALL_PREFIX/include/avogadro/svn.h This allows applications using
  libavogadro to be aware of which revision they are using.   

2007-09-06  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/aboutdialog.cpp: revert until Johannes is able to fix the
  issue 

  * avogadro/src/aboutdialog.cpp: This is a test if this SVN thingy works. Will
  revert if it doesn't 

2007-09-06  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/application.cpp: set the LC_NUMERIC locale to "C" to work
  around an OB bug. Currently Qt already did this for us but might stop doing
  so in a future version.   

2007-08-28  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.h, libavogadro/src/tools/navigate.cpp: remove two
  useless includes, add a copyright line for myself   

2007-08-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/gamessinputdata.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Updated GLWidget to include the ::current()
  function which returns the current GLWidget.  This isn't the best solution
  but it's required for extensions to get the current GLWidget.  Also fixed up
  all the GAMESS EFP stuff so that it works correctly.   

2007-08-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ribbonengine.cpp,
  libavogadro/src/engines/ribbonengine.h,
  libavogadro/src/engines/ribbonsettingswidget.ui,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h: Some small updates to the POVPainter. Added
  drawLine and drawSpline to the Painters, but spline is commented out as it
  still requires more work. Started some very early work on the ribbon view but
  it is far from working right now. Depends on implementing a spline function
  to draw B-splines.  

  * ChangeLog, libavogadro/src/glwidget.cpp: Fixed regression with bond
  picking.  

  * ChangeLog: Updated the ChangeLog.  

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  Added the computeClickedPrimitive/Atom/Bond functions to the GLWidget class
  as these functions have been used in several tools and are quite generic.
  Ported the tools to use the new computeClicked* functions and removed the
  local ones.  

2007-08-19  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog: ChangeLog updates.  

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h, libavogadro/src/tools/navigate.cpp,
  libavogadro/src/tools/navigate.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Added a new navigation class with
  static member functions to perform the navigation functions common to three
  tools right now. Ported the tools to use the new Navigate class and removed
  all duplicated code.  

2007-08-18  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp: Added the display of
  the angle sector under consideration with the current selection of atoms.  

  * ChangeLog, libavogadro/src/tools/clickmeasuretool.cpp: Added units to the
  output.  

2007-08-16  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/action.cpp,
  avogadro/src/action.h, avogadro/src/extension.h,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h, avogadro/src/mainwindow.cpp:
  Removed action.cpp/h all together and replaced with ::menuPath(QAction
  *action) in the Extension class 

2007-08-14  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessefpmatchdialog.ui,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h, avogadro/src/main.cpp: Progress on
  the EFP dialog.  Saves the previous selection and interactivley displays the
  current group in the dialog.  Still modal but I believe that works the best. 
  It's a complicated process and might get more complicated with multiple
  dialogs being open.  Plus if the molecule is modified the EFP group
  information becomes invalid. 

  * avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessefpmatchdialog.ui,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h: More EFP Additions.  Still more
  needed.   

  * ChangeLog, avogadro/src/editcommands.cpp,
  avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/gamessefpmatchdialog.cpp,
  avogadro/src/extensions/gamessefpmatchdialog.h,
  avogadro/src/extensions/gamessefpmatchdialog.ui,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/smartsextension.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Refactored
  clearSelection -> clearSelected (needs to be clearSelectedPrimitives
  eventually but it seems wordy.  I prefer wordy and clear over short and
  unclear.  Added some more EFP mechanisms to the GAMESS plugin but it needs
  some more work.   

2007-08-13  Shahzad Ali <saky.org@gmail.com>

  * libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/skeletontree.h: Comments added - Documentation 

2007-08-13  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/bondcentrictool.cpp: A Fix to Text color for the
  BondCentric Tool 

2007-08-11  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: I updated Krazy to the
  latest generation of checks. Several issues have now been found 

2007-08-10  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitivelist.h, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/autorotate.png,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.qrc,
  libavogadro/src/tools/clickmeasuretool.qrc, libavogadro/src/tools/draw.qrc,
  libavogadro/src/tools/drawtool.qrc, libavogadro/src/tools/manipulate.qrc,
  libavogadro/src/tools/manipulatetool.qrc, libavogadro/src/tools/measure.qrc,
  libavogadro/src/tools/navigate.qrc, libavogadro/src/tools/navigatetool.qrc,
  libavogadro/src/tools/select.qrc, libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.qrc: Minor file renaming to match
  correctly, might still need some work.  Also changed the auto-rotate icon
  which could also use some work.   

2007-08-10  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/navigatetool.cpp: Added visual
  representation of atom centred translation. Needs extra features adding to
  the painter and porting. Also need to add something for zoom/tilt.  

2007-08-08  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog: Updated the ChangeLog.  

  * libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h: Added
  multiCylinder support thanks to help from Benoit with the maths. Also tweaked
  the default material parameters in order to improve the look of default
  renders. Still need to improve the translation from OpenGL to POV-Ray coords.
   

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Add visual representation of atom
  centred molecule rotation. Open up modifiers to all - we always planned to
  add this for all architectures. Alt seems to be taken in KDE for Window
  movement though - possibly need an alternate.  

2007-08-07  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/quaternion.h, libavogadro/src/tools/skeletontree.h:
  Added comments to various functions that I wrote. 

2007-08-07  James Bunt <james.bunt@gmail.com>

  * libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/bondcentric.png,
  libavogadro/src/tools/bondcentrictool.cpp,
  libavogadro/src/tools/bondcentrictool.h,
  libavogadro/src/tools/bondcentrictool.qrc,
  libavogadro/src/tools/quaternion.cpp, libavogadro/src/tools/quaternion.h,
  libavogadro/src/tools/skeletontree.cpp, libavogadro/src/tools/skeletontree.h:
  Added the bondcentric tool.  Added a few procedures needed by this tool to
  the painters, and a new signal to the widget that signals when the molecule
  is changed.   

2007-08-06  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitiveitemmodel.h:
  * libavogadro/src/glwidget.cpp: GLWidget is not initialized until it is
  actually called to render.  This hopefully fixes a race condition that
  existed somewhere with makeCurrent().  Not sure why this was happening but I
  believe it had something to do with the fact that we were calling ->run()
  within the constructor and we don't know what magic TT is doing behind the
  scenes.  * libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitiveitemmodel.cpp: there was an issue with the engine
  views when deleting certain atoms which has been fixed.  Basically the model
  needs to notify the view that it's just taking from the end of the list but
  has reordered the contents (just the way we happen to change things in the
  engines).     

2007-08-05  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Reran Krazy. Still no
  issues. Great 

2007-07-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/action.cpp,
  avogadro/src/action.h, avogadro/src/extension.h,
  avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h, avogadro/src/mainwindow.cpp,
  libavogadro/src/primitivelist.h: Made Avogadro::Action so that each action
  also has a menuPath where it should go.  It will also help later, i think we
  can emit signals easier.   

2007-07-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/camera.h, libavogadro/src/glpainter.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/textrenderer.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/navigatetool.cpp: resolved PR 1759321 and 1742953  see
  bug reports for more information and future updates.   

  * libavogadro/src/camera.cpp, libavogadro/src/engines/bsdyengine.cpp:
  camera.cpp: Fixed PR #1759321 bsdyengine.cpp: removed extraneous sorting
  calls (previously inserted to help with transparency)    

2007-07-23  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/povpainter.cpp: Use the camera position and point the same
  way as the camera.  

2007-07-21  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html, krazy/runkrazy.rb: Now
  Krazy is run with --exclude qclasses,license,copyright. This means those
  three scripts are not used which leads to a --tara-- error-free Avogadro! 

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Updating the HTML files
  after I fixed most issues found by Krazy 

  * libavogadro/src/tools/manipulatetool.h: one more krazy fix: explicit
  MoveAtomCommand 

  * avogadro/src/flowlayout.cpp, avogadro/src/mainwindow.cpp: Krazy-fixes:  Fix
  include order and "" → <>  

  * avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.h,
  avogadro/src/enginesetupwidget.h, avogadro/src/extensions/forcefielddialog.h,
  avogadro/src/extensions/gamessinputdialog.h,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/flattabwidget.cpp, avogadro/src/flattabwidget.h,
  avogadro/src/flowlayout.h, avogadro/src/primitivetreeview.h: Krazy fixes: -
  Many explicit ctors - One more const QString& instead of QString in the API  

  * krazy/runkrazy.rb: No longer run the 'qclasses' test as Avogadro is
  Qt-only. That test only makes sense for KDE 

  * avogadro/src/extensions/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/tools/CMakeLists.txt:
  Do not use TRUE in CMake, use true. The TRUE/FALSE macros are obsolete since
  CMake 2.4.2 or something like that. 

  * libavogadro/src/CMakeLists.txt, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/povpainter.cpp, libavogadro/src/povpainter.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/toolgroup.cpp: Krazy fixes
  for libavogadro/src/*:  - Make two ctors explicit - Use #include <config.h>
  and not "config.h" - Marcus forgot a const QString&   (was just a QString) 
  Question:  ../libavogadro/src/painterengine.h: line#38 (1)
  ../libavogadro/src/painter.h: line#39 (1)  Those two clases are derived from
  QObject but are missing the Q_OBJECT macro... Is there a reason for that? If
  not I will add the macro.   

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Updating the Krazy files
  after installing the latest Krazy-version. Also, this is against the latest
  svn trunk 

2007-07-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/elementcombobox.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/include/avogadro/povpainter.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glpainter.cpp, libavogadro/src/glpainter.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/painterdevice.h, libavogadro/src/painterengine.cpp,
  libavogadro/src/painterengine.h, libavogadro/src/povpainter.cpp,
  libavogadro/src/povpainter.h, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h, libavogadro/src/tool.h,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: MERGE OF MULTITHREADED_OPENGL
  BRANCH INTO TRUNK.  svn merge -r 535:572  *** do not work on
  multithreaded_opengl any longer ***   

2007-06-25  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/sphereengine.cpp: trivial fix for the case m_alpha
  == 0.999, if that ever happens.   

  * libavogadro/src/textrenderer.cpp: In TextRenderer: Fix
  avogadro-Bugs-1739848. Improve text outline brush. Print useful error message
  if a char fails to render, and try to fall back to an asterisk (*). Minor
  optimizations.   

2007-06-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/tools/drawtool.cpp: *
  libavogadro/src/tools/drawtool.cpp (DrawTool::mousePress): Fix bugs with
  "alchemy" mode -- clicking on an atom to change the element. PR#1741653 and
  PR#1720879.   

  * libavogadro/src/tools/drawtool.cpp: Fix PR#1741653  

  * ChangeLog, avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp: * avogadro/src/editcommands.[h,cpp]: Support for
  selecting new atoms when pasting. Fixes PR#1739837.  *
  avogadro/src/mainwidnow.cpp: Pass along the widget when creating a paste
  command. Fix minor crashes when copy/cut with selected bonds. (Now we can
  select more than just atoms).   

2007-06-22  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/navigatetool.cpp:
  Add initial one-button Mac support for draw tool and navigate tool.  

2007-06-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/h2methylextension.cpp,
  avogadro/src/extensions/h2methylextension.h: *
  avogadro/src/extensions/h2methylextension.cpp: New extension for "sculpting"
  hydrogen atoms to methyl groups. Works also on selected hydrogens.   

  * ChangeLog, avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h: *
  avogadro/src/extensions/hydrogens*: Fix PR#1739841. Only add or remove
  hydrogens for selected atoms if some atoms are selected.   

2007-06-21  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: adjust the meaning of the aCells, bCells,
  cCells parameters as discussed with Geoff.   

  * avogadro/src/extensions/unitcellextension.cpp,
  libavogadro/src/glwidget.cpp: let GLWidget::setUnitCells auto-update the
  geometry, reinitialize the camera for the new geometry, and update the view. 
   

  * cmake/modules/FindEigen.cmake: First search for Eigen in
  $ENV{KDEDIR}/include.   

2007-06-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extension.h, libavogadro/src/painter.h: removed some function
  definitions that were never implemented. 

2007-06-20  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/axesengine.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp, libavogadro/src/glwidget.cpp:
  Initialise the painter at the start of the GLWidget render function, removed
  all calls to painter begin and end from the engines.  

2007-06-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/sphereengine.cpp: two different calls to enable
  DepthMasking redundant 

2007-06-20  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/sphereengine.cpp: Use the depth mask now
  transparency doesn't use it by default.  

2007-06-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/glwidget.cpp: *
  avogadro/src/extensions/ghemicalextension.cpp: Added threading so that a
  progress dialog is displayed.  Also removed some debuggin code that was left
  over.   

  * avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h: ghemical optimization is now
  threaded 

2007-06-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: * libavogadro/src/glwidget.*: Added
  ::radius function to the GLWidget that way tools and engines only need to ask
  the GLWidget the radius rather than actually going through all engines on
  their own.  Also, engines more accurately give radius.  *
  libavogadro/src/engine.*: updated ::radius function to take the GLWidget as a
  parameter.  * libavogadro/src/engines/*: updated engines to not maintain an
  internal pointer to the GLWidget that was last called.   

  * libavogadro/src/glwidget.cpp: disable depth masking when calling
  ::renderTransparent 

2007-06-19  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/navigatetool.cpp: Updated tooltip to
  reflect current behaviour of this tool.  

  * libavogadro/src/tools/manipulatetool.cpp: Changed translation to the left
  mouse button and rotation to the right as suggested by Donald and Geoff. It
  does seem more intuitive despite not matching navigate tool.  

  * ChangeLog, libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h: Added the ability to initiate
  rotation using mouse movements. Left for x/y, middle for z.  

2007-06-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, libavogadro/src/glwidget.cpp: * libavogadro/src/glwidget.cpp
  (updateGeometry): Initial attempt at updating geometry based on unit cell
  parameters. This *seems* like the correct approach, but I have not checked
  with Benoit or fully tested. This tracks PR#1739844.   

2007-06-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h: move buttonStartStop to member
  pointer so that name can change.   

2007-06-19  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/sphereengine.cpp: Fix error in logic when dealing
  with drawing selection spheres.  

  * ChangeLog, libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/spheresettingswidget.ui: Removed the skeleton
  rendering functions - use the other engines thanks to changes in engine
  rendering order made by Donald. Much simpler implementation that can use any
  engine for the backbone now.  

2007-06-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/src/glwidget.cpp: cleaned up debug code. 

2007-06-18  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/extensions/gamessextension.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.h: *
  libavogadro/src/engine.*: added some engine flags for transparency atoms,
  bonds, molecules so that the glwidget has a better idea of the capabilities
  of the engines.  also added the transparencyDepth relative to others.  this
  needs a conceptual update just because i don't think it's intuitive.  if
  people define theirs higher than other engines they get priority.  i still
  believe this should be dependent on the ::radius response for the specific
  primitive type we're trying to compare.  * libavogadro/src/glwidget.*:
  engines are now sorted on load based on their flags and their
  transparencyDepth.  * libavogadro/src/engines/*: updated engines. 

  * ChangeLog, avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/gamessinputdialog.ui, avogadro/src/mainwindow.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h, libavogadro/src/tools/selectrotatetool.cpp: *
  libavogadro/src/glwidget.*: Fixed a bug in mass selection where	the pointer
  was going past the end of the buffer.  Had to make sure	our pointer stays
  sane.  * libavogadro/src/primitive.*: Removed old selection code.  *
  libavogadro/src/selectrotate.cpp: Updated so that if there are       
  multiple engines, the toggling of selection only happens once per       
  primitive.  * avogadro/src/extensions/gamessinputdialog.cpp: Fixed bug
  1720467. 

2007-06-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog: Add in missing ChangeLog entries from the SVN log. (Bad
  ghutchis!)  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: *
  avogadro/src/mainwindow.*: Remove quit() event -- Mac clients should receive
  a closeEvent for every window (advice from Trolltech).   

  * ChangeLog, avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/extensions/unitcellparamdialog.ui: *
  avogadro/src/extensions/unitcell*: Add support for controlling unit cell
  dimensions and angles. Add a warning if the molecule does not yet have a unit
  cell record -- extension will suggest a possible box dimenison.   

2007-06-17  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/axesengine.cpp: Small tweak to the engine display. 

2007-06-16  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/engines/axesengine.cpp: Improvements to the axes
  engine rendering - all axes should be of equal length now.  

  * ChangeLog, libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/spheresettingswidget.ui: Some improvements to the
  rendering code and the setup widget, as suggested by Benoit.  

  * ChangeLog, avogadro/src/settingsdialog.ui, libavogadro/src/painter.cpp:
  Added some higher detail levels, probably only useful on accelerated systems.
  Kept the default level at 2.  

2007-06-15  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/autorotatetool.cpp: Removed shortcuts for the
  buttons.  

  * ChangeLog, libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h: Added a start/stop button and a reset
  button to the config widget.  

  * ChangeLog, cmake/modules/FindOpenBabel2.cmake: Added more verbosity to the
  cmake messages about the required version.  

