Avogadro 0.9.4

Avogadro 0.9.4 was released on 2 May 2009. This is the fifth 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 0.9.3. This is mainly a bug fix release with a few new features implemented over the last month of development.

  • Installs CMake configuration files making it easier to find and build against the installed Avogadro.
  • General changes and improvements to the build system and testing framework.
  • First network aware extension - PDB downloader.
  • Now load contributed plugins from the contrib subdirectory.
  • More unit tests and a new benchmarking test for the Molecule class.

  • More bugs found and fixed.

  • Export of generated cubes now possible again.

  • 2D cleanup code improvements for 2D molecule files.

  • Calculation of cubes for output from MolPro added.

  • Improvements to the plotting support of IR spectra.
  • New NWChem input file dialog.
  • New MolPro input file dialog.
  • Improvements and optimization of the super cell builder.

Dependencies

  1. Eigen 2.0.0 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 <pre>tar xvjf avogadro-0.9.4.tar.bz2</pre>

make the build directory <pre> cd avogadro-0.9.4 mkdir build </pre>

configure <pre> cd build cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_GLSL=ON -DENABLE_PYTHON=ON .. </pre>

CMake takes a few optional parameters:

  • -DCMAKE_INSTALL_PREFIX= : specify the installation prefix (default /usr)
  • -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).

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

build <pre>make</pre>

install <pre>make install</pre>

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.
  • Opening a SMILES file will not create 3D coordinates either (although you can insert SMILES as fragments into an Avogadro window)

  • Saving to a 2D format will not necessarily produce correct 2D stereochemistry.

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

Categories:

Updated: