Java applet

Sofh are applications can mainly be divided into stand-alone programs that have to be installed on a local computer, and web-based appUcation.s. Furthermore, there arc two different tcchniquc.s u.scd in web-based applications for providing the programs applets and plug-ins. Whereas plug-ins (helper applications) have to be installed to be displayed correctly in a browser, java applets are loaded by the browser on demand. The basic requirement for executing java applets is that the java Virtual Machine (jVM) must be pre-installed on the local computer, which is oltcn the case. 

The molecular editor consists of a java applet that is embedded in the HTML document. It encodes the drawing into a connection table in inol-format, which is sent to the web server. 

The predictions are sent back to the client web browser and visualized using a combination of HTML, JavaScript [50], MDL Chime [51] scripting, and Java applets. 

Any software that includes matrix reduction can be used similariy. For example, wilh Maple (Watedoo Maple, Inc.), the first three steps in Example 1-3 are initiated by (1) with (linalg) (2) transpose (array ([list of species as in (1)])) (3) rref ( ). In many cases, the matrix reduction can be done conveniently by hand manipulation. 5Chemical reaction stoichiometry is described more fully on a Web site located athttp //www.chemical-stoichiometry.net. The site includes a tutorial and a Java applet to implement the matrix reduction method used in the examples here. 

For an excellent introduction to genetic algorithms, see the website constructed by Marek Obitko of the Czech Technical University at http //cs.felk.cvut.cz/ xobitko/ga1. It contains a genetic algorithm, coded as a Java Applet, which the user can run interactively, specifying his or her own objective if desired. 

The designers will provide Java applets for displaying the following ... 

The Student Web Site, www.whfreeman.com/cica7e, has directions for experiments that may be reproduced for your use. At this Web site, you will also find lists of experiments from the Journal of Chemical Education, a few downloadable Excel spreadsheets, and a few Living Graph Java applets that allow students to manipulate graphs by altering data points and variables. Supplementary topics at the Web site include spreadsheets for precipitation titrations, microequilibrium constants, spreadsheets for redox titration curves, and analysis of variance. 

From the top, the client layer resides on an end user s desktop, laptop, or handheld device, which is typically, but not limited to, a Windows PC with a Web browser. Usually a Web-based client layer is called thin client, which is lightweight. The programs that run inside the browser are typically JavaScript, VB Script, Java Applets, ActiveX, or Web browser plug-in. Using a rich client such as. NET or Java Swing is another choice, although this book focuses on a Web-based architecture. 

When the FDA ESG has received a complete submission, a backup copy is made before the Java applet receives a reply from the server confirming the submission is complete. For large submissions (V7.5GB), this can take many minutes. Since there is no network activity for such a long time, the session has time-outs and the Java applet never receives the response. The FDA ESG has received the submission successfully, but the Java applet returns an error and indicates that the submission needs to be resumed. Receipt of the first acknowledgment [Message Delivery Notification (MDN)] confirms that the submission was successfully received by the FDA ESG and that it is okay to cancel the resume request. Since this is a large submission, it will take several hours before the first acknowledgment is received. 

Java Applets and Applications Java applets are small programs written in Java, which can be deployed over the Internet to the users computers and viewed within a HTML page. Java applications are formal computer programs written in Java, but are stand-alone programs not requiring a browser to run. 

The former approach gives the user an environment specializing in chemistry, with options and tools not found in general software (such as the ability to choose between ball and stick, wire-frame, and other representations of a molecule). The programs are usually able to work with many input formats, such as Molfile or CML, and there is therefore often no need to convert the published data. Of the tools mentioned above, Jmol deserves special attention because it is an open-source program that works as a Java applet inside the browser, so the user does not need to install any special tools (of course, Java is mandatory). 

Java applets, another kind of J2EE components, are also embedded in the client tier. These applets are the containers holding visualization programs written in Java3D... 

Use your Weh browser to connect to http //chemistry.brookscole.com/skoogfac/. From the Chapter Resources menu, choose Web Works. Locate the Chapter 13 section, and click on the link to the Virtual Titrator. Click on the indicated frame to invoke the Virtual Titrator Java applet and display two windows the Menu Panel and the Virtual Titrator main window. To begin, click on Acids on the main window menu bar, and select the diprotic acid o-phthalic acid. Examine the titration curve that results. Then click on Graphs/Alpha Plot vs. pH and observe the result. Click on Graphs/Alpha Plot vs. mL base. Repeat the process for several monoprotic and polyprotic acids, and note the results. 

ChemDraw plug-in This is claimed as being more than a mere structure viewer or a slow Java applet, rather it runs as fast and is as familiar as the regular ChemDraw application. Available without charge, it enables searching of web databases by structure or substructure, and viewing of ChemDraw documents that others have placed on the web. http //www.camsoft.com... 

JME molecular editor JME is a free Java applet which allows generation and editing of molecules and reactions, and creation of molecule SMILES. The JME applet, written by Peter Ertl from Novartis, has become a standard for molecule structure input on the internet. http //www.molinspiration.com/ jme/index.html... 

The Java applet that comes with NMRShiftDB includes an array of features for molecular display (such as ball-and-stick, wireframe, space-fill, etc.), translation into SMILES nomenclature, and possibility of structure editing. Searching of chemicals can be based on (amongst others) chemical name, keyword, CAS number, literature title/author, and chemical formula. 

From the meta definition layer, it is also possible to use alternative viewer adaptors. The view adaptor is given a meta definition, which describes the input that the viewer requires. This is currently used to allow graphical Java applets to use information from SRS for data visualization. 

A final section describes how to display one s own BugView comparisons on the web using a special version of the program (a Java applet). 

Such a graphical display problem occurs because of an incompatibility between the quizzing exercises and older versions of the Macintosh Runtime for Java (which is a piece of software that allows Internet Explorer to view Java applets such as the Quizzing exercises). To resolve this problem ... 

Figure 5.3. Testing a three-dimensional viewer for sequence numbering artifacts with the structure 3TS1 (Brick et al., 1989). WebMol, a Java applet, correctly indicates both the explicit and implicit sequences of the structure. Note the off-by-two difference in the numbering in the two columns of numbers in the inset window on the lower right. The actual sequence embedded in the PDB file is 419 residues long, but the COOH-terminal portion of the protein is lacking coordinates it also has two missing residues. (See color plate.)...

Java A programming language developed by Sun Microsystems that allows small programs (applets) to be run on any computer. Java applets are typically invoked when a user clicks on a hyperlink. 

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