  * ChangeLog, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h: Added undo/redo support to the
  manipulation tool.  

2007-06-14  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: update the krazy status 

  * libavogadro/src/engines/axesengine.h, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.h, libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.h, libavogadro/src/engines/wireengine.h:
  remove 23 includes from the engine headers... We really need a script to do
  this! 

2007-06-14  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog: Updated the ChangeLog with various stuff I have done this week. 

2007-06-14  Carsten Niehaus <carsten.niehaus@gmail.com>

  * CMakeLists.txt, ChangeLog, INSTALL: Require Qt 4.3.0 now. Marcus told me
  with 4.2.x Avo doesn't even compile right now because of some .ui-files.  Ok,
  I have *no* clue whatsoever what these lines are all about... Shall I simple
  s/4.2.3/4.3.0/?  File C:\Qt\4.2.3\lib\QtGui4.dll File
  C:\Qt\4.2.3\lib\QtCore4.dll File C:\Qt\4.2.3\lib\QtOpenGL4.dll    

2007-06-14  Marcus D. Hanwell <marcus@cryos.org>

  * avogadro/src/extensions/unitcellparamdialog.cpp: Small fix to close the
  dialog when clicking cancel.  

  * libavogadro/src/tools/selectrotatetool.cpp: Fixed the selection bug when
  using a selection box - should work fine now.  

2007-06-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/unitcellextension.cpp,
  avogadro/src/extensions/unitcellextension.h,
  avogadro/src/extensions/unitcellparamdialog.cpp,
  avogadro/src/extensions/unitcellparamdialog.h,
  avogadro/src/extensions/unitcellparamdialog.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added full unit cell display support -- new
  extension can allow you to specify how many unit cells in each direction to
  display. (Still need to fix selection.)  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Add a small random
  vector offset to pasted molecules, so they do not fall on top of each other.
  (Best solution would be to mirror drawing programs, a small increasing offset
  with every paste.)  

  * libavogadro/src/tools/drawtool.cpp: Fix minor bug with periodic table
  widget loosing focus.  

2007-06-13  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/autorotatetool.cpp: Allow both positive and negative
  rotation about all axes.  

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/autorotatetool.cpp,
  libavogadro/src/tools/autorotatetool.h: Added new auto rotation tool. The
  rotation speed about the x, y and z axes can be set using sliders. It needs
  an icon.  

2007-06-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/navigatetool.cpp: Corrected incorrect tooltip text.  

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/axesengine.cpp, libavogadro/src/engines/axesengine.h:
  Added an axes engine - draws the x, y and z axes in the bottom left of the
  GLWidget. Added new transformedAxis() functions for x, y and z to the camera
  class. Thanks to Benoit for his help in figuring this one out - still need to
  add drawing of axis labels.  

  * libavogadro/src/engines/sphereengine.cpp: Two pass rendering of the
  transparent spheres to remove spheres that are internal to the VdW surface.  

2007-06-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui,
  libavogadro/src/engines/stickengine.cpp: Added support for bond labels too.
  They are not drawn for engines that do not draw bonds or the wireframe engine
  - they both return a zero bond radius. Also updated the engines that needed
  it to return the radius of their bonds.  

  * libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/spheresettingswidget.ui: A few small optimisations of
  the OpenGL code and the settings widget.  

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/spheresettingswidget.ui: Extend the VdW sphere engine
  for transparent rendering of the VdW spheres and draw a ball and stick
  structure inside if the VdW spheres are transparent. Added setAlpha function
  to the Color class to accomplish this.  

2007-06-06  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/textrenderer.cpp: render all outlines before the rendering
  the actual glyphs. being able to do so was the main reason for splitting the
  outline texture from the actual glyph texture. Now the letters don't "eat"
  each other anymore, as used to be the case e.g. between the "x" and the "y"
  in "Oxygen".   

  * libavogadro/src/textrenderer.cpp: make the new text outlining engine work
  also when the texture_rectangle extension is absent.   

  * libavogadro/src/textrenderer.cpp: a whole new text outlining engine.   

2007-06-05  Carsten Niehaus <carsten.niehaus@gmail.com>

  * libavogadro/src/tools/periodictabledialog.ui: Adding a layout for the PSE
  widget 

2007-06-05  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/engineconfigurationwidget.ui,
  avogadro/src/enginetabwidget.cpp, avogadro/src/enginetabwidget.h,
  avogadro/src/mainwindow.cpp: Minor class refactoring / cleanup 

2007-06-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/periodictabledialog.cpp: Update draw tool to update
  periodic table when visible. (e.g., if element is picked from menu, table
  will update correctly).  

  * libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/periodictabledialog.h,
  libavogadro/src/tools/periodictabledialog.ui: Make the periodic table more
  like a palette -- no "ok" or "cancel" buttons -- can leave it open on the
  screen while changing elements.  

  * libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/periodictabledialog.h: Add periodic table which
  actually sets elements! (What a concept.)  

  * avogadro/src/mainwindow.cpp: Added titles to open/save dialogs.  

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/periodictabledialog.ui: Minor periodic table fixes  

2007-05-31  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/periodicTable.ui,
  libavogadro/src/tools/periodictabledialog.cpp,
  libavogadro/src/tools/periodictabledialog.h,
  libavogadro/src/tools/periodictabledialog.ui: Added slim periodic table
  widget to draw tool, but does not yet set custom elements.  

2007-05-28  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/textrenderer.cpp: tweaking internal parameters of the text
  renderer. tell me if you like/dislike it.   

2007-05-27  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: merge a patch by Alexandr Goncearenco from
  the kalzium snapshot, to avoid hitting a bug in the Radeon DRI driver.   

2007-05-26  Carsten Niehaus <carsten.niehaus@gmail.com>

  * cmake/modules/COPYING-CMAKE-SCRIPTS: adding the COPYING-CMAKE-SCRIPTS file 

  * cmake/modules/FindOpenBabel2.cmake: We require OpenBabel 2.1.0+ and not
  2.0.0+ 

2007-05-26  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: forward-port a fix for a crash in kalzium   

2007-05-26  Marcus D. Hanwell <marcus@cryos.org>

  * AUTHORS, ChangeLog, authors.xml, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Updated my details in the author
  files. Added bond selection support to the stick engine, small clean ups in
  bsdyengine and sphereengine.  

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Fix a bug where the 0 indexed
  bond is not selectable. 

  * ChangeLog, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Use left mouse button for rotation
  and right mouse button for translation.  

2007-05-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/engineconfigurationwidget.ui: &Settings tab conflicted with
  alt-key for &Settings menu 

2007-05-25  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/extension.h,
  avogadro/src/extensions/ghemicalextension.h, avogadro/src/mainwindow.cpp: *
  avogadro/src/extension.h, avogadro/src/mainwindow.cpp: Add
  Extension::menuPath() which defines menus and submenus for extensions.
  Default is to use "&Tools" -- existing Tools menu.  *
  avogadro/src/extensions/ghemicalextension.h: Use above for a "Molecular
  Mechanics" submenu for all actions.   

2007-05-25  Marcus D. Hanwell <marcus@cryos.org>

  * ChangeLog, libavogadro/src/tools/selectrotatetool.cpp: Extended code to
  support bond selection for selection boxes too.  

  * ChangeLog, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/global.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Added some initial bond selection
  support in bsdyengine, refactored the engine a little. Added some support to
  selectrotatetool to pick bonds and some extra checks in manipulatetool as it
  previously assumed all selected items were atoms. Also added
  SEL_BOND_EXTRA_RADIUS for rendering selected bonds.  

2007-05-25  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/application.cpp, avogadro/src/mainwindow.cpp: *
  avogadro/src/application.cpp: Fix bug 1717423 -- Mac interface fix for
  opening files from Finder.  

  * avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h: Remove undo/redo support for
  selection extensions. Selections are handled by views, which are volatile.
  There's no way to reliably undo a selection and people probably don't care.  

2007-05-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: * avogadro/src/mainwindow.*: Mac interface fixes.
  Duplicate menu and toolbar actions for  new, open, save, close, quit. Remove
  icons from menu items. Fix bug 1720872: don't close the last MainWindow, hide
  it and disable menu items. Restore upon open or new.   

2007-05-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/src/editcommands.cpp,
  avogadro/src/engineconfigurationwidget.ui, avogadro/src/engineitemmodel.cpp,
  avogadro/src/enginetabwidget.cpp, avogadro/src/enginetabwidget.h,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/smartsextension.cpp, avogadro/src/flattabwidget.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/settingsdialog.cpp,
  libavogadro/src/color.cpp, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitiveitemmodel.cpp,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: * libavogadro/src/glwidget.*: Did a
  bunch of API cleanup.  I know i know. How you guys loath my long function
  names.  Moved from ::selection to ::selectedPrimitives.  Now have
  ::setSelected and ::isSelect.  Thanks KDevelop for nice refactoring.  This
  naming method follows more of the Qt style "view" naming conventions (ie
  ::selectedItems).  * .: Fixed a few compiler warnings.   

2007-05-23  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/selectrotatetool.cpp: Small fix for extra brace in
  the selectrotate tool code. 

2007-05-23  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/extension.h,
  avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/smartsextension.cpp, avogadro/src/mainwindow.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitivelist.cpp,
  libavogadro/src/primitivelist.h, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp: Fix selection to use new
  PrimitiveList. The selectrotate tool still needs some updating to properly
  handle non-atom selections and hits. Eliminate duplicate
  GLWidget::selection() and selectedItems() calls.  

2007-05-23  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/wireengine.cpp: add frustum culling also to the
  wireengine.   

  * libavogadro/src/painter.cpp: adopt a more aggressive setting for frustum
  culling, reap increased benefit. This slightly breaks things when the
  glwidget's aspect ratio (width/height) is extremely high (above 2.0), but
  that shouldn't be a problem in practice.   

  * libavogadro/src/painter.cpp: generalize frustum culling to all painted
  objects. Now the speed boost can be as high as +300% (open a very large
  molecule and get a viewpoint from which only a small portion of the molecule
  is visible).    

  * libavogadro/src/painter.cpp: perform a basic form of frustum culling. When
  navigating through a large molecule, this increases the framerate by
  somewhere between +10% and +50%.   

  * libavogadro/src/color.cpp, libavogadro/src/glwidget.cpp: Fine-tune
  materials and light: The black background suggests that we're in deep space,
  so there's no wall around to reflect the light, so the "ambient" component of
  the light is lowered (0.4 -> 0.2). To sharpen this effect, the "ambient"
  component of materials is also lowered (1/2 -> 1/3). Another change is that
  the "diffuse" light is increased to 1.0 (from 0.8) so that the effective
  color is as saturated as the color given by openbabel for the atom. There was
  no good reason not to set it to 1.0 and it's also visually more beautiful.   

2007-05-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, avogadro/ChangeLog, avogadro/src/CMakeLists.txt,
  avogadro/src/avogadro.qrc, avogadro/src/engineconfigurationwidget.ui,
  avogadro/src/enginetabwidget.cpp, avogadro/src/enginetabwidget.h,
  avogadro/src/extensions/smartsextension.cpp, avogadro/src/icons/edit_add.png,
  avogadro/src/icons/edit_remove.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.ui, avogadro/src/primitivetreeview.cpp,
  avogadro/src/primitivetreeview.h,
  libavogadro/include/avogadro/primitiveitemmodel.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitiveitemmodel.cpp, libavogadro/src/primitiveitemmodel.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: *
  avogadro/src/enginetabwidget.*: Now uses a .ui file to design the widget. 
  this is much easier.  * avogadro/src/primitivetreeview.*: Added the
  PrimitiveTreeView class as a helper class for displaying PrimitiveItemModels.
   Just looks a bit prettier.  * libavogadro/src/primitivelist.*: Added the
  ::contains(Primitive *) operator for checking if a primitive is already in
  the list.  * .: Lots of other stuff for doing selective rendering.   

2007-05-22  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/engineitemmodel.cpp: Fix Mac problem discussed on IRC --
  qobject_cast strikes again. (Any advice on making a minimum test case for
  Trolltech would be very welcome. -Geoff)  

  * ChangeLog, avogadro/src/mainwindow.cpp: * avogadro/src/mainwindow.cpp: Fix
  bug 1722691. Show preferences in the correct spot on Mac.   

2007-05-22  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: improvement in drawtool: when creating an
  atom by dragging from an existing atom, the newly created atom is placed and
  moved within the plane passing through the existing atom, and parallel to the
  window. This feels more intuitive than the former behavior, where the new
  atom was placed and moved within the plane passing through the molecule
  center.  Also fix a comment in camera.cpp.   

2007-05-22  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/primitive.cpp: Trivial fixes to initialisation order in the
  constructors.  

  * libavogadro/src/tools/manipulatetool.h,
  libavogadro/src/tools/navigatetool.h: Small clean up in variable
  initialisation order.  

2007-05-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Some more code clean ups. Deleted
  old code and fixed some compiler warnings.  

  * libavogadro/src/engine.cpp, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/painter.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Various small clean ups for compiler
  warnings - unused variables etc.  

2007-05-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, libavogadro/include/avogadro/primitivelist.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/primitivelist.cpp, libavogadro/src/primitivelist.h:
  Refactored PrimitiveQueue -> PrimitiveList.  Within the class renamed
  ::primitiveQueue to ::subList which returns a subList based on type.  Fixed
  changes due to refactoring in various files.   

  * ChangeLog, avogadro/src/enginelistview.cpp, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.h: *
  libavogadro/src/primitive.h: Fixed compiler warnings. *
  libavogadro/src/glwidget.cpp: Fixed compiler warnings. *
  libavogadro/src/color.cpp: Added virtual deconstructor and reformatted. *
  libavogadro/src/engines/bsdyengine.cpp: Fixed compiler warnings. *
  avogadro/src/enginelistview.cpp: Cleaned commented code and fixed bug caused
  by previous approach.   

2007-05-21  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/labelsettingswidget.ui: Added confguration for label
  settings. Can now display atom number as before, element symbol or element
  name.  

2007-05-21  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Update the krazy issues 

2007-05-21  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h: Merge
  TextRenderer improvements made in the Kalzium branch: -- simplifications --
  3D-text is now centered around the specified position. This makes the atom
  labels look better, especially the longer ones (like full element names). 2D
  text (as in debugengine) is left unchanged.   

  * avogadro/src/engineitemmodel.cpp: Quick fix for a failed assert in QList,
  triggered by EngineItemModel::index, that has been preventing Carsten and
  myself from running avogadro since yesterday.  Donald: please read my FIXME
  comment. My solution probably isn't the best one.   

2007-05-20  Carsten Niehaus <carsten.niehaus@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/color.cpp,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/painter.cpp: Silence Krazy: We can #include <config.h>
  because of the way CMake works. 

  * CMakeLists.txt: Ok, using CMAKE_COMPILER_IS_GNUCXX is better here. Thanks
  Benoit 

  * CMakeLists.txt: add more drastic GCC-flags to get more warnings (agreed
  with Benoit). As you can see we need to fix a million issues in Avogadro!
  Especially the virtual destructor thing 

2007-05-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/elementcombobox.cpp,
  avogadro/src/elementcombobox.h, avogadro/src/engineitemmodel.cpp,
  avogadro/src/engineitemmodel.h, avogadro/src/enginelistview.cpp,
  avogadro/src/enginelistview.h, avogadro/src/enginetabwidget.cpp,
  avogadro/src/enginetabwidget.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.ui, libavogadro/src/engine.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/tools/manipulatetool.cpp: Added a item model for managing
  engines for a GLWidget.  This will make it easier whenw e need to add /
  remove / edit engines.  Updated the engine interface for name and
  description.  Added new configuration widget layout.  Now there is a dock
  widget for for configuring an engines, this includes engine settings plus
  *eventually* the primitives that are rendered by an engine.  Created the
  EngineTabWidget that will display the configuration for a GLWidget (one
  engine at a time).  It is possible that it should be called a
  GLWidgetStackedWidget but it does some weird stuff to save GUI memory.  The
  tab for settings is a stack, but when we add a tab for editing primitive,
  this will be a single widget for all engines.   

2007-05-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp: make the default viewpoint a bit farther from
  the moleculer (step backwards by CAMERA_NEAR_DISTANCE).   

2007-05-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/CMakeLists.txt: Fixed a small typo.   

2007-05-18  Tim Vandermeersch <tim.vandermeersch@gmail.com>

  * ChangeLog, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/forcefielddialog.cpp,
  avogadro/src/extensions/forcefielddialog.h,
  avogadro/src/extensions/forcefielddialog.ui,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h: Added Setup Force Field dialog,
  Calculate Energy and Rotor Search  

2007-05-18  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/settingsdialog.cpp, avogadro/src/settingsdialog.h,
  avogadro/src/settingsdialog.ui, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/navigatetool.cpp: Added a settings dialog.  Updated the
  painter class to use ::begin ::end all the time.  This is good but needs to
  be better.  It needs to check to make sure it's in the correct context, if a
  painter is used in more than one context it should probably at least give a
  warning.  Can lead to data corruption.  (check email to list)  Updated
  engines to use the new painter class.   

