Avogadro 0.9.8

From Avogadro - Free cross-platform molecule editor

Avogadro 0.9.8 was released on 9 September 2009. This is the ninth 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 0.9.7. This is a bug fix release with some feature enhancements since our last release.

General

• Updated user interface and icons.
• Introduced a menu option to reset display types.
• Updated translations, fixed encoding issues that affected some translations on Windows.
• Avogadro will now run correctly from the build directory on the Mac too.
• Fixes to display type labels.
• Improved recent file list handling.
• Fixes to dipole moment reading and display.
• Fixes to file saving, marking of modified windows.
• More bugs found and fixed.

Rendering

• Speed and efficiency enhancements for single colored meshes.

Tools

• Various draw tool bugs fixed.
• Aesthetic fixes to the autorotate slider -- easier to see central position.

Extensions

• New Chemical Identifier Resolver extension -- type in a chemical name and search http://cactus.nci.nih.gov/chemical/structure for structures.

Dependencies

1. Eigen 2.0.3 or later http://eigen.tuxfamily.org/ -- for compiling only.
2. OpenBabel 2.2.2 or later http://openbabel.org
3. CMake 2.6.0 or later http://www.cmake.org
4. Qt 4.5.1 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-0.9.8.tar.bz2

make the build directory

cd avogadro-0.9.8
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

• 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.