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

<p>Abstract</p> <p>Background</p> <p>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 type, Avogadro seeks to enhance the semantic accessibility of chemical data types.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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 <url>http://avogadro.openmolecules.net</url>.</p

A tropological theory of institutionalization

We address the co-evolution of language and material practices during institutionalization by proposing a tropological model of institutionalization that integrates linguistic and practice-oriented approaches into a four-stage sequence: Metaphor enables members to inaugurate institutional change by inspiring and energizing initial movement. Members use metonymy to operationalize the emerging institution by demonstrating how it can become expected practice. Synecdoche is used to facilitate diffusion, standardizing the institution across time and space. When material practice is noticeably contrary to linguistic claims, however, members use irony to bring about deinstitutionalization and generate another inaugurating metaphor. The model further proposes that ritualized actions dramatize each trope, highlighting its symbolic meaning and embedding distinct material practices that serve both to institutionalize the practice and to facilitate boundary crossing to the next trope. The paper goes beyond current literature by offering an integrated theory of trope and ritual as an explanation of how institutions are simultaneously symbolic-linguistic and practice-material