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ABSTRACT: BACKGROUND: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platformuse in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Itoffers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include buildingmolecular structures, formatting input files, and analyzing output of a wide variety of computational chemistrypackages. By using the CML file format as its native document type, Avogadro seeks to enhance the semanticaccessibility of chemical data types. RESULTS: The work presented here details the Avogadro library, which is a framework providing a code library andapplication programming interface (API) with three-dimensional visualization capabilities; and has directapplications to research and education in the fields of chemistry, physics, materials science, and biology. TheAvogadro 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 toexplore different visualization techniques, build/manipulate molecular structures, and interact with otherprograms. We describe some example extensions, one which uses a genetic algorithm to find stable crystalstructures, and one which interfaces with the PackMol program to create packed, solvated structures formolecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussedhere. CONCLUSIONS: Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers aneasy-to-use builder, integrated support for downloading from common databases such as PubChem and theProtein Data Bank, extracting chemical data from a wide variety of formats, including computationalchemistry output, and native, semantic support for the CML file format. For developers, it can be easilyextended 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-sourcelicense from http://avogadro.openmolecules.net.

Posts

We are pleased to announce the first beta release of the Open Chemistry suite of cross platform, open-source, BSD-licensed tools and libraries - Avogadro 2, MoleQueue and MongoChem. They are being released in beta, before all planned features are complete,...
Take a look at our ten most accessed papers for January.One of the latest articles to be published as part of our InChI thematic series is among the most accessed papers from last month. The paper presents a database called UniChem – a compound identifier...
Take a look at our ten most accessed papers for December.Among the most accessed articles is a research article in Journal of Cheminformatics from Saber Akhondi et al. published as part of a thematic series on the IUPAC International Chemical Identifier. The...
In an earlier post, I showed the accesses in the first month for the Blue Obelisk and Open Babel papers from late last year. I should have stopped there. Instead I decided to see how the recent Avogadro paper compared (Update 15/09/12: thanks to Geoff for filling...
from: http://avogadro.openmolecules.net/wiki/File:Avogadro-unitcell.pngReaders of this blog will know that I am a fan of Avogadro.   A paper describing Avogadro has now been published in the open access Journal of Cheminformatics.  I am telling...
Take a look at our ten most accessed papers for November.One of the most popular articles from the past month comes from a supplement published in Chemistry Central Journal earlier this year on Roles for chemistry in the worlds energy problems. The paper, entitled...
Take a look at our ten most accessed papers for October.A study by Monica Butnariu and Cristina Coradini that aimed to identify and characterise the phenolic and flavonoid components of marigold flowers was the most read paper last month. Due to the diverse...
Take a look at our ten most accessed papers for September.Among the most popular articles last month was an article in Journal of Cheminformatics covering the Open Molecule Generator software. The program represents the first general purpose open source structure...
Take a look at our ten most accessed papers for August.A software article published in Journal of Cheminformatics was the most popular paper last month, with over 2000 accesses in the first two weeks of publication. The paper describes Avogadro – an advanced...