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External Databases ================== Biojava provides access to a number of external structural databases. These often use [caching](caching.md) to reduce the amount of data which must be downloaded from the database. SCOP ----

(Top) The structure 1dan contains four chains.
(Bottom) These chains are broken up into six SCOP domains. The green chain L becomes 3 domains, while a combination of chains U (red) and T (orange) go to form the central purpal domain.

The Structural Classification of Proteins (SCOP) is a manually curated classification of protein structural domains. It provides two pieces of data: * The breakdown of a protein into structural domains * A classification of domains according to their structure. The structure for a known SCOP domain can be fetched via its 7-letter domain ID (eg 'd2bq6a1') via ```StructureIO.getStructure()```, as described in [Local PDB Installations](caching.md#Caching of other SCOP, CATH). The SCOP classification can be accessed through the [```ScopDatabase```](http://www.biojava.org/docs/api/org/biojava/nbio/structure/scop/ScopDatabase.html) class. ```java ScopDatabase scop = ScopFactory.getSCOP(); ``` ### Inspecting SCOP domains A list of domains can be retrieved for a given protein. ```java List domains = scop.getDomainsForPDB("4HHB"); ``` You can get lots of useful information from the [```ScopDomain```](http://www.biojava.org/docs/api/org/biojava/nbio/structure/scop/ScopDomain.html) object. ScopDomain domain = domains.get(0); String scopID = domain.getScopId(); // d4hhba_ String classification = domain.getClassificationId(); // a.1.1.2 int sunId = domain.getSunId(); // 15251 ### Viewing the SCOP hierarchy The full hierarchy is available as a tree of [```ScopNode```](http://www.biojava.org/docs/api/org/biojava/nbio/structure/scop/ScopNode.html)s, which can be easily traversed using their ```getParentSunid()``` and ```getChildren()``` methods. ```java 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. ```java List superfams = scop.getByCategory(ScopCategory.Superfamily); System.out.println("Total nr. of superfamilies:" + superfams.size()); ``` ### Types of ScopDatabase Several types of ```ScopDatabase``` are available. These can be instantiated manually when more control is needed. * __RemoteScopInstallation__ (default) Fetches data one node at a time from the internet. Useful when perfoming a small number of operations. * __ScopeInstallation__ Downloads all SCOP data as a batch and caches it for later use. Much faster when performing many operations. 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. ```java ScopDatabase scop = new ScopInstallation(); ScopFactory.setScopDatabase(scop); ``` Several versions of SCOP are available. ```java // 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 ---- Cath can be accessed in a very similar fashion to SCOP. In parallel to the ScopInstallation class, there is a CathInstallation. Also, the StructureIO class allows to request by CATH ID. ```java private static final String DEFAULT_SCRIPT ="select * ; cartoon on; spacefill off; wireframe off; select ligands; wireframe on; spacefill on;"; private static final String[] colors = new String[]{"red","green","blue","yellow"}; public static void main(String args[]){ UserConfiguration config = new UserConfiguration(); config.setPdbFilePath("/tmp/"); String pdbID = "1DAN"; CathDatabase cath = new CathInstallation(config.getPdbFilePath()); List domains = cath.getDomainsForPdb(pdbID); try { // show the structure in 3D BiojavaJmol jmol = new BiojavaJmol(); jmol.setStructure(StructureIO.getStructure(pdbID)); jmol.evalString(DEFAULT_SCRIPT); System.out.println("got " + domains.size() + " domains"); // now color the domains on the structure int colorpos = -1; for ( CathDomain domain : domains){ colorpos++; showDomain(jmol, domain,colorpos); } } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } private static void showDomain(BiojavaJmol jmol, CathDomain domain, int colorpos) { List segments = domain.getSegments(); StructureName key = new StructureName(domain.getDomainName()); String chainId = key.getChainId(); String color = colors[colorpos]; System.out.println(" * domain " + domain.getDomainName() + " has # segments: " + domain.getSegments().size() + " color: " + color); for ( CathSegment segment : segments){ System.out.println(" * " + segment); String start = segment.getStart(); String stop = segment.getStop(); String script = "select " + start + "-" + stop+":"+chainId + "; color " + color +";"; jmol.evalString(script ); } } ```

This will show the following

and the text:

                   
got 4 domains
 * domain 1danH01 has # segments: 2 color: red
   * CathSegment [segmentId=1, start=16, stop=27, length=12, sequenceHeader=null, sequence=null]
   * CathSegment [segmentId=2, start=121, stop=232, length=112, sequenceHeader=null, sequence=null]
 * domain 1danH02 has # segments: 2 color: green
   * CathSegment [segmentId=1, start=28, stop=120, length=93, sequenceHeader=null, sequence=null]
   * CathSegment [segmentId=2, start=233, stop=246, length=14, sequenceHeader=null, sequence=null]
 * domain 1danU00 has # segments: 1 color: blue
   * CathSegment [segmentId=1, start=91, stop=210, length=120, sequenceHeader=null, sequence=null]
 * domain 1danT00 has # segments: 1 color: yellow
   * CathSegment [segmentId=1, start=6, stop=80, length=75, sequenceHeader=null, sequence=null]

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