2007-05-18  Carsten Niehaus <carsten.niehaus@gmail.com>

  * krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavogadro-src-engines.html, krazy/libavogadro-src-tools.html,
  krazy/libavogadro-src.html, krazy/libavogadro.html: Updates of the html files

  * krazy/runkrazy.rb: Adding a nice little script which runs krazy.  

  * krazy/libavo-src.html, krazy/libavogadro-src-engines.html,
  krazy/libavogadro-src-tools.html, krazy/libavogadro-src.html: some new files 

  * avogadro/src/extensions/issues.html, avogadro/src/issues.html,
  krazy/avogadro-src-extensions.html, krazy/avogadro-src.html,
  krazy/libavo-src.html: They files should go in one directory 

  * avogadro/src/extensions/issues.html: First round of Krazy checks 

  * avogadro/src/issues.html: First round of Krazy checks 

  * libavogadro/src/moleculetreeview.cpp, testfiles/2-aminoethanol.cml,
  testfiles/2-thioethanol.cml, testfiles/2_2_2-trifluoroethanol.cml,
  testfiles/COPYING, testfiles/but-2-yne-1_4-diol.cml, testfiles/butane.cml,
  testfiles/ethane-1_2-diol.cml, testfiles/ethane.cml, testfiles/ethanol.cml,
  testfiles/methane.cml, testfiles/methanol.cml, testfiles/porphyrin.cml,
  testfiles/propan-1-ol.cml, testfiles/propan-2-ol.cml, testfiles/propane.cml,
  testfiles/thiophene.cml: Adding a couple of deme/test molecules  

2007-05-18  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: this slot is
  needed in Kalzium, and it's needed anyway.   

2007-05-18  Carsten Niehaus <carsten.niehaus@gmail.com>

  * libavogadro/src/tools/manipulatetool.h: Forgot two places 

  * libavogadro/src/engine.h, libavogadro/src/primitive.h,
  libavogadro/src/tool.h, libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.h: Ok, doing funny ";" fixes. GCC 4.3
  is issuing a million warning it seems and Stephan Binner is fixing them in
  Kalziums copy of avogadro. I am forward porting all fixes now so that they
  are not lost!  Example: -Q_DECLARE_INTERFACE(Avogadro::ToolFactory,
  "net.sourceforge.avogadro.toolfactory/1.0");
  +Q_DECLARE_INTERFACE(Avogadro::ToolFactory,
  "net.sourceforge.avogadro.toolfactory/1.0")   

  * libavogadro/src/camera.h, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitive.h, libavogadro/src/tool.cpp: Several EBN fixes: 
  explit ctors newer compare a QString to == "" but use ".isEmpty"  

  * libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/sphereengine.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h:
  Fixing a couple of EBN issues. Benoit ack'ed the explicit patch  

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tool.h, libavogadro/src/tools/manipulatetool.cpp: Fix several
  typos found by 
  
  ex.html   

2007-05-17  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/periodicTable.ui: Adding initial periodic table UI --
  for the draw tool.  

2007-05-17  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * AUTHORS, CMakeLists.txt, COPYING, ChangeLog, INSTALL, authors.xml,
  avogadro/src/extensions/CMakeLists.txt,
  cmake/modules/cmake_uninstall.cmake.in, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/tools/CMakeLists.txt:
  Merged all changes from tag loschmidt/0.1.0.  Final merge. (r407, r409, r410,
  r411, r412, r413) 

2007-05-17  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/bsdyengine.cpp: fix bug where the bonds drawn by
  bsdyengine were too short. After all, the optimization trying to avoid
  painting the hidden portion of bonds inside the atoms was useless and unsafe.
    

2007-05-16  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/textrenderer.cpp: Committing to trunk because i have 15 min
  battery left and I left my AC adapter at office yesterday :/ so I can't look
  in the SVN book right now for how to merge, branch, switch, and whatnot. 
  This makes the TextRenderer work even on "old" OpenGL implementations without
  GL_ARB_texture_rectangle extension.  The presence of this extension is
  checked for when text is first painted. If this extension is absent, we fall
  back to using square, power-of-two textures. Of course this is not optimal
  since some whitespace is added around each glyph, wasting a significant
  amount of texture memory, but what do you want...  anyway this is far better
  than falling back to QGLWidget::renderText(): i can't imagine how slow that
  would be on old hardware, and think of how long the lag would be at startup! 
   

2007-05-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp: Fix for issue 1719699.  

  * libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp: Fix for issue 1719080 

  * avogadro.nsi, avogadro/src/CMakeLists.txt, avogadro/src/application.cpp,
  avogadro/src/extension.h, avogadro/src/extensions/gamessextension.h,
  avogadro/src/icons/avogadro.ico, avogadro/src/mainwindow.cpp,
  avogadro/src/windows/avogadro.rc, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitive.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/manipulatetool.cpp, libavogadro/src/undosequence.h:
  Merging changes from 0.1.0 tag; r400, r401, r402, r403, r404 

2007-05-14  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/manipulatetool.cpp: fix again tooltip in
  manipulatetool -- i had misunderstood something   

  * libavogadro/src/glwidget.h, libavogadro/src/painter.h: Clarify/add
  documentation; remove my copyright from glwidget.h because really I only
  edited a few lines in it.   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/labelengine.cpp, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h, libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: add documentation and internal
  comments for Painter class rename Camera::backTransformed* to
  Camera::backtransformed*, add documentation, make a bit more use of them in
  labelengine. clarify tooltip of manipulatetool   

2007-05-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/aboutdialog.cpp: Fix PR#1718302 for link to Avo webpage.  

  * libavogadro/src/tools/selectrotatetool.cpp: Add tooltip to indicate click
  and drag  

2007-05-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Few UI bugs and
  removed debugging line that was unneeded.   

2007-05-13  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/manipulatetool.cpp: Fixed small bug with the zoom
  manipulation, not sure how that crept in there ;)  

  * libavogadro/src/tools/selectrotatetool.cpp: Fix for bug 1717975 - molecules
  and residues now behave more intuitively across views. Still may not be
  perfect but a definite improvement.  

2007-05-13  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: fix the preceding fix :)   

  * libavogadro/src/glwidget.cpp: Make a ugly hack so that the labelengine
  works with Sphereengine and Sticksengine correctly.   

  * libavogadro/src/textrenderer.cpp: Close bug 1717985; some simplification in
  TextRenderer.   

2007-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Added function to
  easily determine if a Primitive is selected in the GLWidget. Modified the
  toggleSelected function to behave as expected with multiple views. Found and
  fixed a subtle crash in the engines when radius was called before render and
  ported all engines to render correctly with multiple views.  

2007-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/extension.cpp,
  avogadro/src/extension.h, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h: Extension cleanup. Base Extension
  class is not QObject, but extensions are.  

2007-05-12  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/selectrotatetool.cpp: fix bug where the selection
  rectangle was not drawn because of back-face culling. I think I introduced
  this bug a while ago, in an "optimization".   

2007-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extension.h, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h,
  avogadro/src/extensions/smartsextension.cpp,
  avogadro/src/extensions/smartsextension.h, avogadro/src/mainwindow.cpp: Pass
  a GLWidget to extensions (so selection can be modified, auto-rotate, etc.)
  Add example SMARTS selection extension -- select atoms by SMARTS pattern.  

  * avogadro/src/aboutdialog.cpp: Update version to 0.1.0  

2007-05-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt, Doxyfile, Doxyfileext, avogadro/src/extension.h,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  libavogadro/src/CMakeLists.txt, libavogadro/src/camera.cpp,
  libavogadro/src/camera.h, libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/global.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/internal/cylinder.cpp,
  libavogadro/src/internal/cylinder.h, libavogadro/src/internal/sphere.cpp,
  libavogadro/src/internal/sphere.h, libavogadro/src/internal/textrenderer.cpp,
  libavogadro/src/internal/textrenderer.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/drawcommand.cpp, libavogadro/src/tools/drawcommand.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h, libavogadro/src/undosequence.cpp,
  libavogadro/src/undosequence.h: Updated documentation.  Removed dependancy on
  4.3 (make sure you do editing of .ui files with designer of qt4.2)  Added
  documentation.  Updated copyright information on all files.  There is now a
  Doxyfileext which generates external docs.   

2007-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/tools/manipulatetool.cpp: Fix inconsistencies between what is
  drawn and what the manipulate tool does when using multiple views. The other
  engines still need their behaviour to be fixed.  

2007-05-12  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Minor API improvements; make use
  of these at various places; close bug 1717437 in clickmeasuretool.   

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/internal/textrenderer.cpp: fix bug in dynamic-bs where the
  separation between the two colors of a bond was not made at the middle of the
  bond. Also don't draw the portion of the bond that's inside the sphere.   

2007-05-12  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/manipulatetool.cpp: Added the tilt ability to the
  middle mouse press - tilt selected atoms.  

  * libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Fix a bug with atoms selected using
  the selection box. Performed some clean up in the selectrotatetool code.  

2007-05-12  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/internal/textrenderer.cpp: safety/performance fixes in the
  textrenderer. in particular, avoid large arithmetic operations involving
  GLubytes: too risky wrt overflow!   

2007-05-12  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: Add support for
  setting the number of unit cells to display. Not exposed in the user
  interface, but it's now in the library. Just need to build the window for the
  extension (after this beta release).  

  * libavogadro/src/tools/manipulate.png, libavogadro/src/tools/manipulate.qrc,
  libavogadro/src/tools/manipulatetool.cpp: Add "hand" icon for manipulate
  tool.  

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Add "select all" and "select none" edit menu
  actions.  

2007-05-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Added some shortcut keys for the
  tools. These may not be optimal and probably need further discussion. Also
  added the drawing of the selection centroid sphere for the manipulate tool.  

2007-05-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Support for cut/copy
  of just selected atoms.  

2007-05-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/manipulatetool.cpp: Added selection manipulation for
  the zoom function too - move selections in to and out of the display.  

  * libavogadro/src/tools/selectrotatetool.cpp: Comment out the atom
  manipulation code - moved to manipulatetool. Should be removed once the code
  in manipulatetool is better tested.  

  * libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h: Adapted the methods implemented by
  Geoff in the selectrotatetool source. Now translation (LMB) and rotation
  (RMB) of selected atoms works. Currently uses the selection list maintained
  by GLWidget.  

2007-05-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/application.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Improve behavior when
  opening files while launching on Mac.  

2007-05-11  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/manipulate.qrc,
  libavogadro/src/tools/manipulatetool.cpp,
  libavogadro/src/tools/manipulatetool.h: Initial version of the manipulation
  tool. Currently only operates on single atoms. Currently the left mouse
  button translates the atom position in x and y. The middle mouse button moves
  the atom into and out of the screen (zoom). This tool needs its own icon.  

2007-05-11  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp: Fix quit action on Mac.  

  * avogadro/src/editcommands.cpp, avogadro/src/editcommands.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Add initial cut
  support, as well as undo/redo for clear.  

2007-05-11  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * Doxyfile, libavogadro/src/CMakeLists.txt,
  libavogadro/src/internal/sphere.h: Updated indenting in CMakeLists.txt,
  corrected some comments in sphere.h, updated Doxygen configuration.   

2007-05-10  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/global.h, libavogadro/src/glwidget.cpp: remove some useless
  OpenGL commands. Make sure GL_TEXTURE_RECTANGLE_ARB is defined.   

  * libavogadro/src/internal/textrenderer.cpp,
  libavogadro/src/internal/textrenderer.h: some cleanup in TextRenderer   

2007-05-10  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h:
  Remove old bsengine code  

2007-05-10  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h: add method needed by
  cryos (and needed anyway): Camera::backTransformedZAxis()   

2007-05-10  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Add some initial support for
  "selection modes" and tracking selected atoms (in the GLWidget). Probably
  needs some work.  

2007-05-10  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/internal/textrenderer.cpp: Fix small mistake in
  TextRenderer. As a result: better visual quality for the outlining effect !  

  * libavogadro/src/internal/textrenderer.cpp: Fix the bug where the text was
  misrendered as blank rectangles. You know what? after all it _was_ a bug in
  my own code! I was using GL_TEXTURE_2D with non-rectangular, non-power-of-2
  textures. Using GL_TEXTURE_RECTANGLE_ARB instead did the trick (btw: we need
  to add this define to global.h in case glext.h doesn't provide it).
  Apparently some drivers were more liberal than others in that respect, which
  is why the bug only showed with some drivers, giving the wrong impression
  that it was a driver issue. I closed the bug report -- with apologies -- at
  bugs.freedesktop.org.   

2007-05-09  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.h: remove outdated #include that were
  breaking compilation. Sorry rbraith :)   

  * avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  libavogadro/CMakeLists.txt, libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/sphere.h,
  libavogadro/include/avogadro/textrenderer.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/internal/cylinder.cpp, libavogadro/src/internal/cylinder.h,
  libavogadro/src/internal/sphere.cpp, libavogadro/src/internal/sphere.h,
  libavogadro/src/internal/textrenderer.cpp,
  libavogadro/src/internal/textrenderer.h, libavogadro/src/painter.cpp,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/textrenderer.cpp, libavogadro/src/textrenderer.h: Move the
  Sphere, Cylinder and TextRenderer to a internal/ subdirectory, don't expose
  them publicly. These classes are only used by the Painter class. Also replace
  tabs with 2 spaces in the CMakeLists.txt files, to be consistent with the
  indenting style of the source code.   

2007-05-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/extensions/CMakeLists.txt: Make sure to link against
  extension.cpp for support on Mac.  

2007-05-09  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/sphere.cpp, libavogadro/src/textrenderer.cpp,
  libavogadro/src/textrenderer.h: In TextRenderer: quality improvements, API
  changes, indentation fixing, and most importantly, documentation (both API
  and internal code comments). Also fix indentation in Sphere.   

2007-05-08  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/painter.cpp, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: In GLWidget, make the Camera live
  as a pointer and let GLWidget::camera() return this pointer instead of a
  reference. Adapt the rest of the code to that change.   

2007-05-08  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Added improved "manipulate" rotate
  thanks to Benoit. Shift + left mouse. Much cleaner rotation.  

2007-05-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp: Small bug fix for opening windows.  Have to
  check the UndoStack.  If it is in a clean state we know there are no
  modifications.   

  * avogadro/src/CMakeLists.txt, avogadro/src/application.cpp,
  avogadro/src/application.h, avogadro/src/extension.cpp,
  avogadro/src/extension.h, avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Update Extensions to separate instances per
  MainWindow.  Added true SDI functionality.  For more info see
  
  
  l  This should fix our Mac errors.   

2007-05-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/primitive.cpp: Copy/paste now
  prefers MDL molfile mimetype (ensures bond orders, etc. copied) Paste will
  now select atoms pasted for automatic manipulation.  

  * libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Initial "manipulate mode" for
  select tool. Hold down the shift key: left button rotates (needs work) right
  translates  

2007-05-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/enginelistview.cpp, avogadro/src/enginelistview.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdysettingswidget.ui,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitive.cpp, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h: Added the settings dialogs to Engines. 
  Modified the preexisting toolSettings interface to return a 0 if there is no
  settings available for the tool.  This is done to mimic the engines settings
  interface and it is done in the engines settings so that we know if we should
  create a new window or not.  It is better than testing against null QWidgets
  or whatever the alternative would be.  Also added GLWidget::setStable(bool)
  and GLWidget::isStable() to see if the GLWidget is in an unstable state. 
  This would occur as the result of some tool setting it.   

2007-05-07  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/global.h, libavogadro/src/tools/clickmeasuretool.cpp: Fix
  compile error (extra closing parenthesis -- sorry!) Tweak detail level of
  spheres.   

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h, libavogadro/src/global.h,
  libavogadro/src/painter.cpp, libavogadro/src/painter.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  rework class Cylinder; make Painter able to draw Cylinders; make use of that
  in all engines; also change Tools so they no longer have their own
  Cylinders/Spheres and use Painter instead.   

2007-05-07  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.ui: Minor fixes.
  Remove "select all" (not ready) and fudge "cut" with current copy() code.  

  * avogadro/src/CMakeLists.txt, avogadro/src/editcommands.cpp,
  avogadro/src/editcommands.h, avogadro/src/enginelistview.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui: Add initial support for copy commands (includes
  copy to text, image, chemical/x-xyz). Still needs work tomorrow.  

2007-05-06  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h, libavogadro/src/global.h,
  libavogadro/src/painter.cpp: make use of Painter to draw spheres in all
  engines. Introduce SEL_ATOM_EXTRA_RADIUS constant to control the radius of
  selection highlighting spheres (added to the atom's radius).   

