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

Abstract

Background: 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.

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.

Figure 1

General code architecture of Avogadro. General code architecture of Avogadro, indicating major plugin interfaces for colors, display engines, tools, and extensions. Red boxes indicate code dependencies of Avogadro, blue boxes indicate plugin API classes, and green boxes inidicate examples of each plugin type.

Figure 2

Standard molecular structure representations. Several molecular representations of thiophene, (a) wireframe, (b) stick/licorice, (c) ball and stick, (d) ball and stick with ring, (e) Van der Waals/CPK and (f) transparent Van der Waal’s with stick.

Figure 3

Python scripting terminal, printing atomic numbers.

Figure 4

The Avogadro graphical user interface. Taken on Mac OS X, showing the editing interface for a molecule.

Figure 5

Dialogs for inserting pre-built fragments. The left shows molecules, and the right amino-acid sequences.

Figure 6

Dialog for generating input for quantum codes. Dialogs for generating input for Q-Chem, NWChem, Molpro and MOPAC200x. Note that the dialogs are similar in interface, allowing users to use multiple computational chemistry packages.

Figure 7

The GAMESS-US input deck generator. This input generator has an advanced panel and syntax highlighting.

Figure 8

The measurement tool. The measurement tool being used to measure bond angles and lengths (on Linux with KDE 4).

Figure 9

Molecular orbitals and surfaces. Rendering of a molecular orbital isosurface (left) and an electrostatic surface potential mapped onto the electron density (right).

Figure 10

Molecular orbitals rendering using GLSL shaders. Rendering of a molecular orbital isosurface using two GLSL shaders to highlight the edges of the surfaces. The X-ray effect (left) and red and blue (right) showing the positive and negative molecular orbital shapes.

Figure 11

Ray-traced HOMO isosurfaces of varying cube density. Rendering of a molecular orbital isosurface using POV-Ray with cubes of low (left) and high (right) density.

Figure 12

The Kalzium application in KDE using Avogadro to render molecular structures.

Figure 13

The PackMol lipid layer as produced by the PackMol extension.

Figure 14

The XtalOpt extension. XtalOpt extension showing a plot of stability vs. search progress for a TiO₂ supercell.