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JSmol and the Next‐Generation Web‐Based Representation of 3D Molecular Structure as Applied to Proteopedia
Author(s) -
Hanson Robert M.,
Prilusky Jaime,
Renjian Zhou,
Nakane Takanori,
Sussman Joel L.
Publication year - 2013
Publication title -
israel journal of chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.908
H-Index - 54
eISSN - 1869-5868
pISSN - 0021-2148
DOI - 10.1002/ijch.201300024
Subject(s) - java applet , javascript , scripting language , java , computer science , rich internet application , rendering (computer graphics) , web application , world wide web , mobile device , unobtrusive javascript , java api for xml based rpc , graphical user interface , operating system , computer graphics (images) , java annotation
Although Java does not run on some handheld devices, e.g., iPads and iPhones, JavaScript does. The development of JSmol, a JavaScript‐only version of Jmol, is described, and its use in Proteopedia is demonstrated. A key aspect of JSmol is that it includes the full implementation of the entire set of Jmol functionalities, including file reading and writing, scripting, and rendering. The relative performances of Java‐based Jmol and JavaScript‐only JSmol are discussed. We can now confirm that the guiding principles of Java programming can be completely and relatively straightforwardly transformed directly into JavaScript, requiring no Java applet, and producing identical graphical results. JSmol is thus the first full‐featured molecular viewer, and the first ever viewer for proteins, which can be utilized with an internet browser on handheld devices lacking Java. Since the MediaWiki features of Proteopedia have been modified to optionally use JSmol, the wealth of crowd‐sourced content in Proteopedia is now directly available on such devices, without the need to download any additional applet.