  * libavogadro/src/engines/labelengine.cpp: Fix Z-fighting (nothing related to
  dragonball Z) issue. cryos: i hope this fixes the visual artifacts you were
  getting   

  * libavogadro/include/avogadro/painter.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/global.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/painter.cpp,
  libavogadro/src/painter.h: Introduce Painter class and global quality
  setting. Currently it can only paint spheres. Make bsdyengine use it.   

  * libavogadro/src/sphere.cpp, libavogadro/src/sphere.h: implement level 0 as
  a octahedron, d-pointerify, and many simplifications   

  * libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h: Fix typo in Ross's name. Sorry!   

2007-05-06  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h: Added operator+= and copy constructor to the
  Molecule class.  Added pasting operation.  Currently only works with
  cartesian coordinates.  It is setup to work with Mime data but i pick the
  default text case (assumed to be cartesian coordinates).   

2007-05-05  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp: Add hooks for options dialog for engines.  

2007-05-05  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp: Draw outlined text in labelengine, for
  readibility on all backgrounds. Had to change the depthFunc from GL_LESS to
  GL_LEQUAL. Hope that doesn't break anything. This is very slow so I propose
  that text should be hidden while moving the camera with the mouse, to get
  smoother movement. That suggests the following: in Engine, we could have
  renderOpaque, renderTransparent and renderText. What do you think? Tools
  would inform the GLWidget that they are moving the view using callbacks
  GLWidget::beginMoveCamera() and GLWidget::endMoveCamera().   

2007-05-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Fix compile problems with radius()
  function  

2007-05-04  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/stickengine.cpp: Added radius function to stick
  engine.   

2007-05-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp: Add support for classes of color maps
  (subclasses of Color). This includes setting a color map for any engine.
  (e.g., color by element, color by atom type, color by reside...)  

2007-05-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/labelengine.cpp, libavogadro/src/global.h: fix
  position of label in the labelengine (now the label is always placed on top
  of the atom, from the camera's point of view) however there remains an issue
  caused by the fact that we still don't make sure all opaque objects have been
  drawn *before* transparent objects are drawn.   

2007-05-04  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Removed d-pointer stuff as it is not
  required for tools - see mailing list.  

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h: Improved the label engine to use the
  radius method an so labels can be seen using the sphere engine now. Still
  needs work on label placement.  

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Updated visual effects in NaviateTool
  to cover all atom centred operations. After discussion with Benoit added
  d-pointer to NavigateTool too.  

2007-05-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: fix #including in tools and
  engines. In particular, don't include the meta-header <QtGui> when the much
  smaller <QtPlugin> is enough. Also fix comment in debugengine.   

  * libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h: fix copyright lines in debug engine   

2007-05-04  Carsten Niehaus <carsten.niehaus@gmail.com>

  * CMakeLists.txt, avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: -- I
  moved the FindFoo instructions in the toplevel CMakeLists.txt. I see no
  reason why we should check for it twice...  -- We now officially require Qt
  4.2.0 (set(QT_MIN_VERSION)). Benoit told me that 4.1 is totally broken wrt to
  something in QtGl and all developers are using 4.2 anyway. Before we we just
  looking for "Qt4" which would even have worked for 4.0-beta I think!  

  * INSTALL, avogadro/INSTALL: Update the installation instructions  

2007-05-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/mainwindow.cpp: restoreOverrideCursor immediately whenever a
  failure occurs.   

  * libavogadro/src/engines/debugengine.cpp: in debugengine: in FPS, show only
  3 significant digits show GLWidget height and width   

2007-05-04  Carsten Niehaus <carsten.niehaus@gmail.com>

  * INSTALL: This file really belong to the top level directory as you cannot
  build avo without compiling libavo  

2007-05-04  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: remove _setup : Sphere::setup is clever
  enough to notice that new_detail==old_detail and exit in that case.  remove
  some unnecessary state changes. Donald: it is possible to draw spheres with
  GL_NORMALIZE, only it's not optimally fast. But if we're only drawing one
  sphere, it's not worth the four state changes enabling GL_RESCALE_NORMAL
  instead.   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/stickengine.cpp, libavogadro/src/global.h: replace
  #defines with constants in global.h remove a qDebug and other negligible
  cleanup   

2007-05-04  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/sphereengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h,
  libavogadro/src/tools/navigatetool.cpp, libavogadro/src/tools/navigatetool.h:
  Updated Tool interface. Now there is a ::paint function which gets called
  after the engines render allowing Tools a better way to render to the
  GLWidget (as opposed to using a displayList).  I updated the NavigateTool and
  ClickMeasure tool (it now shows proper colors).  Also added the ::radius
  function to the dynamic ball and stick engine.  As a note if an atom is
  selected, radius(Primitive *) needs to reflect that.   

2007-05-03  Ross Braithwaite <dark.nz@gmail.com>

  * libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Made the changes that Benoit recommended, code in
  the glwidget was removed and new code was put into the debug engine.  When
  the debug engine is turned on now it repeatedly calles gl->update() thereby
  makeing the glwidget constantly re-render.  This gives FPS a reasonably
  accurate value.  

2007-05-03  Marcus D. Hanwell <marcus@cryos.org>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h: Added radius function to Engine,
  ported bsengine and sphereengine to use the new function. 

2007-05-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/icons/avogadro.svg: Adding the SVG for the icon.   

  * avogadro/src/avogadro.qrc, avogadro/src/icons/navigate.png,
  avogadro/src/icons/navigateN.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui, gpltemplate,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/navigate.png,
  libavogadro/src/tools/navigate.qrc, libavogadro/src/tools/navigatetool.cpp:
  Added template for licensing.  Added navigate icon taken from the crystal
  clear office set.  Added "Center View" action.  There are times things are
  not updateing the glwidget's geometry info.  we need to fix this so that
  things are required to call it.  there is a callback from primitiveAdded /
  primitiveUpdate / primitiveRemoved that should be sufficient to set a flag
  that the geometry data needs to be updated.  I'll look at this more tomorrow,
  tomorrow, i'll love ya, tomorrow, you're only a day away.   

2007-05-03  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/engines/stickengine.cpp: fix the sticks-engine (lighting
  bug and level of detail)   

2007-05-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/extensions/CMakeLists.txt, avogadro/src/extensions/gamess.cpp,
  avogadro/src/extensions/gamess.h,
  avogadro/src/extensions/gamessextension.cpp,
  avogadro/src/extensions/gamessextension.h,
  avogadro/src/extensions/ghemical.cpp, avogadro/src/extensions/ghemical.h,
  avogadro/src/extensions/ghemicalextension.cpp,
  avogadro/src/extensions/ghemicalextension.h,
  avogadro/src/extensions/hydrogens.cpp, avogadro/src/extensions/hydrogens.h,
  avogadro/src/extensions/hydrogensextension.cpp,
  avogadro/src/extensions/hydrogensextension.h: Refactored classes so that
  extensions are named *Extension (GamessExtension, etc etc)  Renamed source
  files accordingly.   

  * avogadro/src/application.cpp, avogadro/src/enginelistview.cpp,
  avogadro/src/extension.h, avogadro/src/extensions/gamess.cpp,
  avogadro/src/extensions/gamess.h, avogadro/src/extensions/ghemical.cpp,
  avogadro/src/extensions/ghemical.h, avogadro/src/extensions/hydrogens.cpp,
  avogadro/src/extensions/hydrogens.h, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  libavogadro/include/avogadro/undosequence.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitive.cpp,
  libavogadro/src/primitive.h, libavogadro/src/tool.cpp,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/drawcommand.cpp,
  libavogadro/src/tools/drawcommand.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h, libavogadro/src/undosequence.cpp,
  libavogadro/src/undosequence.h: ****Big Huge Changes****  Undo/Redo is
  implemented and all of the extensions and tools have been updated. The
  interface to tools and extensions now requires that you return a
  QUndoCommand* or 0 (NULL).  The only important things to remember when
  creating QUndoCommands is to make sure that the state after undo is exactly
  how it was before you performed your action.  Worst case you need to
  duplicate all the Molecule data.  This is somewhat intense but it runs quite
  quickly as there are no calls to NewAtom meaning no callbacks.  There is a
  new class UndoSequence which is essentially a list of QUndoCommands which are
  all compiled into one.  This is handy for our drawing tool.  I apologize as i
  haven't had time to document any of this code.   

2007-05-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tool.h: The last patch introduced a new tool interface to
  allow for undo/redo.  I am working on the QUndoCommand subclasses to help our
  tools do these things.   

  * avogadro/src/elementcombobox.h, avogadro/src/extension.h,
  avogadro/src/extensions/gamess.cpp,
  avogadro/src/extensions/gamessinputdata.h,
  avogadro/src/extensions/ghemical.cpp, avogadro/src/extensions/hydrogens.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/include/avogadro/primitive.h,
  libavogadro/include/avogadro/primitives.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitive.cpp, libavogadro/src/primitive.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: primtives.h was defining the
  Primitive class.  Minor refactoring that was buggin me.  *sigh*.   

  * libavogadro/src/glwidget.cpp: Fix error when minimizing and restoring.  

  * avogadro/src/mainwindow.cpp: Whoops.  Environment should *replace* the
  default.   

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/debugengine.cpp,
  libavogadro/src/engines/debugengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added new Debug Engine which lists the number of
  atoms and molcules along with the FPS.  Contributed by James, Ross and
  Shahzad.  I modified to only perform one division.  As a result there are
  some added hooks to GLWidget to keep track of time to render a scene. 
  Hopefully we can say this is trivial.   

2007-05-02  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/glwidget.cpp: Better unit cell crystal support.  

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/stickengine.cpp,
  libavogadro/src/engines/stickengine.h: Added stick engine  

  * libavogadro/src/glwidget.cpp: Added unit cell rendering if an OBUnitCell is
  present.  

2007-05-01  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/CMakeLists.txt, avogadro/config.h.in, avogadro/src/CMakeLists.txt,
  avogadro/src/config.h.in, avogadro/src/extensions/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/CMakeLists.txt, libavogadro/config.h.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/config.h.in,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/toolgroup.cpp, libavogadro/src/tools/CMakeLists.txt: tools,
  engines, extensions are now installed and loaded by default to their correct
  locations: ${CMAKE_INSTALL_PREFIX}/lib/avogadro/{tools|engines|extensions} 
  added the define INSTALL_PREFIX to the CMAKE_INSTALL_PREFIX path.  this does
  not get installed with the other header files.  modified the environment
  variables:  AVOGADRO_{ENGINES|TOOLS|EXTENSIONS}  AVOAGDOR_EXTENSIONS was
  previously AVOGADRO_PLUGINS   

2007-05-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/ResidueSphereEngine.cpp,
  libavogadro/src/engines/ResidueSphereEngine.h,
  libavogadro/src/engines/StickEngine.cpp,
  libavogadro/src/engines/StickEngine.h,
  libavogadro/src/engines/WireframeEngine.cpp,
  libavogadro/src/engines/WireframeEngine.h: Remove old engines to allow
  updated stick engine.  

2007-05-01  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp: fix bug found by carsten/valgrind:
  GLWidgetPrivate::selectBufSize wasn't getting initialized.   

2007-05-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/SphereEngine.cpp,
  libavogadro/src/engines/SphereEngine.h,
  libavogadro/src/engines/sphereengine.cpp,
  libavogadro/src/engines/sphereengine.h: Remove old SphereEngine code --
  conflicts on capitalization-sensitive file systems. Clean up class names,
  etc. in new sphere engine.  

2007-04-29  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/cylinder.cpp, libavogadro/src/sphere.cpp,
  libavogadro/src/sphere.h: Fix errors (not leaks) found by valgrind:
  "Conditional jump or move depends on uninitialised value(s)"   

2007-04-27  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/global.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/tools/navigatetool.cpp: add another missing {} after a
  one-line if in my code :)  simplification in navigatetool  more clever
  handling of the selection buffer. Instead of resizing at molecule loading (as
  done before), resize in GLWidget::hits(). To prevent too frequent resizing,
  add some margin to the buffer size. The advantages are: -- new approach never
  fails, the user may add as many atoms as he likes (like when doing "add
  hydrogens"). -- old approach required a large margin in order to let user add
  atoms; this is no longer needed. Old margin was 256*8=2048 ints. New margin
  is 128 ints only.    

2007-04-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/glwidget.cpp, libavogadro/src/tools/clickmeasuretool.cpp:
  Added check for correct hit type (AtomType)   

2007-04-26  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/selectrotatetool.cpp: minor optimization in painting
  selection boxes   

  * libavogadro/src/global.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: -- introduce defines in global.h
  for the size of the small selection boxes used in tools. The former size,
  5x5, was too small in wireframe mode (selection-wise, the atoms were single
  pixels regardless of the "point size"). We now use 9x9 boxes. -- cleanup in
  drawtool   

  * libavogadro/src/engines/wireengine.cpp: cleanup in wireengine. Also revert
  something stupid I did earlier today.   

  * libavogadro/src/cylinder.cpp, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/sphere.cpp: minor cleanup in
  bsdyengine; only toggle client state inside Sphere and Cylinder, since it's
  not needed elsewhere.   

  * libavogadro/src/sphere.cpp: port memleak fix by Laurent Montel 
  CCMAIL:montel@kde.org   

  * libavogadro/src/camera.cpp: fix bug in Camera::normalize. I think i
  introduced it in the last "simplification". Oops!   

  * libavogadro/src/camera.cpp, libavogadro/src/tools/navigatetool.cpp:
  simplification in Camera::normalize(), remove qDebug()   

  * avogadro/ChangeLog, avogadro/src/enginelistview.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/tools/navigatetool.cpp:
  complete the updateGL() -> update() move   

  * libavogadro/src/tools/navigatetool.cpp: fix bug where it was impossible to
  zoom out after one had zoomed in to the max   

  * avogadro/src/enginelistview.cpp: remove a qDebug().   

  * avogadro/src/enginelistview.cpp, libavogadro/src/engine.cpp: start with
  only dynbs engine enabled. That's pretty much a hack as I don't really
  understand how avogadro (the app) works. So I did it in enginelistview. Sorry
  if that's not the right place.  CCMAIL:Donald Ephraim Curtis
  <donald-curtis@uiowa.edu>   

  * libavogadro/src/engines/wireengine.cpp: in wireframe engine, disable
  lighting and paint atoms even when they are selected. (instead of painting
  only the translucent layer)   

  * libavogadro/src/global.h, libavogadro/src/glwidget.cpp: dynamically resize
  the selection buffer at molecule loading, to adapt to any number of atoms. At
  mol loading, a margin is added in case the user creates new atoms (current
  margin is for 256 new atoms).   

  * libavogadro/src/glwidget.cpp: don't crash when GL selection fails
  (typically when there are too many selected atoms) increase value of
  SELECTION_BUFFER_SIZE to 4096 so that it fails less often   

  * libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: updateGL() -> update()   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/global.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Hey, the Navigate Tool now feels
  very solid, even when cruising through very large proteins!! 
  -simplifications and improvements in Camera wrt clipping planes
  -reorganization in NavigateTool: -- move much code to helper functions -- fix
  at last the problem with zoom-in passing beyond the goal -- swap left and
  right buttons -- use a member glwidget pointer to reduce argument-passing.
  the pointer is obtained from the mouse callbacks. - move numeric constants to
  #defines in global.h   

2007-04-25  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: have the camera auto-normalize
  after each rotation. no need to explicitly normalize anymore.   

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: Now mouse wheel is also sensitive to
  the atom below mouse pointer.   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/selectrotatetool.cpp: Solve a numerical instability
  issue : after a large number of rotations, the camera matrix got more and
  more corrupt, eventually resulting in a blank GLwidget.  Solved by adding
  method Camera::normalizeRotation(), to be called after each frequent rotation
  (typically in user input handling). Already used in navigatetool and
  selectrotatetool.    

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/navigatetool.cpp: much improved right-button movement
  in navigatetool. Now the molecule precisely follows the mouse movement. This
  required further tweaking of the unProject API.   

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: change
  prototype of unProject(double, double) to unProject(const QPoint&).  This
  simplifies some code since this method is always being called on QPoint
  coordinates.   

  * libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/drawtool.cpp, libavogadro/src/tools/drawtool.h: Rework
  API and documentataion for project/unproject, const-correctify, make use of
  class Vector3d. Move to GLWidget the special unproject method from DrawTool
  taking only x and y coords and unprojecting to the plane of the mol center
  parallel to the screen. Will be useful in NavigateTool.    

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: fixes and simplifications in mid-button
  zoom. No longer center on atom; instead keep atom center at fixed position on
  screen. Centering is no longer needed since right-button allows to center
  manually. Keeping atom at fixed position is also more consistent with
  left-button rotation.   

