BioJava supports by default the original SCOP version from the UK (currently at version 1.75). As of version 3.0.4 it also allows to work with the newer (version 1.75A) version of SCOP that is available from Berkeley.


import org.biojava.nbio.structure.scop.BerkeleyScopInstallation; import org.biojava.nbio.structure.scop.ScopDatabase; import org.biojava.nbio.structure.scop.ScopFactory;

/** A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP

* @since 3.0.4

public class DemoBerkeleyScop {

   public static void main(String[]args){

       ScopDatabase berkeley = new BerkeleyScopInstallation();


       // whenever you want to get access to SCOP now request it like this:
       ScopDatabase scop = ScopFactory.getSCOP();
       // ... and do something with it

       // eg. you can run all the demos that work for the UK - SCOP (currently at version 1.75) 
       // this demo no automatically picks up the Berkeley version (currently 1.75A)
       DemoSCOP scopDemo = new DemoSCOP();