Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey R Hutchison
2012 Journal of Cheminformatics  
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. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document
more » ... , Avogadro seeks to enhance the semantic accessibility of chemical data types. Results: 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. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. 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. 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 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions: Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. Background Many fields such as chemistry, materials science, physics, and biology, need efficient computer programs to both build and visualize molecular structures. The field of molecular graphics is dominated by viewers with little or no editing capabilities, such as RasMol [1], Jmol [2], PyMOL [3], VMD [4], QuteMol [5], BALLView [6], VESTA [7], and XCrySDen [8,9], among many others. The aforementioned viewers are all freely available, and most of them are available under open-source licenses and work on the most common operating systems (Linux, Apple Mac OS X, Microsoft Windows, and BSD). The choice of software capable of building chemical structures in three dimensions is far smaller. There are existing commercial packages, such as CAChe/Scigress [10], ChemBio3D [11], GaussView [12], HyperChem [13], CrystalMaker [14], Materials Studio [15], and Spartan [16], which are polished and capable of constructing many different types of molecular structures. They are, however, not available for all operating systems (most of them only run on Microsoft Windows), and are not easily extensible, customized, or integrated into automated workflows.
doi:10.1186/1758-2946-4-17 pmid:22889332 pmcid:PMC3542060 fatcat:e2mdy6dfjfai5gcnexaaiyvjg4