2007-04-24  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h: simplifications   

2007-04-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/clickmeasure.cpp, libavogadro/src/tools/clickmeasure.h,
  libavogadro/src/tools/clickmeasuretool.cpp,
  libavogadro/src/tools/clickmeasuretool.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h, libavogadro/src/tools/drawtool.cpp,
  libavogadro/src/tools/drawtool.h, libavogadro/src/tools/navigate.cpp,
  libavogadro/src/tools/navigate.h, libavogadro/src/tools/navigatetool.cpp,
  libavogadro/src/tools/navigatetool.h, libavogadro/src/tools/selectrotate.cpp,
  libavogadro/src/tools/selectrotate.h,
  libavogadro/src/tools/selectrotatetool.cpp,
  libavogadro/src/tools/selectrotatetool.h: Renamed tool filenames to match
  their class names.   

  * libavogadro/src/engine.h, libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsdyengine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/toolgroup.h,
  libavogadro/src/tools/clickmeasure.cpp, libavogadro/src/tools/clickmeasure.h,
  libavogadro/src/tools/draw.cpp, libavogadro/src/tools/draw.h,
  libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigate.h,
  libavogadro/src/tools/selectrotate.cpp, libavogadro/src/tools/selectrotate.h:
  Updated Engine interface to recieve the GLWidget as a pointer.  This as
  opposed to using the ::parent() for two reasons: 1) we can duplicate
  GLWidgets (so that they share engines) 2) we may also want to allow programs
  using libavogadro to load their own engines and pass them to the GLWidget. 
  Updated Tools so that they are named correctly.  ie. DrawTool
  SelectRotateTool ...  This to match the *Engine form with engines. renaming
  coming soon.   

2007-04-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/enginelistview.cpp, avogadro/src/enginelistview.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: MainWindow now has functionality to create
  multiple views.  View->New View / View->Close View.  GLWidget optimized
  functionality so that unactive GLContexts to not get rendered.  This will
  need to be updated if/when we allow two views to be shown at once. 
  EngineListView now handles enabling and disabling engines for the current
  GLWidget. (opposed to MainWindow binding to the signals).  

2007-04-23  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigate.h:
  cleanup and bugfixing in the navigate tool. -- fix molecule-centered rotation
  when center is not at origin -- don't recompute GL hits at every mouse move  

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/labelengine.cpp: Fix camera bug cause by
  miscalculation of distance to molecule. Fix comment explaining how this is
  computed. Introduce Camera::distance(Vector&) method performing this
  computation in the correct way. Make use of this new method in bsdynengine
  and labelengine, and do cleanup there. Remove method
  Camera::translationVector().   

2007-04-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engine.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Added d-pointer to Cylinder class + formatting
  updated.  Primitive and Molecule now share d-pointer.   

  * avogadro/src/application.cpp, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: new / open now
  perform correctly; ie, check for modified status (handled by the QMainWindow)
  and ask to save if changes have been made.  also, 'new' simply clears our the
  editor rather than creating a new window.   

2007-04-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Updating to qt
  style d-ptrs.   

  * libavogadro/src/tool.cpp: Renamed the d pointer properties.   

  * libavogadro/src/tools/clickmeasure.cpp,
  libavogadro/src/tools/clickmeasure.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h: more updates based off the new tool interface. 

  * libavogadro/src/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/tool.cpp, libavogadro/src/tool.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/tools/clickmeasure.cpp,
  libavogadro/src/tools/clickmeasure.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h, libavogadro/src/tools/navigate.cpp,
  libavogadro/src/tools/navigate.h, libavogadro/src/tools/selectrotate.cpp,
  libavogadro/src/tools/selectrotate.h:
  libavogadro/src/tool.h,libavogadro/src/tool.cpp; updated interface. removed
  ::initialize() and ::cleanup() functions.  Unneeded.  If plugins need to use
  these functions they can attach functions to the signals of the
  ::activateAction().  libavogadro/src/toolgroup.cpp; we can now use
  Tool::parent() to get the plugin which it belongs to, rather than relying on
  the Tool::data() to do the same.  libavogadro/src/CMakeLists.txt; added the
  tool.cpp file so that the tool object gets compiled into libavogadro. 
  libavogadro/src/glwidget.cpp; tool interface was updated.  Updated interface
  to all tools.  

2007-04-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/select.png,
  libavogadro/src/tools/select.qrc, libavogadro/src/tools/selectrotate.cpp: Add
  pointer icon for selectrotate tool  

2007-04-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/tools/clickmeasure.cpp,
  libavogadro/src/tools/clickmeasure.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h: libavogadro/src/tools/draw.h,
  libavogadro/src/tools/draw.cpp; updated tooltip to include how the tool
  works.  added code to replace atoms and bonds if they are different. 
  clicking on a lone atom will change it to the new type.. drawing bonds over
  preexisting bonds updates them. 
  libavogadro/src/tools/clickmeasure.cpp,libavogadro/src/tools/clickmeasure.h;
  updated tooltip to include how the tool works.  renamed the tag so that as
  you select you get atom 1,2,3 rather than 0,1,2.  

  * libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/tools/clickmeasure.cpp:
  libavogadro/src/engines/labelengine.cpp; push all GL attribute bits and use
  white text.  libavogadro/src/tools/clickmeasure.cpp; push all GL attributes,
  give feedback on initial click (marked with *0) for now.  

  * libavogadro/src/tools/measure.png: Forgot to add my neat measure icon.   

  * libavogadro/src/tools/measure.qrc: tools/measure.qrc : forgot to add. 
  sorry about this.  resource for the measure icon.  

  * libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/tool.h,
  libavogadro/src/tools/CMakeLists.txt, libavogadro/src/tools/clickmeasure.cpp,
  libavogadro/src/tools/clickmeasure.h, libavogadro/src/tools/draw.cpp,
  libavogadro/src/tools/draw.h, libavogadro/src/tools/selectrotate.cpp:
  libavogadro/src/glwidget.h libavogadro/src/glwidget.cpp : added unProject and
  project functions, also fixed the ::hits function so it restore the previous
  projection and modelview matrices  libavogadro/src/engines/bsdyengine.cpp :
  fixed compiler warning  libavogadro/src/tools/selectrotate.cpp : free the
  display list  libavogadro/src/tools/clickmeasure.cpp
  libavogadro/src/tools/clickmeasure.h : new click to measure tool.  Displays
  results in the GL Widget.  libavogadro/src/tools/CMakeLists.txt : added
  clickmeasure build instructions  libavogadro/src/tools/draw.cpp
  libavogadro/src/tools/draw.h : make use of the new GLWidget::project and
  GLWidget::unProject functions  libavogadro/src/tool.h : renamed ::init to
  ::initialize.  can't be sure we actually need these functions.  we have the
  option to let the tool decide what initialization it needs to do by
  connection to the action signals.  

2007-04-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsdyengine.cpp,
  libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/glwidget.cpp: Switch
  to use dynamic_cast instead of qobject_cast  

  * libavogadro/src/color.cpp, libavogadro/src/cylinder.cpp,
  libavogadro/src/sphere.cpp: Namespace fixes.  

2007-04-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/include/avogadro/tool.h: Needed to use quotes instead of <>'s
  on the relative include.   

2007-04-14  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/include/avogadro/tool.h: Replaced with truly fake. Probably
  something happened in the riggermerow<sp?>...   

2007-04-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/include/avogadro/camera.h,
  libavogadro/include/avogadro/color.h,
  libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/engine.h, libavogadro/include/avogadro/global.h,
  libavogadro/include/avogadro/glwidget.h,
  libavogadro/include/avogadro/moleculetreeview.h,
  libavogadro/include/avogadro/primitives.h,
  libavogadro/include/avogadro/sphere.h, libavogadro/include/avogadro/tool.h,
  libavogadro/include/avogadro/toolgroup.h: Fix "fake" includes.  

  * libavogadro/include/avogadro/camera.h,
  libavogadro/include/avogadro/color.h,
  libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/engine.h, libavogadro/include/avogadro/global.h,
  libavogadro/include/avogadro/glwidget.h,
  libavogadro/include/avogadro/moleculetreeview.h,
  libavogadro/include/avogadro/primitives.h,
  libavogadro/include/avogadro/sphere.h, libavogadro/include/avogadro/tool.h,
  libavogadro/include/avogadro/toolgroup.h: Moving headers from src/ to
  include/avogadro -- two pass job.  

2007-04-14  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h:
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h:
  added dynamics for bonds.  libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h:  when detail < 0 we generate a single line rather
  than a cylinder.  Also added constructor with default parameter to 0.  

2007-04-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engine.cpp, libavogadro/src/engine.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsdyengine.cpp, libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/labelengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/primitives.cpp,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h,
  libavogadro/src/toolgroup.cpp, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/draw.cpp, libavogadro/src/tools/selectrotate.cpp:
  libavogadro/src/moleculetreeview.cpp: removed debug code 
  libavogadro/src/sphere.cpp: added constructor and cleaned up code 
  libavogadro/src/toolgroup.cpp: removed debug code 
  libavogadro/src/primitives.cpp: removed debug code  libavogadro/src/sphere.h:
  added constructor which takes as a parameter the detail 
  libavogadro/src/engine.h, libavogadro/src/engine.cpp : added interface
  function to inform the engine to update the primitive.  This is a cautionary
  function for optimization.  libavogadro/src/glwidget.cpp: cleaned up the
  code, added use of new engine function. 
  libavogadro/src/engines/labelengine.cpp: added clause to not label when far
  from camera libavogadro/src/engines/bsdyengine.h,
  libavogadro/src/engines/bsdyengine.cpp: proof of concept for optimization of
  the ball & stick engine.  Added this as to not disturb the old code until the
  new code can be cleaned up.  I will get around to this just haven't had the
  time to think about the best way to do it. 
  libavogadro/src/engines/bsengine.cpp: removed debug code. 
  libavogadro/src/engines/CMakeLists.txt: added bsdyengine 
  libavogadro/src/tools/CMakeLists.txt: commented test tool code. 
  libavogadro/src/tools/selectrotate.cpp: added atom::update call after
  selection  libavogadro/src/tools/draw.cpp: removed debug code  

2007-04-09  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h:
  Minor reorganization of BS engine to improve performance. (Need to add
  "options" ability to set level of detail, etc.)  

  * avogadro/src/CMakeLists.txt, avogadro/src/mac/MacOSXBundleInfo.plist.in,
  avogadro/src/mac/atom.icns, avogadro/src/mac/avogadro.icns: Renamed Mac icon
  to avogadro.icns  

2007-04-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/avogadro.qrc: Misspelling of 'avogadro.png'.  Thanks to Steven
  Di Rocco for bringing this to our attention.   

2007-04-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/aboutdialog.cpp, avogadro/src/avogadro.qrc,
  avogadro/src/avogadro.ui, avogadro/src/icons/atom2.png,
  avogadro/src/icons/avogadro.png, libavogadro/src/tools/CMakeLists.txt: Update
  logo name to avogadro.png.  Lets not get too lazy with naming it's important!
   atom2.png does not describe what the png is really of.   

2007-04-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Updated PrimitiveQueue to allocate statically
  instead of dynamically.  Changed PrimitiveQueue::primitiveList to return a
  const QList<Primitive *>  Updated the engines to use "foreach" loops.   

2007-04-02  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/wireengine.cpp, libavogadro/src/engines/wireengine.h:
  Add wireframe engine (partly to help debug label issues)   

2007-04-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/labelengine.cpp,
  libavogadro/src/engines/labelengine.h: Label rendering engine added.  Needs
  work.  Possibly using an overlay?   

  * libavogadro/src/engine.cpp: Forgotten File   

  * avogadro/src/CMakeLists.txt, avogadro/src/application.cpp,
  avogadro/src/application.h, avogadro/src/avogadroapp.cpp,
  avogadro/src/avogadroapp.h, avogadro/src/enginelistview.cpp,
  avogadro/src/enginelistview.h, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Refactored AvogadroApp -> Application to maintain
  naming scheme.  Added EngineListView to list the engines and allow them to be
  enabled/disabled accordingly.  Engines now maintain their own PrimitiveQueue.
   This will allow us (in the future) to allow advanced users to add/remove
  atoms/bond/residues accordingly from an engine.  (in the case that i only
  want a certain atom or set of atoms rendered.   

2007-03-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/avogadroapp.cpp,
  avogadro/src/avogadroapp.h, avogadro/src/main.cpp: Added open events for Mac
  (i.e., now can drag-and-drop files from the Finder)  

  * avogadro/src/CMakeLists.txt: Add Mac OS X app bundle target  

  * avogadro/src/aboutdialog.cpp: Scale icon to 256x256  

  * avogadro/src/mac/MacOSXBundleInfo.plist.in, avogadro/src/mac/atom.icns:
  Added Mac OS X resources directory  

  * libavogadro/src/tools/CMakeLists.txt: Make sure to install in "tools"
  subdirectory  

2007-03-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/tools/draw.cpp: Refactored SetVector3d and GetVector3d to
  setPos and pos after discussing with Benoit.  We agreed that this sticks with
  our Avogadro API convention.   

  * libavogadro/include/avogadro/toolmanager.h: Deleted trash file.   

  * avogadro/include/avogadro/extension.h, avogadro/include/avogadro/plugin.h,
  avogadro/src/CMakeLists.txt, avogadro/src/extension.h,
  avogadro/src/extensions/CMakeLists.txt, avogadro/src/extensions/gamess.cpp,
  avogadro/src/extensions/gamess.h,
  avogadro/src/extensions/gamessinputdata.cpp,
  avogadro/src/extensions/gamessinputdata.h,
  avogadro/src/extensions/gamessinputdialog.cpp,
  avogadro/src/extensions/gamessinputdialog.h,
  avogadro/src/extensions/gamessinputdialog.ui,
  avogadro/src/extensions/ghemical.cpp, avogadro/src/extensions/ghemical.h,
  avogadro/src/extensions/hydrogens.cpp, avogadro/src/extensions/hydrogens.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, avogadro/src/plugin.h,
  avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/draw.cpp,
  avogadro/src/plugins/draw.h, avogadro/src/plugins/draw.png,
  avogadro/src/plugins/draw.qrc, avogadro/src/plugins/gamess.cpp,
  avogadro/src/plugins/gamess.h, avogadro/src/plugins/gamessinputdata.cpp,
  avogadro/src/plugins/gamessinputdata.h,
  avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.h,
  avogadro/src/plugins/gamessinputdialog.ui, avogadro/src/plugins/ghemical.cpp,
  avogadro/src/plugins/ghemical.h, avogadro/src/plugins/hydrogens.cpp,
  avogadro/src/plugins/hydrogens.h, avogadro/src/plugins/navigate.cpp,
  avogadro/src/plugins/navigate.h, avogadro/src/plugins/selectrotate.cpp,
  avogadro/src/plugins/selectrotate.h,
  avogadro/src/plugins/ui_gamessinputdialog.h,
  libavogadro/include/avogadro/molgeominfo.h,
  libavogadro/include/avogadro/tool.h,
  libavogadro/include/avogadro/toolgroup.h,
  libavogadro/include/avogadro/toolmanager.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/tool.h, libavogadro/src/toolgroup.cpp,
  libavogadro/src/toolgroup.h, libavogadro/src/tools/CMakeLists.txt,
  libavogadro/src/tools/draw.cpp, libavogadro/src/tools/draw.h,
  libavogadro/src/tools/draw.png, libavogadro/src/tools/draw.qrc,
  libavogadro/src/tools/navigate.cpp, libavogadro/src/tools/navigate.h,
  libavogadro/src/tools/selectrotate.cpp, libavogadro/src/tools/selectrotate.h:
  Moved tools to libavogadro: - Added ToolGroup which manages a group of tools.
  - Moved avogadro "plugins" to "extensions".  (removed tools)   

2007-03-24  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/primitives.h: adapt to latest constness change in OpenBabel
    

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h: In Draw:
  standardize on passing GLWidget *widget to the various methods, from which
  both the molecule and the center can be retrieved. Maybe evaluate letting the
  Tool know which GLWidget it's operating in, gettable with glwidget()? That
  would spare much argument-passing.  Add API documentation and explanatory
  code comments to unProject().   

  * avogadro/src/plugins/draw.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: In class Atom:
  Rename position() to GetVector3d() and setPosition() to SetVector3d(). This
  underlines the fact that they're just wrappers for GetVector() and
  SetVector() from OBAtom, doing casts with Eigen::Vector3d.  Rewrite these
  functions to make sure they don't cause copies, and inline them. Add
  documentation. A "rationale for inlining" is provided in comment, to justify
  that inlining isn't dangerous here.   

2007-03-23  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/aboutdialog.cpp, avogadro/src/avogadro.qrc,
  avogadro/src/icons/atom2.png: Add contributed icon to about dialog  

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/ui_gamessinputdialog.h:
  Add full third-row elements (e.g., sulfur, phosphorus...)  

  * avogadro/src/plugins/CMakeLists.txt: Switch GAMESS automoc -- don't know
  why, but this one actually works.  

2007-03-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/navigate.cpp,
  avogadro/src/plugins/navigate.h: Commiting cryo's patch for the navigate
  plugin.  (ie. importing navigation functionality from Kalzium.   

