Java Code Examples for org.biojava.nbio.structure.io.FileParsingParameters#setParseSecStruc()

private static void demoAtomCache() {
	AtomCache cache = new AtomCache();

	FileParsingParameters params = cache.getFileParsingParams();

	params.setAlignSeqRes(true);
	params.setHeaderOnly(false);
	params.setParseCAOnly(false);
	params.setParseSecStruc(false);

	String[] pdbIDs = new String[]{"4hhb", "1cdg","5pti","1gav", "WRONGID" };

	for (String pdbID : pdbIDs){

		try {
			Structure s = cache.getStructure(pdbID);
			if ( s == null) {
				System.out.println("could not find structure " + pdbID);
				continue;
			}
			// do something with the structure
			System.out.println(s);

		} catch (Exception e){
			// something crazy happened...
			System.err.println("Can't load structure " + pdbID + " reason: " + e.getMessage());
			//e.printStackTrace();
		}
	}

}
 

public static void main(String[] args) throws IOException,
		StructureException {

	String pdbID = "5pti";

	// Only change needed to the DEFAULT Structure loading
	FileParsingParameters params = new FileParsingParameters();
	params.setParseSecStruc(true);

	AtomCache cache = new AtomCache();
	cache.setFileParsingParams(params);

	// Use PDB format, because SS cannot be parsed from mmCIF yet
	cache.setUseMmCif(false);

	// The loaded Structure contains the SS assigned by Author (simple)
	Structure s = cache.getStructure(pdbID);

	// Print the Author's assignment (from PDB file)
	System.out.println("Author's assignment: ");
	printSecStruc(s);

	// If the more detailed DSSP prediction is required call this
	DSSPParser.fetch(pdbID, s, true);

	// Print the assignment residue by residue
	System.out.println("DSSP assignment: ");
	printSecStruc(s);

	// finally use BioJava's built in DSSP-like secondary structure assigner
	SecStrucCalc secStrucCalc = new SecStrucCalc();

	// calculate and assign
	secStrucCalc.calculate(s,true);
	printSecStruc(s);

}
 

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 basicLoad(String pdbId){

		try {

			// This utility class can automatically download missing PDB files.
			AtomCache cache = new AtomCache();

			//
			// configure the parameters of file parsing (optional)

			FileParsingParameters params = new FileParsingParameters();

			// should the ATOM and SEQRES residues be aligned when creating the internal data model?
			params.setAlignSeqRes(true);
			// should secondary structure get parsed from the file
			params.setParseSecStruc(false);

			// and set the params in the cache.
			cache.setFileParsingParams(params);

			// end of optional part

			Structure struc = cache.getStructure(pdbId);

			System.out.println("structure loaded: " + struc);

			List<Domain> domains = LocalProteinDomainParser.suggestDomains(struc);

			System.out.println("RESULTS: =====");
			for ( Domain dom : domains){
				System.out.println("DOMAIN:" + dom.getSize() + " " +  dom.getScore());
				List<Segment> segments = dom.getSegments();
				for ( Segment s : segments){
					System.out.println("   Segment: " + s);
				}
			}
		} catch (Exception e){
			e.printStackTrace();
		}

	}
 

@Test
public void test1REP() throws StructureException, IOException{

	PDBFileReader reader = new PDBFileReader();
	FileParsingParameters params = new FileParsingParameters();
	params.setParseSecStruc(true);
	params.setAlignSeqRes(true);
	params.setParseCAOnly(false);
	reader.setFileParsingParameters(params);



	Structure s = reader.getStructureById("1REP");
	//System.out.println(s);
	//System.out.println(s.toPDB());
	Chain b = s.getPolyChainByPDB("B");

	assertEquals(22,b.getSeqResGroups().size());
	assertEquals(21,b.getAtomGroups().size());

