Avogadro 0.9.5

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Avogadro 0.9.5 was released on 2 June 2009. This is the sixth of our final beta series before Avogadro 1.0.0 is released. Please help us by providing feedback. New beta releases are expected roughly once per month until the 1.0.0 release. You can download this release here.

What's New

The following list includes some of the changes since Avogadro 0.9.4. This is mainly a bug fix release with a few new features implemented over the last month of development.

General

  • More build system improvements - external plugins can easily be built against libavogadro on Linux and Mac.
  • Includes a standard Mac "app bundle" -- completely relocatable disk image
  • Added a check for updated versions of Avogadro on the network (e.g., when 0.9.6 or 1.0 is released)
  • Includes improved translations and localization, including localized numbers everywhere and a full translation in Indonesian
  • More bugs found and fixed.

Interface

  • Updated interface allows more screen space for drawing / viewing
    • Tools moved to a new toolbar
    • Tool and Display Settings appear on demand
    • Updated keyboard shortcuts for switching tools
  • Keyboard shortcuts for switching elements in the Draw tool: type the element symbol (e.g., Fe for iron) screencast
  • Visual cues can now be disabled for the navigation tool
  • Moved "insert fragment" to Build menu

Rendering

  • Significantly improved protein "Cartoon" display type
  • Added a custom color option
  • Display of forces from geometry optimization is fixed (was broken in previous 0.9 releases)

Extensions

  • Added "Insert Peptide" builder for oligopeptides.
  • Added visualization of NMR spectra.
  • Atom, bond, angle, and torsion property tables now allow editing. This means you can now set a bond length, angle or dihedral exactly.
  • Allow sorting of property tables for each column.
  • Improved vibration plugin, fixing many bugs, and smoothing the animation.
  • Added syntax highlighting for GAMESS-US.
  • Now can run local Gaussian 03 jobs.

Dependencies

  1. Eigen 2.0.2 http://eigen.tuxfamily.org/ -- for compiling only.
  2. OpenBabel 2.2.1 or later http://openbabel.org
  3. CMake 2.6.0 or later http://www.cmake.org
  4. Qt 4.4.0 or later http://www.trolltech.com
  5. Boost 1.35 or later http://www.boost.org/ -- for Python support (optional).
  6. GLEW 1.5.0 or later http://glew.sourceforge.net/ -- for GLSL support (optional)

Building

untar the source

tar xvjf avogadro-0.9.5.tar.bz2

make the build directory

cd avogadro-0.9.5
mkdir build

configure

cd build
cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_GLSL=ON -DENABLE_PYTHON=ON ..
CMake takes a few optional parameters:
  • -DCMAKE_INSTALL_PREFIX= : specify the installation prefix (default /usr/local)
  • -DOPENBABEL2_LIBRARIES= : specify the OpenBabel2 libraries
  • -DOPENBABEL2_INCLUDE_DIR : specify the OpenBabel2 include directory
  • -DEIGEN_INCLUDE_DIR : specify the Eigen include directory
  • -DCMAKE_BUILD_TYPE : specify the build type (Debug, Release etc)
  • -DENABLE_GLSL : set to ON to enable, or OFF to disable GLSL support.
  • -DENABLE_PYTHON : set to ON to enable, or OFF to disable Python support.
  • -DENABLE_RPATH: set to ON to install binaries with relative RPaths (no need to set LD_LIBRARY_PATH).
  • -DENABLE_UPDATE_CHECKER: set to ON to enable checks for updated versions over the network - Linux distributions might want to disable this to avoid user confusion.

For more information see the CMake website; http://www.cmake.org/

build

make

install

make install

Known Issues & Limitations

This release is a beta release and is intended to gain feedback and interest in the project.

The code currently expects to be editing one 3D molecule per file with one coordinate set. This means:

  • Editing a multi-molecule file will only edit the first molecule. Saving will overwrite all records except the first.
  • Saving to a 2D format will not necessarily produce correct 2D stereochemistry.

Tools / Building

  • Several builder features are not implemented, including:
    • Crystal structure builder
    • Carbon Nanotube builder
    • Z-matrix editor (early version committed - needs more work)

Interface

  • Views cannot yet be removed into separate windows. In future releases, you will be able to have separate views of the same molecule in separate windows. Early support is in but disabled.
  • Export graphics will only save the current resolution in the window in bitmap form.

Troubleshooting

Problem: OpenBabel2 / Eigen libraries are not found.

Solution: The most likely the cause of this problem is non-standard install locations. Additionally, the detection system for finding libraries and includes is not flawless. The most likely remedy is to manually specify the library location and include directory for the package using the cmake arguments specified above.