2007-03-21  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/camera.cpp: add comments to the code of
  Camera::initializeViewPoint()   

  * libavogadro/src/camera.cpp: Simplification and improvement of
  Camera::applyPerspective() Now it should have reached it's "canonical" form. 
   

  * libavogadro/src/camera.cpp, libavogadro/src/camera.h,
  libavogadro/src/glwidget.cpp: Document class Camera   

  * libavogadro/src/camera.cpp: Rework Camera::applyPerspective(). That fixes
  the clipping bug for very small molecules.   

2007-03-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/gamessinputdialog.cpp: Fixes linking error.  Was not
  generating moc file because the cpp file was missing #include
  "gamessinputdialog.moc" at the bottom of the file.  This caused by change to
  MOC generation to more KDE-like operation.   

2007-03-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/plugin.h, avogadro/src/plugins/draw.cpp,
  avogadro/src/plugins/draw.h, avogadro/src/plugins/selectrotate.cpp,
  avogadro/src/plugins/selectrotate.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h: Added wheel function to plugins to allow handling
  of wheel events on the GLWidget.   

2007-03-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/plugins/draw.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/engine.h, libavogadro/src/glwidget.h: Fix compilation (after
  removal of molgeominfo.*).   

2007-03-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h,
  avogadro/src/plugins/selectrotate.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/molgeominfo.cpp,
  libavogadro/src/molgeominfo.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Removed the MolGeomInfo class.  It's really not
  needed as all this info can happily exist in the Molecule class and
  techincally should.  The GLWidget makes it's own copies of this info when it
  wants to by GLWidget::updateGeometry().  I believe this class was most likely
  introduced as a way to get the info to the Engines, but really they should
  know their parent.   

2007-03-19  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/engine.h, libavogadro/src/engines/StickEngine.cpp,
  libavogadro/src/engines/StickEngine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp: fix the
  auto-multiple-bonds-oritentation feature from kalzium That is, now when you
  load a molecule the double bonds are automatically oriented to face the
  camera in the default viewpoint. So that they don't look like single bonds. 
  This implied API changes in engines: now render must be passed the
  molGeomInfo structure, as it needs to know the normal vector of the
  molecule's fitting plane.   

  * avogadro/src/plugins/draw.cpp, libavogadro/src/camera.cpp: adjust initial
  viewpoint on loaded molecule. remove unused define.   

  * avogadro/src/plugins/draw.cpp, libavogadro/src/camera.cpp,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/molgeominfo.cpp: Fix bug where atoms created on an empty
  molecule were not shown. The problem was twofold: -molGeomInfo wasn't getting
  updated -with an empty molecule, applyPerspective set nearPlane==farPlane,
  thus nothing would be drawn until molGeomInfo would be updated.   

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h,
  avogadro/src/plugins/selectrotate.cpp,
  libavogadro/include/avogadro/molgeominfo.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/camera.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/molgeominfo.cpp,
  libavogadro/src/molgeominfo.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: - much improved Draw::moveAtom: now moves the
  atom within the iso-z-distance of the molecule's center - introduce
  MolGeomInfo class, stores the geometric info of a molecule - take geom info
  out of class Molecule - remove Molecule's d-pointer (nothing left there) -
  remove mutex stuff in Molecule - add d->molGeomInfo member to GLWidget, MUST
  BE UPDATED BY HAND - fix Atom::position() (interfacing coord vectors with
  Eigen)   

2007-03-18  Benoit Jacob <jacob.benoit.1@gmail.com>

  * avogadro/src/plugins/selectrotate.cpp, avogadro/src/plugins/selectrotate.h:
  Unscrew the selectrotate tool, after migration to the Camera class caused
  some damage. Donald: I hope I reproduced the original behavior, if not, just
  tell me.   

  * libavogadro/src/glwidget.cpp: rename GL_SEL_BUF_SIZE : the GL_ prefix
  should be reserved to the OpenGL API. Move that define to top of file.   

2007-03-16  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/primitives.cpp: use a mutex in the Molecule class to make
  sure that recomputing geom info blocks any operation that might access it
  concurrently.   

  * libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Make
  Primitive's d-pointer private Move Molecule's data to a d-pointer Cache the
  molecule geometric info. Still need to evaluate potential thread-safeness
  issues.   

  * libavogadro/src/primitives.cpp: remove unneeded variable numAtoms and
  remove "using namespace OpenBabel"   

2007-03-15  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/primitives.h: Cleaning commented code.   

  * libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Removed
  _vatom / _vbond from Molecule class (not needed) and fixed up the iterator
  stuff in primitives.cpp for Benoit.  (specifically the computGeometricInfo
  function).   

  * Doxyfile, avogadro/src/main.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/engine.h, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Document
  Changes. Merged in Benoit's changes.    

2007-03-15  Carsten Niehaus <carsten.niehaus@gmail.com>

  * cmake/modules/FindOpenBabel2.cmake: This syncs Avo with KDE again. Beside
  some cosmetic sugar this adds much improved support for Windows (I think...).
  Anyway, we now have for example this line in the file: 
  [HKEY_CURRENT_USER\\SOFTWARE\\OpenBabel\ 2.0.2]  I think that we all agree
  that both Kalzium and Avo want to depend on OB 2.1.0, right? The current beta
  still installs as 2.0.2 which cannot be the correct way to do, I think. Geoff
  told us yesterday that branching is about 2 weeks in the future, please lets
  increase that version number then so that those clashes can be fixed!  

  * cmake/modules/FindEigen.cmake: sync with KDE. FindEigen moved to kdelibs
  now! In the future (from next monday on) it will only be in kdelibs, no
  longer in kdeedu or koffice! 

2007-03-14  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/glwidget.cpp, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Implement computation and storage of geometric
  information in the Molecule class, replacing the former approach consisting
  in changing molecule coordinates.   

2007-03-13  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/aboutdialog.cpp,
  avogadro/src/flattabwidget.cpp, avogadro/src/mainwindow.cpp,
  avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/draw.cpp,
  avogadro/src/plugins/gamess.cpp, avogadro/src/plugins/ghemical.cpp,
  avogadro/src/plugins/hydrogens.cpp, avogadro/src/plugins/selectrotate.cpp,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/primitives.cpp:
  Converted cmake files to use qt4_automoc format.  More KDE like.   

  * avogadro/src/CMakeLists.txt, avogadro/src/aboutdialog.cpp: about dialog
  compilation fixed.  thanks carsten.   

2007-03-12  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/CMakeLists.txt, avogadro/src/aboutdialog.cpp,
  avogadro/src/aboutdialog.h, avogadro/src/mainwindow.cpp: New about dialog.
  Here it works but I think the moc-thing is wrong. Could somebody with more
  moc-foo check this, please?  

2007-03-12  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/cylinder.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/sphere.cpp: Add Molecule::centerAndFitInXYPlane() method.
  Just to demonstrate it, call it from GLWidget::setMolecule(). Some sparse
  cleanup in Cylinder and Sphere.   

2007-03-09  Carsten Niehaus <carsten.niehaus@gmail.com>

  * CMakeLists.txt: Make CMake 2.4.3 the minimumversion needed. KDE will move
  to require 2.4.5 on March, 19th. 

2007-03-09  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro.nsi: Release 0.0.3 updates.  Fixed avogadro.nsi to include
  ghemical.prm so that the optimization parameters are included in the install.
   Booyah. 

  * avogadro/CMakeLists.txt, libavogadro/CMakeLists.txt: Misspelled
  USING_DYNAMIC_LIBS.  What a mistake.  Fixed the CMakeLists.txt files. 

  * avogadro/CMakeLists.txt: Added USING_OBDLL and USING_DYNAMIC_LIBS to build
  defines. 

2007-03-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui,
  avogadro/src/plugins/gamessinputdialog.ui: Updated mainwindow.ui.  TODO:
  Refactor so that variables are named descriptionType instead of
  typeDescription.  All mainwindow actions need to be renamed.   

2007-03-08  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.h: Remove a lot unused includes.
  Includes shouldn't be in .h-files, use forward declaration here 

2007-03-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.ui: Minor misspellings and added units
  to the recalculate hessian spin box.   

  * avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.h,
  avogadro/src/plugins/gamessinputdialog.ui: Done with ui and working.   

2007-03-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/gamess.cpp,
  avogadro/src/plugins/gamess.h, avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputbuilder.ui,
  avogadro/src/plugins/gamessinputdialog.cpp,
  avogadro/src/plugins/gamessinputdialog.h,
  avogadro/src/plugins/gamessinputdialog.ui: Refactoring GamessInputBuilder ->
  GamessInputDialog.  More appropriately named.   

  * avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputbuilder.ui: My version of the dialog.  With
  tree and tabs etc etc.  Widgets named accordingly.  

  * libavogadro/src/cylinder.h, libavogadro/src/sphere.h: Needed Qt4OpenGL
  include so that GLuint named a type.   

  * avogadro/src/CMakeLists.txt, avogadro/src/plugins/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt: Updated include precedence.  Should fix some
  compile errors.  Just so that when you build you are getting the header files
  from your build directory and not the installed ones.   

2007-03-07  Carsten Niehaus <carsten.niehaus@gmail.com>

  * avogadro/src/plugins/gamessinputbuilder.ui: adding those strange string. No
  idea what they are for, though 

  * avogadro/src/plugins/gamessinputbuilder.ui: * Bling, about 3000 lines diff.
  Oh my god :)  

  * avogadro/src/plugins/gamessinputbuilder.ui: Muhu, a big step, another 500
  lines of diff :-) I added default values, added some new widgets, improved
  layout...  

  * avogadro/src/plugins/gamessinputbuilder.ui: One more tab done  

  * avogadro/src/plugins/gamessinputbuilder.ui: 2 more tabs done 

  * avogadro/src/plugins/gamessinputbuilder.ui: muha, integrating Donalds
  stuff, some this and that 

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Commit my patch: No
  inludes in the .h-file if possible 

  * avogadro/src/plugins/gamessinputbuilder.ui: More close to the original 

  * avogadro/src/plugins/gamessinputbuilder.ui: First version of the dialog,
  now in Designer  

2007-03-07  Benoit Jacob <jacob.benoit.1@gmail.com>

  * libavogadro/src/cylinder.h, libavogadro/src/sphere.h: don't include
  QGLWidget when not needed; documentation fixes   

  * libavogadro/src/cylinder.cpp, libavogadro/src/sphere.cpp: Remove all
  mentions of the USE_DISPLAY_LISTS define, always use display lists (instead
  of never) for the sphere and cylinder.  This fixes an issue with the way avo
  reused the sphere/cylinder code from Kalzium: avo used a display list for the
  whole molecule, but not for the spheres and cylinders, which caused the
  geometric data and the opengl traffic of each sphere/cylinder to be
  replicated into the molecule display list. This caused the rendering to be
  unnecessarily slow and memory-consuming.   

2007-03-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/CMakeLists.txt: Added GAMESS plugin install line.   

  * avogadro.nsi: Update for building 0.0.3alpha Win32 release. 

  * avogadro/src/flattabwidget.cpp, avogadro/src/plugins/CMakeLists.txt:
  flattabwidget.cpp: return proper integer CMakeLists.txt: remove garbage left
  over from initial testing of gamess plugin. 

2007-03-06  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro.nsi: installer file changes 

  * avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/gamess.cpp,
  avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h: GAMESS Input Deck Plugin Complete.
   Non-Modal Dialog.  

  * avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputdata.cpp,
  avogadro/src/plugins/gamessinputdata.h: Gamess Interface Updates.  Still not
  incorporated into the plugin.  This will happen tomorrow.   

2007-03-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputdata.cpp: More changes to the GAMESS Input
  Deck Generator.  Almost finished.  Need to add some more specific
  information.  At some point a lot of the callbacks need to be refactored to
  another class.  For now they are alright.  This is very big and complex.  Not
  fun.   

  * avogadro/src/plugins/gamess.cpp, avogadro/src/plugins/gamess.h,
  avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputdata.cpp,
  avogadro/src/plugins/gamessinputdata.h: Working good so far.  Not yet a
  plugin.   

2007-03-01  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/gamess.cpp, avogadro/src/plugins/gamess.h,
  avogadro/src/plugins/gamessinputbuilder.cpp,
  avogadro/src/plugins/gamessinputbuilder.h,
  avogadro/src/plugins/gamessinputdata.cpp,
  avogadro/src/plugins/gamessinputdata.h: Backing up before deleteing a bunch
  of unnecisary functions. Code taken from WxMacMolPlt GNU Licensed.   

2007-02-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/CMakeLists.txt: More ugly.  My Bad.   

  * cmake/modules/FindAvogadro.cmake, cmake/modules/FindEigen.cmake: cmake
  files needed updating for finding paths correctly.   

2007-02-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.h, avogadro/src/plugins/ghemical.cpp: Tim
  Vandermeersch's Patch for ghemical.  Cleaned up mainwindow.h so it'd compile.
   

  * avogadro/src/CMakeLists.txt, avogadro/src/flattabwidget.cpp,
  avogadro/src/flattabwidget.h, avogadro/src/flowlayout.h,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h: Added new
  FlatTabWidget for Messages.  Needs working on but will be really sweet.   

2007-02-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, avogadro/src/plugin.h,
  avogadro/src/plugins/ghemical.cpp, avogadro/src/plugins/ghemical.h,
  avogadro/src/plugins/hydrogens.cpp, avogadro/src/plugins/hydrogens.h:
  Messages are now printed to the messages window.  It's very hard to see but
  it's at the bottom of the GL area.  You can see a small dotten line, which
  you can drag up and see the messages.  I'm working on a better interface for
  this, unfortanly it's not built into the default QT widgets.  More to come.  

2007-02-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h: Some repeated
  code.  Factored out into the newBond function.   

2007-02-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/plugins/hydrogens.cpp: Fix problem with zero'ed coordinates.
  Begin/EndModify strike again!  

  * avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt: Update build
  environment  

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/hydrogens.cpp: Update
  to fix draw and hydrogen problems from Begin/EndModify in OBMol.  

  * avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/ghemical.cpp,
  avogadro/src/plugins/ghemical.h: Add support for Ghemical minimization using
  Open Babel OBForceField  

2007-02-19  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt, avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui, avogadro/src/plugin.h,
  avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/hydrogens.cpp,
  avogadro/src/plugins/hydrogens.h, libavogadro/CMakeLists.txt,
  libavogadro/src/engines/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Fixed bug in
  glwidget.h with GLHit constructure being ill-defined. Updated cmake files to
  incorporated dependancy (multi-threaded make now works). Added plugin to
  Add/Removed Hydrogens.  Having problems which i believe are in OpenBabel.   

2007-02-09  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro.nsi, avogadro/avogadro.nsi: moved nsis file 

2007-02-08  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp: Removed STL dependancy. (Should reduce windows
  QT dlls).    

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/selectrotate.cpp,
  libavogadro/src/engines/bsengine.cpp: corrected names. 

  * avogadro/avogadro.nsi: added mxvc2005 file. 

2007-02-04  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h: Add bond order
  to draw tool.   

2007-02-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/main.cpp: had extra include in there. 

  * avogadro/avogadro.nsi, avogadro/src/CMakeLists.txt,
  avogadro/src/icons/avogadro.ico, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/plugins/draw.cpp,
  avogadro/src/plugins/draw.h, avogadro/src/plugins/selectrotate.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/primitives.h: Updated WIN32
  compiling parameters, added icons/avogadro.ico and nsis installer file. 

  * libavogadro/CMakeLists.txt, libavogadro/src/global.h,
  libavogadro/src/glwidget.cpp: more WIN32 changes.  Added some GL defines that
  were missing.  added return value on GLHit = operator. 

  * libavogadro/src/global.h: Updates for windows. 

  * libavogadro/include/avogadro/global.h: Added global header.   

  * avogadro/config.h.in, libavogadro/config.h.in: Cleaned up config.h 
  config.h should contain the install paths and version and package name. 
  Needs updating.   

  * avogadro/CMakeLists.txt, avogadro/config.h.in, libavogadro/CMakeLists.txt:
  Rather than using an include file for WIN32 we should just define it as a
  compile time definition.   

  * libavogadro/CMakeLists.txt, libavogadro/config-libavogadro.h.in,
  libavogadro/config.h.in, libavogadro/global.h.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.cpp,
  libavogadro/src/color.h, libavogadro/src/cylinder.cpp,
  libavogadro/src/cylinder.h, libavogadro/src/engine.h,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h: Done with changes. 
  Defines are properly setup.   

  * libavogadro/global.h.in: about to be renamed again.   

2007-02-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/CMakeLists.txt, libavogadro/config-libavogadro.h.in,
  libavogadro/config.h.in, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.h, libavogadro/src/cylinder.h,
  libavogadro/src/engine.h, libavogadro/src/engines/bsengine.h,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.h, libavogadro/src/sphere.h: Broken for two min.  

  * libavogadro/src/moleculetreeview.h, libavogadro/src/sphere.cpp:
  MoleculeTreeView no longer has ambiguous constructor. Sphere no longer has
  ambiguous call to sqrt. 

