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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

The Open Chemistry Group have just announced the availability of the first beta release of a suite of software packages for chemists.It consists of Avogadro 2 an update to the well established molecular editing package, see a recent paper describing it for...
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...
In January of last year I was invited to attend the Semantic Physical Science Workshop in Cambridge, England. That was a great meeting where I met like-minded scientists and developers working on adding semantic structure to data in the physical sciences. Peter...
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...
Here's a quick question, for what shape distribution does the mean convey the least useful information? Well, there are many answers, but a prime candidate is a one-sided long-tail distribution of the type exhibited by journal citations. The mean, standard...
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...
A new version (1.1.0) of Avogadro was released recently and contains a very useful new building tool, where molecule-fragments can be added to selected atoms.  The screencast shows how. Remember: please cite the Avogadro paper if you use Avogadro in research...
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...
From the latest issue of Journal of CheminformaticsAvogadro: An advanced semantic chemical editor, visualization, and analysis platformThe work presented here details the Avogadro library, which is a framework providing a code library and application programming...