The Java version of the OpenEye Toolkits is a JNI (Java Native Interface) wrapper created using SWIG. It is important to note that this is not a new version of the toolkits written in Java nor is it a Java interpretation of the toolkit API, but a rather faithful reproduction of the toolkit API in Java. As such there are some features that might not be as Java-like as a toolkit written entirely in Java, but most of these are minor issues and consistency with all the supported languages makes translation from one to another relatively easy and greatly enhances our ability to support all the language versions.
A few of these idiomatic differences include:
There are relatively few classes in OEChem and they have a rather shallow inheritance hierarchy.
Most OEChem algorithms are in C++ free functions. These are mapped to static methods in the class oechem.
Method names in most OEChem TK classes start with uppercase letters.
Java doesn’t support operator overloading, so C++ operators are mapped to methods. For example, operator bool() is mapped to a member function called IsValid(), operator() is mapped to call() and operator() const is mapped to constCall().
Java doesn’t support direct access to class attributes, so for some simple C++ classes and structs, direct access is mapped to a get/set pair of functions.
Calling close() is required for all objects that provide a close() method.
delete() should be explicitly called on all objects that come from the following toolkits:
The user should interact with these particular libraries from only a single Java thread. Failing to do so can lead to subtle race conditions.
There is a known bug concerning OpenEye constants that occurs when compiling against an older version of the OpenEye jar and running against a newer version of the OpenEye jar. Please make sure to run against java programs against the same version it was compiled with.
A Java version of the toolkits allows integration into Java desktop and server-side applications. However, the Java toolkits are not necessarily suited for applet programming since they require native code and platform- specific shared libraries. This can be achieved by building a multi-platform JAR as described in the final section, but this is considered for experts only.
In general, due to the wrapping of native code, using explicit
obj.delete() calls on class instances obtained from any toolkit
is highly recommended as it minimizes issues with early or delayed
deletion activity by the Java garbage collector on OpenEye class instances.
In order to use the OpenEye Java toolkits, a compatible version the Java SDK must be installed. For the most part, this means installing a version of OpenJDK8 or OpenJDK11. See https://openjdk.org/ for your platform.
Linux installation also requires the zlib and libcairo libraries be available. These are usually available on Desktop Linux installations by default, but may not be available on Linux server installations.
OpenEye’s support of operating systems changes from the time to time, with older systems retired and newer ones validated. For the current set of supported platforms, see the current release notes.
Additional software requirements are spelled out in the following sections.
Download the OpenEye Java distribution¶
Picking a distribution is relatively easy. For each platform (Windows, Linux, and macOS), we only have 1 download, a 64-bit version (x64).
Download from http://www.eyesopen.com/downloads.
Untar or unzip the distribution into a directory of your choice. This will create the following structure:
OpenEye-Java-|pkgversion|-OSName-xArch/ docs/ lib/ oejava-|pkgversion|-OSName-xArch.jar verify/ verify.py examples/ build.xml openeye/ examples/ docexamples/
For Windows, the distribution should be unzipped to a directory with a short pathname, so the longest directory pathname in the tree can be specified in less than 260 characters. Otherwise, one may see errors when running the verify.py mentioned below due to the 260 character maximum path limit in Windows.
All the examples are found in the examples directory. Use ant to compile the examples jar then you can run an OEChem example using:
cd OpenEye-Java-|pkgversion|-OSName-xArch/examples ant java -cp ../lib/oejava-|pkgversion|-Linux-x64.jar:openeye.examples.jar openeye.examples.oechem.OEChemInfo
For Windows, note the use of semi-colon instead of a colon in the class path argument:
cd OpenEye-Java-|pkgversion|-OSName-xArch/examples ant java -cp ../lib/oejava-|pkgversion|-Windows-x64.jar;openeye.examples.jar openeye.examples.oechem.OEChemInfo
The verify.py script can also be run to ensure a properly working distribution in the current environment. If there are problems with the distribution or environment the script will fail. To run verify.py:
cd OpenEye-Java-|pkgversion|-OSName-xArch/verify python verify.py
If an error similar to
java.lang.OutOfMemoryError: Java heap space
occurs, one can increase the heap size of the JVM using the ‘JAVAFLAGS’
environment variable. The ‘-Xmx’ option controls the size of Java heap
used. For example, add
export JAVAFLAGS=-Xmx4G in bash, and then