  * libavogadro/src/engines/bsengine.h: Added #include "config.h"   

  * libavogadro/CMakeLists.txt, libavogadro/config.h.in,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.h,
  libavogadro/src/cylinder.h, libavogadro/src/engine.h,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h, libavogadro/src/sphere.h: Update for WIN32
  defines for compilation on windows.  Exporting of DLL classes.  

2007-02-02  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/glwidget.cpp: Updated plugin
  paths: split by colon...  PATH=/usr/bin:/bin:/usr/sbin (etc)  

2007-01-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * avogadro/src/plugins/CMakeLists.txt, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/moleculetreeview.cpp: Updated link commands to work on Mac OS
  X.  

2007-01-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp: Updated changes from library.   

  * libavogadro/src/engines/bsengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Changed names /
  added QT_PROPERTIES.  Bulked up the lib.   

  * avogadro/include/avogadro/tool.h, avogadro/src/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/plugin.h, avogadro/src/plugins/CMakeLists.txt,
  avogadro/src/plugins/draw.cpp, avogadro/src/plugins/draw.h,
  avogadro/src/plugins/draw.png, avogadro/src/plugins/draw.qrc,
  avogadro/src/plugins/selectrotate.cpp, avogadro/src/plugins/selectrotate.h,
  avogadro/src/tool.h, avogadro/src/tools/CMakeLists.txt,
  avogadro/src/tools/draw.cpp, avogadro/src/tools/draw.h,
  avogadro/src/tools/draw.png, avogadro/src/tools/draw.qrc,
  avogadro/src/tools/selectrotate.cpp, avogadro/src/tools/selectrotate.h,
  libavogadro/src/glwidget.cpp: Merged Tools + Extensions = Plugins.   

2007-01-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/plugin.h: Fixed plugin.h to
  compile.   

2007-01-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/include/avogadro/plugin.h, avogadro/include/avogadro/tool.h,
  avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui, avogadro/src/plugin.h,
  avogadro/src/plugins/CMakeLists.txt, avogadro/src/plugins/ghemical.cpp,
  avogadro/src/plugins/ghemical.h, avogadro/src/tool.cpp,
  avogadro/src/tools/CMakeLists.txt, avogadro/src/tools/draw.h,
  avogadro/src/tools/selectrotate.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp: Added
  plugin interface (incomplete).  Added tabs at bottom for messages and other
  information we wish to have.   

  * avogadro/src/elementcombobox.cpp, avogadro/src/elementcombobox.h,
  libavogadro/src/elementcombobox.cpp, libavogadro/src/elementcombobox.h: Moved
  combobox to avogadro app.    

  * libavogadro/src/elementcombobox.cpp, libavogadro/src/elementcombobox.h:
  Modifications... will be moved.   

  * libavogadro/src/CMakeLists.txt: Extra Line   

  * libavogadro/src/CMakeLists.txt: Working CMakeLists   

  * libavogadro/src/elementbox.cpp, libavogadro/src/elementbox.h,
  libavogadro/src/elementcombobox.cpp, libavogadro/src/elementcombobox.h:
  Rename   

  * avogadro/src/CMakeLists.txt, avogadro/src/flowlayout.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/mainwindow.ui, avogadro/src/tool.h, avogadro/src/tools/draw.cpp,
  avogadro/src/tools/draw.h, avogadro/src/ui_mainwindow.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/elementbox.cpp,
  libavogadro/src/elementbox.h: Using generated ui.  Added tool properties. 
  adding ElementComboBox   

2007-01-23  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/bsengine.cpp: NORMALIZE bonds instead of
  RESCALE_NORMAL   

  * cmake/modules/FindEigen.cmake: Updated FindEigen.cmake from pinotree.   

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/tools/CMakeLists.txt, avogadro/src/tools/draw.cpp,
  avogadro/src/tools/selectrotate.cpp, libavogadro/CMakeLists.txt,
  libavogadro/include/avogadro/color.h,
  libavogadro/include/avogadro/cylinder.h,
  libavogadro/include/avogadro/engine.h,
  libavogadro/include/avogadro/glwidget.h,
  libavogadro/include/avogadro/moleculetreeview.h,
  libavogadro/include/avogadro/primitives.h,
  libavogadro/include/avogadro/sphere.h, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.cpp, libavogadro/src/cylinder.cpp,
  libavogadro/src/engine.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/sphere.cpp: Updated cmake
  files and added psuedo include dir.   

  * avogadro/src/flowlayout.cpp, avogadro/src/flowlayout.h: Missing files!   

  * avogadro/src/tool.h, avogadro/src/tools/draw.cpp: updated tooltip / text
  minor change.   

  * avogadro/src/CMakeLists.txt, avogadro/src/tool.h,
  avogadro/src/tools/draw.cpp, avogadro/src/tools/draw.h,
  avogadro/src/tools/selectrotate.cpp, avogadro/src/tools/selectrotate.h:
  Updated name() and description() to const functions.  Made it so that if a
  tool doesn't defined an Icon / Text / Tooltip it will be correctly populated
  using name() and description().   

  * avogadro/src/CMakeLists.txt, avogadro/src/avogadro.qrc,
  avogadro/src/icons/colorize.png, avogadro/src/icons/exit.png,
  avogadro/src/icons/fileclose.png, avogadro/src/icons/fileexport.png,
  avogadro/src/icons/filenew.png, avogadro/src/icons/fileopen.png,
  avogadro/src/icons/filesave.png, avogadro/src/icons/filesaveas.png,
  avogadro/src/icons/help.png, avogadro/src/icons/redo.png,
  avogadro/src/icons/revert.png, avogadro/src/icons/tool.png,
  avogadro/src/icons/undo.png, avogadro/src/icons/window_fullscreen.png,
  avogadro/src/icons/window_nofullscreen.png, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/mainwindow.ui, avogadro/src/tool.h,
  avogadro/src/tools/CMakeLists.txt, avogadro/src/tools/draw.cpp,
  avogadro/src/tools/draw.h, avogadro/src/tools/draw.png,
  avogadro/src/tools/draw.qrc, avogadro/src/tools/selectrotate.cpp,
  avogadro/src/tools/selectrotate.h, avogadro/src/ui_mainwindow.h,
  libavogadro/src/engine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: ui_mainwindow.h defines Ui::MainWindow which is
  a private member of Avogadro::MainWindow.  QTDesigner does a crappy job with
  naming the layouts and embedding widgets within widgets that don't need to be
  that way.  There is a bit of renaming done so that we can use our FlowLayout
  (ripped from the tutorials).  Added icons to actions.  Images are from
  CrystalClear collection.  Made libavogadro const-correct as well as
  implementing the d-pointer technique in glWidget and Primitives classes. 
  Figured out a memory leak in OpenBabel.  Updated the TreeView to match
  pointers rather than indexes.  This could become a bottleneck if we have to
  delete a lot of primitives from a big molecule. We'll tackle that when we
  cross that bridge.  Would give us something like O(n^2) when we should really
  have O(n).  Although that could be wrong i was never good with big O.  Added
  resource files.  Plugins now define an action which selects them.  They can
  connect to the callback but it doesn't them little good.  The MainWindow
  decides what tool gets called.  This just gives the plugin the ability to
  define it's own tooltips / icon.  tool.h defines a default action but this
  action doesn't get any information from the implemented plugin.   

2007-01-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engine.h, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/bsengine.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitives.h: Added const
  correctness.   

2007-01-07  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/tools/draw.cpp, avogadro/src/tools/draw.h,
  avogadro/src/tools/selectrotate.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.h, libavogadro/src/primitives.cpp: Draw
  tools done.  Fixed some bugs.   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/tools/draw.cpp, avogadro/src/tools/draw.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/moleculetreeview.cpp, libavogadro/src/moleculetreeview.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Can now draw
  atoms into the model.  No bonds yet but it also updates the treewidget
  through callbacks.  However, primitiveAdded(Primitive *) should actually be
  admitted *after* the primitive has been added to the model. Otherwise we
  would need to overload everytime that the indexes change.  Need to discuss
  further with Geoff and crew.   

  * avogadro/src/avogadro.pro, avogadro/src/src.pro,
  avogadro/src/tools/SelectRotate.pro, avogadro/src/tools/tools.pro: Cleanup. 
  Old Project files we don't need.   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  libavogadro/src/CMakeLists.txt, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/moleculetreeview.cpp,
  libavogadro/src/moleculetreeview.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Rather than using a view on top of a model i
  created a custom view widget for our Primitive::Molecule.  I haven't updated
  all the signals but this is now what we will use.  It looks better and is
  easier to manage.  Plus I got it looking sweeet.   

2007-01-06  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/mainwindow.cpp, libavogadro/src/CMakeLists.txt,
  libavogadro/src/primitives.cpp: New Molecule is Working... signal to GLWidget
  needs to be updated.   

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/projectmodel.cpp,
  avogadro/src/projectmodel.h: Updated to use new Molecule which has
  QAbstractItemModel.   

  * libavogadro/src/moleculemodel.cpp, libavogadro/src/moleculemodel.h:
  Cleanup!   

  * libavogadro/src/moleculemodel.cpp, libavogadro/src/moleculemodel.h,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h,
  libavogadro/src/projectmodel.cpp, libavogadro/src/projectmodel.h: Moved
  MoleculeModel *into* Molecule.  Thus, a Molecule acts as a
  QAbstractItemModel.   

  * libavogadro/src/CMakeLists.txt, libavogadro/src/projectmodel.cpp,
  libavogadro/src/projectmodel.h: Moved ProjectModel to library.   

  * avogadro/src/mainwindow.cpp, avogadro/src/projectmodel.cpp,
  avogadro/src/projectmodel.h, avogadro/src/tools/selectrotate.cpp,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitives.h: Updated the primitives enum.  Also reworked
  ProjectModel so that it works directly with the molecule.  Should be moved to
  the library.  The view needs to be updated so that it subgroups.  This should
  not be part of the model.  (ie. the model should not contain "dummy" nodes
  just so that we have groupings of Atoms, Bonds, Residues.). 
  Avogadro::GLWidget needs to be updated to use the MoleculeModel instead of
  working on the Molecule itself.   

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/projectmodel.cpp,
  avogadro/src/projectmodel.h, avogadro/src/projecttree.cpp,
  avogadro/src/projecttree.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Added Docks for
  Tools and for the Project Layout.  The project layout is model/view. 
  ProjectModel, given a molecule, sets up the model for the molecular view. 
  I'm not sure if this is the correct place for this.  I believe it could go
  into the libavogadro.  It's a tossup because we may want to have our Model be
  the basis for interaction with the library but the way the GL engine is
  setup, it takes primitives directly to render them. This isn't a problem as
  we can setup our primitives to act as nodes of the model.  Will think about
  this more.   

  * avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/projecttree.cpp, avogadro/src/projecttree.h: Adding project
  model.   

2007-01-05  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * libavogadro/src/engines/bsengine.cpp, libavogadro/src/glwidget.cpp: Minor
  Changes   

  * avogadro/src/tools/draw.cpp, avogadro/src/tools/selectrotate.cpp,
  avogadro/src/tools/selectrotate.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/primitives.cpp, libavogadro/src/primitives.h: Draw tool now
  draws.  Need to refine these tools.  Also need configuration system
  implemented for the tools.  TODO: create a Tool Properties Dialog.   

  * CMakeLists.txt, avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h,
  avogadro/src/tools/CMakeLists.txt, avogadro/src/tools/draw.cpp,
  avogadro/src/tools/draw.h, avogadro/src/tools/selectrotate.cpp,
  avogadro/src/tools/selectrotate.h, libavogadro/CMakeLists.txt,
  libavogadro/src/CMakeLists.txt, libavogadro/src/engines/bsengine.cpp,
  libavogadro/src/engines/vertexarray.cpp,
  libavogadro/src/engines/vertexarray.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h: Added the drawing tool but it doesn't work. 
  There is no code.  Had an issue where the header files were included from the
  wrong location.  Should be easy to implement the drawing tool in the next
  day.  Also need to build an extension for other plugins (gamess /
  libghemical).  Should be interesting then.   

  * avogadro/src/tools/CMakeLists.txt: Added tools/CMakeLists.txt   

2007-01-04  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * avogadro/src/CMakeLists.txt, avogadro/src/mainwindow.cpp,
  avogadro/src/mainwindow.h, avogadro/src/tool.h,
  avogadro/src/tools/selectrotate.cpp, avogadro/src/tools/selectrotate.h,
  libavogadro/src/engine.h, libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/glwidget.cpp, libavogadro/src/glwidget.h,
  libavogadro/src/primitives.h: Should compile and run.  bsengine is Ball and
  Stick and currently works.  Need to bring the other stuff up to date.  the
  select&rotate tool now works too.  haven't finished cleaning up the functions
  and working on creating the drawing tool.   

  * avogadro/CMakeLists.txt, avogadro/src/CMakeLists.txt,
  avogadro/src/tools/SelectRotate.cpp, avogadro/src/tools/SelectRotate.h,
  avogadro/src/tools/selectrotate.cpp, avogadro/src/tools/selectrotate.h,
  libavogadro/CMakeLists.txt, libavogadro/FindOpenBabel.cmake,
  libavogadro/src/CMakeLists.txt, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/sphere.cpp: Should compile now.
   Must checkout the whole trunk to build the cmake files.   

2007-01-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * CMakeLists.txt: Minor changes..  Still won't build..  Need to finish up the
  work tonite.   

  * CMakeLists.txt, avogadro/FindAvogadro.cmake,
  cmake/modules/FindAvogadro.cmake, cmake/modules/FindEigen.cmake,
  cmake/modules/FindOpenBabel2.cmake, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.cpp, libavogadro/src/color.h,
  libavogadro/src/cylinder.cpp, libavogadro/src/cylinder.h,
  libavogadro/src/sphere.cpp, libavogadro/src/sphere.h: Added cmake/modules for
  CMAKE building.   

  * COPYING, ChangeLog, Doxyfile, INSTALL, README, avogadro.pro,
  avogadro/CMakeLists.txt, avogadro/COPYING, avogadro/ChangeLog,
  avogadro/Doxyfile, avogadro/FindAvogadro.cmake, avogadro/FindOpenBabel.cmake,
  avogadro/INSTALL, avogadro/README, avogadro/avogadro.pro,
  avogadro/src/avogadro.pro, avogadro/src/avogadro.ui, avogadro/src/main.cpp,
  avogadro/src/mainwindow.cpp, avogadro/src/mainwindow.h, avogadro/src/src.pro,
  avogadro/src/tool.cpp, avogadro/src/tool.h,
  avogadro/src/tools/SelectRotate.cpp, avogadro/src/tools/SelectRotate.h,
  avogadro/src/tools/SelectRotate.pro, avogadro/src/tools/tools.pro,
  avogadro/untitled01.gpr, libavogadro/CMakeLists.txt,
  libavogadro/FindOpenBabel.cmake, libavogadro/src/CMakeLists.txt,
  libavogadro/src/color.cpp, libavogadro/src/color.h, libavogadro/src/engine.h,
  libavogadro/src/engines/CMakeLists.txt,
  libavogadro/src/engines/ResidueSphereEngine.cpp,
  libavogadro/src/engines/ResidueSphereEngine.h,
  libavogadro/src/engines/SphereEngine.cpp,
  libavogadro/src/engines/SphereEngine.h,
  libavogadro/src/engines/StickEngine.cpp,
  libavogadro/src/engines/StickEngine.h,
  libavogadro/src/engines/WireframeEngine.cpp,
  libavogadro/src/engines/WireframeEngine.h,
  libavogadro/src/engines/bsengine.cpp, libavogadro/src/engines/bsengine.h,
  libavogadro/src/engines/vertexarray.cpp,
  libavogadro/src/engines/vertexarray.h, libavogadro/src/glwidget.cpp,
  libavogadro/src/glwidget.h, libavogadro/src/primitives.cpp,
  libavogadro/src/primitives.h, src/Engine.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/Primitives.cpp, src/Primitives.h,
  src/Renderer.h, src/Tool.cpp, src/Tool.h, src/Views.cpp, src/Views.h,
  src/avogadro.pro, src/avogadro.ui, src/color.cpp, src/color.h,
  src/engines/BSEngine.cpp, src/engines/BSEngine.h, src/engines/BSEngine.pro,
  src/engines/ResidueSphereEngine.cpp, src/engines/ResidueSphereEngine.h,
  src/engines/ResidueSphereEngine.pro, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.h, src/engines/SphereEngine.pro,
  src/engines/StickEngine.cpp, src/engines/StickEngine.h,
  src/engines/StickEngine.pro, src/engines/WireframeEngine.cpp,
  src/engines/WireframeEngine.h, src/engines/WireframeEngine.pro,
  src/engines/engines.pro, src/engines/vertexarray.cpp,
  src/engines/vertexarray.h, src/main.cpp, src/src.pro,
  src/tools/SelectRotate.cpp, src/tools/SelectRotate.h,
  src/tools/SelectRotate.pro, src/tools/tools.pro: Moving things around. 
  Conforming to a more KDE-like layout in SVN.  I'm going nuts.  SOrry  

2007-01-02  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/GLWidget.cpp, src/GLWidget.h, src/Tool.cpp, src/Tool.h,
  src/avogadro.pro, src/src.pro, src/tools/SelectRotate.cpp,
  src/tools/SelectRotate.h, src/tools/SelectRotate.pro, src/tools/tools.pro:
  Added Tool interface and SelectRotate tool.   

