The SCOP classification can be accessed through the [```ScopDatabase```](http://www.biojava.org/docs/api/org/biojava/bio/structure/scop/ScopDatabase.html) class.

ScopDatabase scop = ScopFactory.getSCOP();

A list of domains can be retrieved for a given protein.

List<ScopDomain> domains = scop.getDomainsForPDB("4HHB");

You can get lots of useful information from the [```ScopDomain```](http://www.biojava.org/docs/api/org/biojava/bio/structure/scop/ScopDomain.html) object.

The full hierarchy is available as a tree of [```ScopNode```](http://www.biojava.org/docs/api/org/biojava/bio/structure/scop/ScopNode.html)s, which can be easily traversed using their ```getParentSunid()``` and ```getChildren()``` methods.

ScopNode node = scop.getScopNode(sunId);

while (node != null){

System.out.println(scop.getScopDescriptionBySunid(node.getSunid()));

node = scop.getScopNode(node.getParentSunid());

}

ScopDatabase also provides access to all nodes at a particular level.

List<ScopDescription> superfams = scop.getByCategory(ScopCategory.Superfamily);

System.out.println("Total nr. of superfamilies:" + superfams.size());

Several internal BioJava classes use ```ScopFactory.getSCOP()``` when they encounter references to SCOP domains, so it is always a good idea to notify the ```ScopFactory``` when using a custom ```ScopDatabase``` instance.

ScopDatabase scop = new ScopInstallation();

ScopFactory.setScopDatabase(scop);

Several versions of SCOP are available.

// Use Steven Brenner's updated version of SCOP

scop = ScopFactory.getSCOP(ScopFactory.VERSION_1_75C);

// Use an old version globally, perhaps for an older benchmark

ScopFactory.setScopDatabase(ScopFactory.VERSION_1_69);

CATH