PUG SOAP with Java and Axis

These examples were created to work with Java classes generated by Axis 1.4. With Axis installed, set CLASSPATH to something like what's shown below, although the details will depend on your Java installation platform and local file paths. The CLASSPATH needs to contain these Axis .jar files (or they can be supplied on the command line):

axis-ant.jar;axis.jar;commons-discovery-0.2.jar;commons-logging-1.0.4.jar;jaxrpc.jar;log4j-1.2.8.jar;saaj.jar;wsdl4j-1.5.1.jar

With that, the command:

java org.apache.axis.wsdl.WSDL2Java 'https://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl'

will generate Java source code that provides the interface to PUG SOAP. (See the Axis documentation for more details.) Then use your favorite Java development environment to compile the Axis-generated code and the samples below into working applications, which will also need the Axis .jar libraries at run-time.

These samples were developed and tested with JDK SE 6 (update 7), but they should also work with earlier versions. Note that some of these save or read information in files on disk, so paths will need to be adjusted for the local filesystem.

Sample applications:

• Download CIDs
• Similarity Search from SMILES
• CID from InChI
• Standardize SDF File
• Substructure Search
• Molecular Formula Search
• ESearch Download - uses Axis-generated classes from eutils.wsdl (NCBI eUtils SOAP v2.0)