  * src/engines/BSEngine.cpp, src/engines/StickEngine.cpp,
  src/engines/WireframeEngine.cpp: Changed GetBgn to GetBeginAtom   

2006-09-26  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/MainWindow.cpp, src/MainWindow.h, src/main.cpp: Change QMessageWindowEx
  to QMessageWindow (for rc1 snapshot)  

2006-09-26  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/Engine.h, src/GLWidget.cpp, src/GLWidget.h, src/Primitives.h,
  src/engines/BSEngine.cpp, src/engines/BSEngine.h,
  src/engines/StickEngine.cpp, src/engines/StickEngine.h: Added PrimitiveQueue
  class to Engine.h which is now instanciated for each Engine.   

2006-09-03  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, src/Engine.h, src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/Primitives.cpp, src/Primitives.h,
  src/Views.cpp, src/Views.h, src/engines/BSEngine.h,
  src/engines/ResidueSphereEngine.h, src/engines/SphereEngine.h,
  src/engines/StickEngine.h, src/engines/WireframeEngine.h: Refactored GLEngine
  to Engine.   

2006-09-01  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/GLWidget.cpp, src/GLWidget.h, src/SphereRender.cpp,
  src/SphereRender.h, src/StickRender.cpp, src/StickRender.h, src/avogadro.pro,
  src/color.cpp, src/color.h, src/engines/BSEngine.cpp,
  src/engines/BSEngine.pro, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.pro, src/engines/StickEngine.cpp,
  src/engines/StickEngine.pro, src/engines/WireframeEngine.cpp,
  src/engines/WireframeEngine.pro, src/engines/vertexarray.cpp,
  src/engines/vertexarray.h: * src/color.h, src/color.cpp: Migrate Color class
  out of vertexarray files, to allow further colormaps (e.g., color by other
  atomic or residue properties).  * src/*: Use Color() class.  

2006-08-31  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, src/GLWidget.cpp, src/GLWidget.h: Added group selection.  see
  GLWidget::selectRegion()   

  * ChangeLog, src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h,
  src/Primitives.cpp, src/Primitives.h, src/Views.cpp, src/Views.h,
  src/engines/BSEngine.cpp, src/engines/BSEngine.h,
  src/engines/ResidueSphereEngine.cpp, src/engines/SphereEngine.cpp,
  src/engines/StickEngine.cpp, src/engines/WireframeEngine.cpp: *
  src/Primitives.h: moved the glnametypeing enum to here as enum primativeType 
  * src/Primitives.cpp: Overwrote OBMol::CreateResidue (trunk version of OB)  *
  src/GLWidget.cpp: _hits now containts both .type and .name corresponding to
  the type if hit and the name of the hit.   

2006-08-30  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/Primitives.h, src/Views.cpp,
  src/Views.h, src/engines/BSEngine.cpp, src/engines/BSEngine.h,
  src/engines/ResidueSphereEngine.cpp, src/engines/ResidueSphereEngine.h,
  src/engines/ResidueSphereEngine.pro, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.h, src/engines/StickEngine.cpp,
  src/engines/StickEngine.h, src/engines/WireframeEngine.cpp,
  src/engines/WireframeEngine.h, src/engines/engines.pro: * src/MainWindow.h,
  src/MainWindow.cpp, src/GLWidget.h, src/GLWidget.cpp: Move molecule storage
  (for now) to the GL widget to allow atom selection.  * src/Primitives.h: Add
  marker to indicate that a particular object was selected by the user.  *
  src/Views.h, src/Views.cpp: Add support for ResidueView, as well as
  whole-molecule rendering.  * src/engines/ResidueSphereEngine.*: New render
  engine drawing spheres for residues in PDB files. Illustrates whole molecule
  render option.  * src/GLEngine.h: Add glSelection enum for glPushName()
  entries to deliniate between molecule, atom, bond, residue, etc. picking.
  Render engines are responsible for using these as appropriate for a
  particular user view.  * src/engines/*: Update for glPushName() for atoms and
  hilights when an atom is selected.   

2006-08-29  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog, src/GLWidget.cpp, src/GLWidget.h: * src/GLWidget.cpp: Initial
  group selection code.  Needs work still.  When you double-click to open a
  file it registers the mouse as having moved.  This generates a selection box.
    

  * ChangeLog, src/GLWidget.cpp: Updated the perspective code and added
  "picking".  Will work on drag to select also.   

2006-08-28  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h, src/Primitives.h,
  src/avogadro.pro, src/engines/BSEngine.cpp, src/engines/BSEngine.h,
  src/engines/BSEngine.pro, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.h, src/engines/StickEngine.cpp,
  src/engines/StickEngine.h, src/engines/StickEngine.pro,
  src/engines/WireframeEngine.cpp, src/engines/WireframeEngine.h,
  src/engines/WireframeEngine.pro, src/engines/vertexarray.h, src/main.cpp:
  Updates to use vertex array classes for rendering. Much, much faster.  

  * ChangeLog, src/MainWindow.cpp, src/MainWindow.h: * src/MainWindow.h,
  src/MainWindow.cpp: Add full screen rendering and background color. (Needed
  for upcoming ACS presentations.)   

  * src/engines/SphereEngine.cpp, src/engines/SphereEngine.h: Minor update to
  actually show atoms. Not sure why previous version shows nothing.  

  * ChangeLog, src/GLWidget.cpp, src/engines/SphereEngine.cpp,
  src/engines/SphereEngine.h, src/engines/SphereEngine.pro,
  src/engines/WireframeEngine.cpp, src/engines/WireframeEngine.h,
  src/engines/WireframeEngine.pro, src/engines/engines.pro,
  src/engines/vertexarray.cpp, src/engines/vertexarray.h: * src/GLWidget.cpp:
  Make sure to enable vertex arrays (for Benoit's sphere/cylinder classes.  *
  src/engines/vertextarray.cpp, src/engines/vertexarray.h: Moved Benoit's
  vertex array sphere and cylinder from Kalzium.  *
  src/engines/WireframeEngine.*: New class for a wireframe view. (Should be
  made a static plugin and the default view, but don't have time right now.)  *
  src/engines/SphereEngine.*: New class for van der Waals spheres using
  Benoit's classes. Very fast.   

2006-08-25  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/GLEngine.h, src/engines/BSEngine.h, src/engines/StickEngine.h: More
  documentation updates.   

  * Doxyfile, src/GLEngine.h, src/engines/BSEngine.h,
  src/engines/StickEngine.h: Added Doxyfile for documentation generation
  through doxygen and added comments to the Engine files.   

2006-08-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/MainWindow.cpp: * src/MainWindow.cpp: Make sure to update
  recent file list when creating a new window, and make sure to call updateGL
  after reading a file. Fixes minor bugs.  

2006-08-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * ChangeLog: Updated ChangLog   

  * src/GLWidget.cpp: Removed	unnecissary debug code.   

  * src/GLWidget.cpp, src/GLWidget.h, src/engines/BSEngine.h,
  src/engines/StickEngine.h: Updated Description (should not include "Engine"
  Added slots for setting the GLWidget renderer.   

  * src/MainWindow.cpp, src/MainWindow.h: Added engine selection ComboBox.   

2006-08-24  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h, src/Primatives.cpp,
  src/Primatives.h, src/Primitives.cpp, src/Primitives.h, src/Renderer.h,
  src/Views.cpp, src/Views.h, src/avogadro.pro, src/engines/BSEngine.cpp,
  src/engines/BSEngine.h, src/engines/BSEngine.pro,
  src/engines/StickEngine.cpp, src/engines/StickEngine.h,
  src/engines/StickEngine.pro: Rename Prim-a-tive to Primitive (correct
  spelling). Add a fallback for finding plugins to environment variable:
  AVOGADRO_PLUGINS  This enables plugin support on Mac OS X.  

2006-08-24  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/GLEngine.h, src/Views.cpp, src/engines/BSEngine.cpp,
  src/engines/BSEngine.h, src/engines/StickEngine.cpp,
  src/engines/StickEngine.h: Updated GLEngine interface to only implement
  .render(<subclass of Primative> *).   

  * src/GLEngine.h, src/GLWidget.cpp, src/GLWidget.h, src/MainWindow.cpp,
  src/MainWindow.h, src/Primatives.cpp, src/Primatives.h, src/Views.cpp,
  src/Views.h, src/avogadro.pro, src/engines/BSEngine.cpp,
  src/engines/BSEngine.h, src/engines/SBSEngine.cpp, src/engines/SBSEngine.h,
  src/engines/SBSEngine.pro, src/engines/StickEngine.cpp,
  src/engines/StickEngine.h, src/engines/StickEngine.pro,
  src/engines/engines.pro: Refactored Renderer -> GLEngine  StickEngine &
  BSEngine both run. (although they need some fixes).  Major Modifications. 
  See mailing list.   

  * src/engines/BSEngine.cpp, src/engines/BSEngine.h, src/engines/BSEngine.pro,
  src/engines/BSRenderer.cpp, src/engines/BSRenderer.h,
  src/engines/BSRenderer.pro, src/engines/SBSEngine.cpp,
  src/engines/SBSEngine.h, src/engines/SBSEngine.pro,
  src/engines/SBSRenderer.cpp, src/engines/SBSRenderer.h,
  src/engines/SBSRenderer.pro, src/engines/engines.pro: Refactoring: Renderer
  -> Engine   

2006-08-22  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/Makefile.am: Removing makefiles.am to fix Carsten's broken heart  

2006-08-21  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/MainWindow.cpp: Fix call to debug from QDir -- wouldn't compile.  

2006-08-21  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * Makefile.am: More cleanup.   

  * autogen.sh, configure.ac: Cleaning up old GNU stuff from the main
  directory.   

  * : We may need this back.  Not sure how it got here.   

  * avogadro.pro: Does a recursive build.   

  * src/MainWindow.cpp, src/MainWindow.h: MainWindow now dynamically loads
  rendering engines.  There is currently no way to select the default and there
  is not NULL check as of yet.  Thats is to come.   

  * src/GLWidget.cpp: GLWidget now calls on the Molecule to render itself.   

  * src/Renderer.h: This is the renderer plugin interface definition.  It is
  used as a template for what functions must be implemented by the engines.   

  * src/avogadro.pro, src/src.pro: src is now a qmake that does recursive
  building.  avogadro.pro builds the binary.   

  * src/Primatives.cpp, src/Primatives.h: These are molecule primatives; ie.
  wrappers around the OBAtom / OBBond / OBMol classes.  They are used to set
  graphical attributes of the primatives and allows us to call render on the
  individuals.   

  * src/BSRender.cpp, src/BSRender.h: These have been moved to the pluggable
  engines directory.   

  * src/engines/BSRenderer.cpp, src/engines/BSRenderer.h,
  src/engines/BSRenderer.pro, src/engines/SBSRenderer.cpp,
  src/engines/SBSRenderer.h, src/engines/SBSRenderer.pro,
  src/engines/engines.pro: Rendering Engines have been added.   

2006-08-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/main.cpp: The 'foreach' command does not ignore the first element in
  the list.  Therefore it was trying to load "./avogadro" everytime it loaded. 
  Reverted back to old way; this isn't wrong it's just not as "pretty" but it's
  a specific issue.   

2006-08-20  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/MainWindow.cpp, src/MainWindow.h: * src/MainWindow.h,
  src/MainWindow.cpp: Fix saveFile -- make sure to call SetOutFormat() not
  SetInFormat()! Works great now. Added code to save settings for window
  position and size.  

  * src/GLWidget.cpp: * src/GLWidget.cpp: Handle mouse events based on
  QMouseEvent, rather than internal members. Fixes occasional "sticking."  

  * src/main.cpp: * src/main.cpp: Update with fix from Carsten Niehaus to use
  cleaner "foreach" mechanism.  

2006-08-20  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/MainWindow.cpp: Rolling back changes.  Previous problems were caused by
  using development versions of OB modules.  

  * src/GLWidget.cpp, src/MainWindow.cpp, src/main.cpp: * MainWindow (see line
  82 TODO) - Temporarily fixed the open bug. * GLWidget - Modified the rotate
  so that the molecule rotates more normal. Also did some reformatting.   

2006-08-19  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/main.cpp: Add template for loading files from the command-line. (But
  when implemented, doesn't work for no-argument.)   

  * ChangeLog, src/MainWindow.cpp, src/MainWindow.h: * src/MainWindow.cpp:
  Check to see if a file is already in a window -- raise it if needed, rather
  than opening another copy. Implement exportGraphics with
  QGLWidget::grabFrameBuffer. Doesn't allow oversampling, but works.  

  * src/GLWidget.cpp, src/GLWidget.h: * src/GLWidget.cpp: Improved scale/zoom
  feature and added calls for adding screen coordinates (e.g., for seelction
  rectangle).   

2006-08-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/BSRender.cpp, src/BSRender.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/SphereRender.cpp,
  src/SphereRender.h, src/StickRender.cpp, src/StickRender.h, src/main.cpp:
  Merge of current development code. Sometimes buggy, as explained in message. 

2006-08-18  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/ABSRender.cpp, src/ABSRender.h, src/AGLWidget.cpp, src/AGLWidget.h,
  src/AMainWindow.cpp, src/AMainWindow.h, src/ASphereRender.cpp,
  src/ASphereRender.h, src/AStickRender.cpp, src/AStickRender.h,
  src/BSRender.cpp, src/BSRender.h, src/GLWidget.cpp, src/GLWidget.h,
  src/MainWindow.cpp, src/MainWindow.h, src/SphereRender.cpp,
  src/SphereRender.h, src/StickRender.cpp, src/StickRender.h, src/avogadro.pro:
  Renamed files.  We user the 'Avogadro' namespace.  Naming the files with A*
  is redundant.   

2006-08-15  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/ABSRender.cpp, src/ABSRender.h, src/AGLWidget.cpp, src/AGLWidget.h,
  src/AMainWindow.cpp, src/AMainWindow.h, src/AStickRender.cpp,
  src/AStickRender.h, src/avogadro.pro, src/avogadro.ui, src/main.cpp: Added
  additional rendering options. Moving towards a more full-featured GUI.  

2006-08-14  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/AGLWidget.cpp, src/AGLWidget.h, src/AMainWindow.cpp,
  src/ASphereRender.cpp: Added initial support for rotation.  

  * ChangeLog, src/AGLWidget.cpp, src/AMainWindow.cpp, src/AMainWindow.h,
  src/ASphereRender.cpp, src/ASphereRender.h, src/avogadro.pro: Sample renderer
  (still OpenGL glitches). When a molecule is opened, a set of VdW spheres is
  rendered with the appropriate colors.  

2006-08-13  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * src/AGLWidget.cpp, src/ASphereRender.cpp, src/ASphereRender.h: More
  experiments.  

  * src/AGLWidget.cpp, src/AMainWindow.cpp, src/AMainWindow.h,
  src/avogadro.pro: More experiments.  

  * ChangeLog, src/AGLWidget.cpp, src/AGLWidget.h: * src/AGLWidget.h,
  src/AGLWidget.cpp: Add support for rendering GL display lists -- renderer
  classes should generate a display list and pass it off to the widget.  

  * src/AMainWindow.cpp, src/AMainWindow.h, src/main.cpp: Switch back to custom
  main window -- easier to add slots for commands. (Not sure why menu doesn't
  show up on Mac OS X.)  

2006-08-08  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * ChangeLog, src/AMainWindow.cpp, src/avogadro.pro, src/avogadro.ui,
  src/main.cpp: * src/avogadro.ui: Use QDesigner to layout some menu items and
  toolbar.  * src/main.cpp, src/AMainWindow.cpp, src/avogadro.pro: Use it.  

2006-05-12  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * src/AGLWidget.cpp, src/AGLWidget.h, src/AMainWindow.cpp, src/AMainWindow.h,
  src/avogadro.pro, src/main.cpp: Demo includes a toolbar and GL widget.   

2006-04-28  Donald Ephraim Curtis <dcurtis3@sourceforge.net>

  * COPYING, INSTALL, src/main.cpp: Tutorial time.   

  * src/AWindow.cpp, src/AWindow.h: Fixed   

  * src/AWindow.cpp, src/AWindow.h, src/main.cpp: Bad Changes.   

  * Makefile.am, autogen.sh, configure.ac, src/Makefile.am: GNU Basics 

2006-04-18  Geoffrey Hutchison <geoff@geoffhutchison.net>

  * README: Initial directory layout import 
