The program has been released under MIT open-source license and is available on. 3DStructGen may play a valuable role in online chemistry education and pre-processing of quantum calculations. Other than local desktop software, it does not require any additional effort to install the system but a web browser supporting HTML5. It can provide web service independently or can be integrated into other web platforms. Additionally, the initial input files for Vienna Ab-initio Simulation Package (VASP) and Gaussian can be obtained by interacting with dialog boxes in 3DStructGen.ģDStructGen is a highly platform-independent program. Four displayed styles, namely “Primitive cell”, “Original”, “In-cell” and “Packing” can be used to visualize a unit cell. A wide range of cheminformatics algorithms for crystal structure are provided, including cleaving surfaces, establishing vacuum layers, and building supercells. The atom, bond, angle and dihedral in a molecule can be viewed and modified using sample mouse operations. Both non-periodic organic molecule and crystal structure can be visualized, built and edited interactively. We developed a user-friendly and versatile program based on standard web techniques, such as Hyper Text Markup Language 5 (HTML5), Cascade Style Sheet (CSS) and JavaScript. But few of these tools can deal with crystal structures. Many web-based three-dimensional (3D) structure tools have been developed for displaying existing models, building new models, and preparing initial input files for external calculations. The increasing number of organic and inorganic structures promotes the development of the “Big Data” in chemistry and material science, and raises the need for cross-platform and web-based methods to search, view and edit structures. Through examples based on JavaScript libraries, web applets, and even full web apps, either alone or coupled to each other, the article puts on the spotlight the potential of these technologies for carrying out numerical calculations, text processing and mining, retrieval and analysis of data through queries to online databases and web services, effective visualization of data including 3D visualization and even virtual and augmented reality all of them in the browser at relatively low programming effort, with applications in cheminformatics, structural biology, biophysics, and genomics, among other molecular sciences. This article reviews the best-established tools for in-browser plugin-less programming, including JavaScript as used in HTML5 as well as related web technologies. Whereas server-side programs are essential to maintain databases and run data analysis pipelines and simulations, client-side web-based computing tools are also important as they allow users to access, visualize and analyze the content delivered to their devices on-the-fly and interactively. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from. Installation on a web server is straightforward and does not require any server-side modules or special permissions. Although this library is designed to create web pages, a web server is not required. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features.Ī light-weight (nearly 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Routines are provided to read structures either from the web server or from the user's computer, and creation of galleries of structures can be accomplished with only a few lines of code. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of webbased applications that should run on any browser capable of rendering HTML5 web pages. While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures.
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