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* BioJava development code

* This code may be freely distributed and modified under the

* terms of the GNU Lesser General Public Licence. This should

* be distributed with the code. If you do not have a copy,

* see:

* http://www.gnu.org/copyleft/lesser.html

* Copyright for this code is held jointly by the individual

* authors. These should be listed in @author doc comments.

* For more information on the BioJava project and its aims,

* or to join the biojava-l mailing list, visit the home page

* at:

* http://www.biojava.org/

* Created on Jun 30, 2010

* Author: Andreas Prlic

package demo;

import org.biojava.nbio.structure.Atom;

import org.biojava.nbio.structure.Structure;

import org.biojava.nbio.structure.StructureTools;

import org.biojava.nbio.structure.align.StructureAlignment;

import org.biojava.nbio.structure.align.StructureAlignmentFactory;

import org.biojava.nbio.structure.align.ce.CeMain;

import org.biojava.nbio.structure.align.model.AFPChain;

import org.biojava.nbio.structure.align.model.AfpChainWriter;

import org.biojava.nbio.structure.align.util.AFPChainScorer;

import org.biojava.nbio.structure.align.util.AtomCache;

import org.biojava.nbio.structure.io.FileParsingParameters;

import org.biojava.nbio.structure.scop.*;

import java.util.List;

/** A class demonstrating the use of the SCOP parsing tools

* @author Andreas Prlic

public class DemoSCOP

{

public static void main(String[] args){

DemoSCOP demo = new DemoSCOP();

// this creates a local copy of SCOP

ScopDatabase scop = new ScopInstallation();

// an alternative would be this one, which fetches data dynamically

//ScopDatabase scop = new RemoteScopInstallation();

ScopFactory.setScopDatabase(scop);

demo.getCategories();

demo.printDomainsForPDB();

demo.traverseHierarchy();

demo.alignSuperfamily();

}

/** Traverse throught the SCOP hierarchy

public void traverseHierarchy()

{

String pdbId = "4HHB";

// download SCOP if required and load into memory

ScopDatabase scop = ScopFactory.getSCOP();

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());

}

/** Get various categories

public void getCategories(){

// download SCOP if required and load into memory

ScopDatabase scop = ScopFactory.getSCOP();

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());

}

public void alignSuperfamily(){

// download SCOP if required and load into memory

ScopDatabase scop = ScopFactory.getSCOP();

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();

FileParsingParameters fileparams = new FileParsingParameters() ;

fileparams.setAlignSeqRes(false);

fileparams.setParseSecStruc(false);

cache.setFileParsingParams(fileparams);

// get tge first superfamily

ScopDescription superfam1 = superfams.get(0);

System.out.println("First superfamily: " + superfam1);

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());

double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2);

afpChain.setTMScore(tmScore);

System.out.println(AfpChainWriter.toScoresList(afpChain));

} catch (Exception e){

e.printStackTrace();

}

public void printDomainsForPDB(){

String pdbId = "4HHB";

// download SCOP if required and load into memory

ScopDatabase scop = ScopFactory.getSCOP();

List<ScopDomain> domains = scop.getDomainsForPDB(pdbId);

System.out.println(domains);

}