Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA.
J Cheminform. 2012 Aug 13;4(1):17. doi: 10.1186/1758-2946-4-17.
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.
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.
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.
Avogadro 项目开发了一个先进的分子编辑和可视化工具，旨在跨平台用于计算化学、分子建模、生物信息学、材料科学和相关领域。它提供了灵活、高质量的渲染和强大的插件架构。典型用途包括构建分子结构、格式化输入文件以及分析各种计算化学软件包的输出。通过使用 CML 文件格式作为其本机文档类型，Avogadro 旨在增强化学数据类型的语义可访问性。
这里介绍的工作详细说明了 Avogadro 库，它是一个提供代码库和应用程序编程接口 (API) 的框架，具有三维可视化功能；并且在化学、物理、材料科学和生物学等领域的研究和教育中有直接的应用。Avogadro 应用程序通过库本身动态加载插件提供了丰富的图形界面。应用程序和库都可以通过实现 C++或 Python 中的插件模块来扩展，以探索不同的可视化技术、构建/操作分子结构以及与其他程序交互。我们描述了一些示例扩展，其中一个使用遗传算法来找到稳定的晶体结构，另一个与 PackMol 程序接口，为分子动力学模拟创建填充、溶剂化结构。这里讨论的结果主要集中在 1.0 版本系列的 Avogadro。
Avogadro 提供了一个语义化学构建器和可视化与分析平台。对于用户，它提供了一个易于使用的构建器，集成了对常见数据库（如 PubChem 和蛋白质数据库）的下载支持，从各种格式（包括计算化学输出）中提取化学数据，并对 CML 文件格式提供原生、语义支持。对于开发人员，它可以通过强大的插件机制轻松扩展，以支持有机化学、无机配合物、药物设计、材料、生物分子和模拟方面的新功能。Avogadro 可以从 http://avogadro.openmolecules.net 获得免费的开源许可证。
