Notes on Java API usage

In addition to the fast similarity search related functionalities this distribution contains various parts of ChemAxon APIs and third party libraries.

API status

Please note that the APIs in the included JAVA API documentation not necessarily part of officially supported ChemAxon public API. Some of the classes appearing in this documentation might be unused, non complete or removed in any subsequent release.

Basic usage

File classpath.jar in directory lib/ has all the libraries (jar files) referenced in its manifest. It is sufficient to use this file in the classpath in case of API usage of this distribution. Note that webapp contents (lib/overlap-examples-ws-<VERSION>-webapp.war) is not referenced in this classpath.jar.

Using custom Java codes

To extend the MadFast distribution with custom functionalities implemented in Java one can use the -classpath <SPEC> option of the launcher scripts. See document Command line interfaces (CLIs) for details.

Advanced usage

With the basic usage many but not all of ChemAxon APIs are available. To use a specific JChem distribution as the source of other ChemAxon APIs further steps needed:

• Selecting fast similarity search related libraries
• Selecting 3rd party libraries not present in JChem distribution
• Compatibility testing of the fast similarity search against the selected JChem distribution

We plan to provide support for this usage scenario in the future.