BioJava:CookBook:PDB:SCOP

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Parsing SCOP with BioJava

The BioJava SCOP parser can

  • automatically download the SCOP release files (if they are not at a specified local directory)
  • parse the SCOP files
  • provides an API to access any level of the SCOP classification.


If you are running out of memory while running any of the examples, increase memory by adding the VM argument: 

-Xmx500M

Print all SCOP domains for a protein structure 

public void printDomainsForPDB(){
      String cacheLocation = "/tmp/";
      String pdbId = "4HHB";
 
      // download SCOP if required and load into memory
      ScopInstallation scop = new ScopInstallation(cacheLocation);
 
      List<ScopDomain> domains = scop.getDomainsForPDB(pdbId);
 
      System.out.println(domains);
 
}

prints: 

[d4hhba_	4hhb	A:	a.1.1.2	15251	cl=46456,cf=46457,sf=46458,fa=46463,dm=46486,sp=46487,px=15251, 
d4hhbc_	4hhb	C:	a.1.1.2	15252	cl=46456,cf=46457,sf=46458,fa=46463,dm=46486,sp=46487,px=15252, 
d4hhbb_	4hhb	B:	a.1.1.2	15428	cl=46456,cf=46457,sf=46458,fa=46463,dm=46500,sp=46501,px=15428, 
d4hhbd_	4hhb	D:	a.1.1.2	15429	cl=46456,cf=46457,sf=46458,fa=46463,dm=46500,sp=46501,px=15429]


Traverse the SCOP hierarchy

This examples loads a domain and traverses through its hierarchy in SCOP. 

private void traverseHierarchy()
   {
      String cacheLocation = "/tmp/";
      String pdbId = "4HHB";
      // download SCOP if required and load into memory
      ScopInstallation scop = new ScopInstallation(cacheLocation);
 
      List<ScopDomain> domains = scop.getDomainsForPDB(pdbId);
 
      // show the hierachy for the first domain:
 
      ScopNode node = scop.getScopNode(domains.get(0).getSunid());
 
      while (node != null){
 
         System.out.println("This node: sunid:" + node.getSunid() );
         System.out.println(scop.getScopDescriptionBySunid(node.getSunid()));
         node = scop.getScopNode(node.getParentSunid());
      }
 
}

Produces this output: 

parsed 110800 scop sunid domains.
parsed 143429 scop sunid nodes.
This node: sunid:15251
parsed 143428 scop sunid descriptions.
15251	px	a.1.1.2	d4hhba_	4hhb A:
This node: sunid:46487
46487	sp	a.1.1.2	-	Human (Homo sapiens) [TaxId: 9606]
This node: sunid:46486
46486	dm	a.1.1.2	-	Hemoglobin, alpha-chain
This node: sunid:46463
46463	fa	a.1.1.2	-	Globins
This node: sunid:46458
46458	sf	a.1.1	-	Globin-like
This node: sunid:46457
46457	cf	a.1	-	Globin-like
This node: sunid:46456
46456	cl	a	-	All alpha proteins
This node: sunid:0
null

Print various SCOP categories 

public void getCategories(){
      String cacheLocation = "/tmp/";
 
      // download SCOP if required and load into memory
      ScopInstallation scop = new ScopInstallation(cacheLocation);
      List<ScopDescription> superfams = scop.getByCategory(ScopCategory.Superfamily);
 
      System.out.println("Total nr. of superfamilies:" + superfams.size());
 
      List<ScopDescription> folds = scop.getByCategory(ScopCategory.Fold);
      System.out.println("Total nr. of folds:" + folds.size());  
 }

prints 

Total nr. of superfamilies:2223
Total nr. of folds:1393

Load a SCOP superfamily and align the first domain against all others

This example loads a superfamily from SCOP and aligns the first domain in this family against all others. 

 public void alignSuperfamily(){
 
      String cacheLocation = "/tmp/";
 
      // download SCOP if required and load into memory
      ScopInstallation scop = new ScopInstallation(cacheLocation);
      List<ScopDescription> superfams = scop.getByCategory(ScopCategory.Superfamily);
 
      System.out.println("Total nr. of superfamilies:" + superfams.size());
 
 
      // configure where to load PDB files from and 
      // what information to load
      AtomCache cache = new AtomCache(cacheLocation, true);      
      FileParsingParameters fileparams = new FileParsingParameters() ;
      fileparams.setAlignSeqRes(false);
      fileparams.setLoadChemCompInfo(true);
      fileparams.setParseSecStruc(false);
      cache.setFileParsingParams(fileparams);
 
      // get the first superfamily
      ScopDescription superfam1 = superfams.get(0);
      System.out.println("First superfamily: " + superfam1);
 
 
      // ScopNodes allow to traverse the SCOP hierarchy      
      ScopNode node = scop.getScopNode(superfam1.getSunID());
      System.out.println("scopNode for first superfamily:" + node);
 
      List<ScopDomain> doms4superfam1 = scop.getScopDomainsBySunid(superfam1.getSunID());
      ScopDomain dom1 = doms4superfam1.get(0);
 
      // align the first domain against all others members of this superfamily
      for ( int i = 1 ; i < doms4superfam1.size() ; i ++){
 
         ScopDomain dom2 = doms4superfam1.get(i);
 
         try {
            Structure s1 = cache.getStructureForDomain(dom1);
            Structure s2 = cache.getStructureForDomain(dom2);
 
            Atom[] ca1 = StructureTools.getAtomCAArray(s1);
            Atom[] ca2 = StructureTools.getAtomCAArray(s2);
            StructureAlignment ce = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);
            AFPChain afpChain = ce.align(ca1, ca2);
 
            //System.out.println(afpChain.toCE(ca1, ca2));
 
            //StructureAlignmentDisplay.display(afpChain, ca1, ca2);
 
            System.out.println(dom1.getScopId() + " vs. " + dom2.getScopId()+ " :" + afpChain.getProbability());
 
         } catch (Exception e){
            e.printStackTrace();
         }
      }
}
Retrieved from "http://www.biojava.org/wiki/BioJava:CookBook:PDB:SCOP"
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