The 1.0 release series of Avogadro is the main focus of the results discussed here. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. It offers flexible, high quality rendering, and a powerful plugin architecture. The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
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