BioSoftwares

Avogadro is a new, open source molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

While still in beta, the recent 0.9.7 release brings general usability to viewing and editing molecules. You can quickly export graphics to PNG, JPEG, or even POV-Ray rendering, or copy from the editor and paste a transparent PNG into programs like OmniGraffle. Avogadro supports reading from over 80 chemical file formats, courtesy of the Open Babel library.

Current features center on interactive molecular building and editing of small molecules. An “auto-optimize” tool will perform molecular mechanics geometry optimization in the background while you edit, and an “adjust hydrogens” feature allows for quick “sculpting” of new molecules.

Since Avogadro is multi-threaded, visualization of hydrogen bonding or other display types is dynamic. For example, during a geometry optimization, one can view the forces acting on each atom (the green arrows) as well as the formation and breaking of hydrogen bonds (the white dashed lines).

Future plans for the Mac version of Avogadro include integration of Spotlight and QuickLook, as well as built-in scripting in Python. Work is also underway to allow copy/paste from ChemDraw and other 2D chemical drawing applications. Additional builders (e.g., for biomolecules, nanotubes, and nanoparticles) and interfaces to other computational chemistry packages are due for future versions as well.

OS: Linux, Unix and Windows

Licence: Open Source under GNU GPL

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