JAVA - SOAP web services
Use the Axis framework to generate the web service client code using the following command line:
java org.apache.axis.wsdl.WSDL2Java "http://www.rcsb.org/pdb/services/pdbws?wsdl"
For a more detailed introduction into how to develop web services using the RCSB soap interface see the developing web services page.
Then you can run e.g. the code below to execute a BLAST search against PDB:
import java.io.PrintStream;
import java.net.URL;
import org.pdb.webservices.PdbWebService;
import org.pdb.webservices.PdbWebServiceServiceLocator;
public class BlastPDB {
public static void main(String[] _args) {
// call the blast method below using this sequence and the ecutoff value
blastThePDB("VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPL", 10);
}
private static void blastThePDB(String _sequence, double _eCutOff) {
// build the service locator object. This object was created by Axis wsdl2java
PdbWebServiceServiceLocator locator = new PdbWebServiceServiceLocator();
try {
// construct my URL object
String _url = "http://www.pdb.org/pdb/services/pdbws";
URL url = new URL(_url);
// Get the web services interface (axis-generated interface)
PdbWebService p = locator.getpdbws(url);
// print some feedback to the standard out
System.out.println("Blasting... ");
// call the blast program on the PDB server using these parameters
String output = p.blastPDB(_sequence, _eCutOff, "BLOSUM62" , "HTML");
// print the output
System.out.println ( "output : " + output );
// save the output into f file
File outputFile = new File ("MyBlastResults.html");
PrintStream printer = new PrintStream ( outputFile );
printer.print(output);
printer.flush();
printer.close();
System.out.println("Blast is complete");
} catch (Exception _e) {
_e.printStackTrace();
}
}
}