Subsections

1.2 Basic installation instructions

Java OEChem comes as a single tar.gz file that contains the jar files, shared libraries, this documentation and numerous examples. Installation is similar for all supported platforms and involves 2 simple steps.

First, Java needs to be able to find the OpenEye JAR files in its CLASSPATH. By default, the all the files are found in a toolkit-version specific directory under the top-level openeye directory. For example, for v1.6.1-1, the path to the JAR files would be "openeye/wrappers/v1.6.1-1/java".

Second, since Java OEChem uses platform-specific shared libraries encapulating the C++ OEChem, we need to tell Java where to find them. In the past, we would set LD_LIBRARY_PATH (Linux), DYLD_LIBRARY_PATH (Mac OS X) or PATH (Windows), but this introduces many problems with mixing shared libraries. As of v1.6.1, we have vastly simplified the process. Instead of setting an environment variable, you instead add the "java/libs" directory to your CLASSPATH along with the JARS. Note also that this allows a single CLASSPATH to work across multiple platforms and Java versions.

1.2.1 Windows Example

As an example for setting this up on Windows, if we un-tar the Java tar file into "C: $\backslash$ ", we end up with the main "java" directory in "C: $\backslash$ OpenEye $\backslash$ wrappers $\backslash$ v1.6.1-1 $\backslash$ java". The CLASSPATH environment variable would then be set to "C: $\backslash$ OpenEye $\backslash$ wrappers $\backslash$ v1.6.1-1 $\backslash$ java $\backslash$ openeye.oechem.jar;...;C: $\backslash$ OpenEye $\backslash$ wrappers $\backslash$ v1.6.1-1 $\backslash$ java $\backslash$ libs", where "..." includes all the other JAR files in that directory.

1.2.2 Linux/Mac OS X Example

If we un-tar the Java tar file into "/usr/local", we end up with the main "java" directory in "/usr/local/openeye/wrappers/v1.6.1-1/java". The CLASSPATH environment variable would then be set to "/usr/local/openeye/wrappers/v1.6.1-1/java/openeye.oechem.jar:...:/usr/local/openeye/wrappers/v1.6.1-1/java/libs"

				OEChem - Java Theory Manual

				OEChem - Java Theory Manual