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Administering JavaGrins

Client Requirements

Though Java bytecode is supposed to run on any 1.1 compatible Java Virtual Machine, the truth as evidenced by varying behavior in differing versions of Netscape is a little distant from reality. However with the latest browsers from Netscape, this is fast changing.

Hence we are publishing a list of all compatible versions of Netscape that run JavaGrins without problem.

The latest version of Netscape Communicator Standard Edition(version 4.05 at the time of creating this document) is downloadable free of charge from their web site. The later versions are recommended over the previous ones especially because of their greatly reduced JVM startup time and their better Java1.1 compatibility. We recommend using Netscape's automatic installer scripts to install the client.

In the event that Netscape's automatic installer scripts are not used to install the Netscape client, the Netscape client must have, access to the Java jar files

in its Java classes directory (usually in $NS_HOME/java/classes where $NS_HOME is the installation directory for the Netscape client). However to run Java correctly, Netscape must also have access to all the jar files that come with Netscape's installation.

Server Requirements and Installation

We expect the web server to have the dayutils server licensed. For reaction capabilities the Reactions Program license is also required. JavaGrins uses a server that needs to be up and running on the web server that Java Grins is hosted off. In case of Solaris this server will need to be running Java 1.1, implying that it should have Solaris 2.5.1 or above (since Java 1.1 won't run correctly on Solaris 2.4). In case of IRIX, the server will need to be running IRIX 5.3 or higher.

The JavaGrins server listens on port 5553. Running the server implies having a Java Runtime Environment(JRE) installed on the server. For Solaris, this Java Runtime Environment is shipped along with the Daylight installation. It is located in $DY_ROOT/exotic/www/sun5 and is named jre116-solaris2-sparc.bin where $DY_ROOT refers to the directory where the daylight software is installed. To install the JRE for Solaris just execute this file (If not executable, you may need to change its mode using the command.

chmod +x jre116-solaris2-sparc.bin

and then execute it.

For SGI's however due to licensing reasons, we ask users to download it from SGI's web site where it is available free of charge. This is explained in detail later below.

While installing the JRE, on either OS, note down the directory where the JRE is installed. The environmental variable JAVA_HOME will have to be set to this value in the web server script, (explained below)

More information on the Java Runtime Environment and its capabilities may be obtained from the JavaSoft web site.

Installing and running the server on Solaris

Note: You must edit the script dayutilserver and verify the setting of the DY_ROOT, JAVA_HOME, and DY_LICENSEDATA environment variables. You must also edit the file $DY_ROOT/data/dayutilsperm.dat (where DY_ROOT is the daylight installation directory).

To run the server

The above command runs the web server in the background.

Installing and running the server on IRIX

With IRIX, it is not clear if we are allowed to redistribute Silicon Graphics' JRE. At this stage, you will have to obtain and install the JDK free of charge from http://www.sgi.com. Download of the JDK from their web site does require that you be a registered member of SurfZone (available at their web site for free). After installing the JDK the following steps need to be done to complete installation and start the servers.

Licensing Issues

The dayutils server is licensed on the number of machines that can use the server. For example if the dayutils server is licensed to 8 machines, only 8 machines on a network can access all the functionality of JavaGrins. The identity of these 8 machines is defined by the first 8 IP numbers which appear in the file $DY_ROOT/data/dayutilsperm.dat. The format in which these numbers may appear in $DY_ROOT/data/dayutilsperm.dat is briefly explained below.

For example a file permitting IP's 128.59.98.1 to 128.59.98.6 and 128.59.97.1 to 128.59.97.6 may be written as 

# this is only a comment. peace love flowers and java.
128.59.98.1
128.59.98.2-4
128.59.98.5:7
128.59.98.4-6
128.59.97.1-6
or as 
128.59.97:98.1-6
or as 
128.59.97:98.1:6
In either case if the server has been licensed for 10 machines, only the first 10 IP numbers that are interpreted from the above will be used and the remaining will be ignored.

Should JavaGrins be invoked on an unlicensed Netscape browser, it will come up with an alert proclaiming the same. It will allow molecule drawing. However it wont permit obtaining SMILES from depictions or vice versa. In this case you are welcome to contact support@daylight.com to obtain additional licenses.

Applet Installation

The files grins.jar and Grins.html are extracted to the desired directory in your web site. To invoke Grins in a browser client browse via your http server (not via the local filesystem) to the Grins.html page(usually at /dayhtml/java/Grins.html). The applet takes about 10-20 seconds to startup once the JVM in your browser has been initialized, a process taking about 15-20 seconds depending on your browser and system. The applet will issue a warning if it either cannot contact the dayutils server on the web server or is running on an unlicensed client. Contact support@daylight.com to resolve any problems that you encounter.

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