![]() The world also insists on changing around us, which always keeps things interesting! The Avogadro 2 libraries were designed to be far more modular from the start, featuring core libraries that only need C++11, then layering on OpenGL, Qt and other dependencies in other libraries or plugins. ![]() The rewrite was not as easy as I originally hoped, and we hit some dead ends in developing some components. We have been working on Avogadro 2 for quite some time, initially funded by a US Army SBIR (the first SBIR grant I obtained after joining Kitware), lots of our own time, and more recently some DOE funding. Everything we learned from the development of Avogadro 1.x led to an ambitious rewrite of Avogadro. Since we first developed Avogadro my ambitions grew. We have also been able to grow a community around the project, and found new, related projects. In those years I have learned a huge amount, grown as a developer, mentor, manager, author, proposal writer, presenter and more. Avogadro has been downloaded over one million times since our first release, and it has been cited over 2,100 times since we published the paper in 2012! That is absolutely mind blowing to me, and I never dreamt that we would garner so much attention when I sat coding for hours on something that was a passion project. Thanks to KDE, GSoC and the Avogadro project my career took on a whole new direction, one that had been a hobby/passion until then-scientific programming, visualization, and forming communities around open source codes.įast forward through a two year postdoc with Geoff Hutchison (one of Avogadro’s founders), and nearly ten years at Kitware (my current employer) and we arrive here. ![]() ![]() I learned a huge amount from my mentor Benoit Jacob that summer, and we were able to land a slew of new features. The group seemed to share many of my goals, and so it seemed like a better idea to work with them. I started a small project that I never published, and had hesitated for a few years to apply for Google Summer of Code but in 2007 I took a look and found what looked like the perfect project. student in Physics, working in an experimental group. In addition, we wanted to provide a library that exposed these features. From the start this was a project founded by a need felt by many of us who got involved in the early days-to have a solid, cross-platform and open source molecular editor. The library we were using was libavogadro, this powered Kalzium and the Avogadro application that provided a fuller interface (also using Qt as its base). The Avogadro project was founded all the way back in 2006, and I participated as a Google Summer of Code student with KDE in 2007 to bring a molecular editor to Kalzium. Avogadro is freely available under an open-source license from. 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. 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. The 1.0 release series of Avogadro is the main focus of the results discussed here.Īvogadro offers a semantic chemical builder and platform for visualization and analysis. 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 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. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. 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. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. It offers flexible, high quality rendering, and a powerful plugin architecture. 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.
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