	Group n1 = b.getSeqResGroup(0);
	Group n2 = b.getAtomGroup(0);
	//System.out.println(n1);
	//System.out.println(n2);
	//System.out.println(n1.getChemComp());


	assertNotNull("Could not acces Chem Comp file!" , n1.getChemComp());
	assertTrue("ChemComp is not DC",n1.getChemComp().getId().equals("DC"));
	assertNotNull("Could not determine polymer type " , n1.getChemComp().getPolymerType());
	//System.out.println(n1.getChemComp().getPolymerType());
	assertTrue(n1.getChemComp().getPolymerType().equals(PolymerType.dna));

	assertNotNull(n1.getPDBName());
	assertNotNull(n1.getResidueNumber());
	assertNotNull(n2.getResidueNumber());
	assertEquals("23", n2.getResidueNumber().toString());
	assertTrue(n1.getResidueNumber().equals(n2.getResidueNumber()));


}
 

public void basicLoad(){
	try {

		PDBFileReader reader = new PDBFileReader();

		// the path to the local PDB installation
		reader.setPath("/tmp");

		// configure the parameters of file parsing

		FileParsingParameters params = new FileParsingParameters();

		// should the ATOM and SEQRES residues be aligned when creating the internal data model?
		params.setAlignSeqRes(true);

		// should secondary structure get parsed from the file
		params.setParseSecStruc(false);

		reader.setFileParsingParameters(params);

		Structure structure = reader.getStructureById("4hhb");

		System.out.println(structure);

		Chain c = structure.getPolyChainByPDB("C");


		System.out.print(c);

		System.out.println(c.getEntityInfo());


	} catch (Exception e){
		e.printStackTrace();
	}

}
 

public void basicLoad(PDBFileReader reader, boolean loadChemComp, String pdbId){

		try {
			// configure the parameters of file parsing

			FileParsingParameters params = new FileParsingParameters();

			// should the ATOM and SEQRES residues be aligned when creating the internal data model?
			// only do this if you need to work with SEQRES sequences. If all you need are ATOMs, then
			// set it to false to have quicker file loading.
			params.setAlignSeqRes(true);

			//
			// should secondary structure get parsed from the file
			params.setParseSecStruc(false);

			reader.setFileParsingParameters(params);

			Structure struc = reader.getStructureById(pdbId);

			printStructure(struc);


		} catch (Exception e){
			e.printStackTrace();
		}

	}
 

@Test
public void test3T5N() throws IOException, StructureException{

	String pdbId = "3T5N";
	Structure s = getStructure(pdbId);


	assertEquals(2,s.getPolyChains().size());

	Chain c = s.getChains().get(1);
	System.out.println(c);
	assertEquals("C", c.getName());
	List<Group> ngr = c.getAtomGroups(GroupType.NUCLEOTIDE);
	assertEquals(6,ngr.size());


	// now test if we download all definitions correctly for this one...
	PDBFileReader reader = new PDBFileReader();
	FileParsingParameters params = new FileParsingParameters();
	params.setParseSecStruc(true);
	params.setAlignSeqRes(true);
	params.setParseCAOnly(false);
	reader.setFileParsingParameters(params);

	ChemCompProvider chemProv = ChemCompGroupFactory.getChemCompProvider();

	DownloadChemCompProvider download = new DownloadChemCompProvider();

	ChemCompGroupFactory.setChemCompProvider(download);

	Structure s1 = reader.getStructureById(pdbId);

	assertNotNull(s1);

	assertEquals(2,s1.getPolyChains().size());

	Chain c1 = s1.getChains().get(1);

	assertEquals("C", c1.getName());

	Group g = c1.getAtomGroup(0);
	assertNotNull(g);
	assertNotNull(g.getChemComp());
	assertNotNull(g.getChemComp().getPolymerType());
	assertNotNull(g.getChemComp().getPolymerType().name());

	assertTrue("Found an unknown polymertype!", (! g.getChemComp().getPolymerType().equals(PolymerType.unknown)));
	//System.out.println(g.getChemComp().getPolymerType());

	List<Group> ngr1 = c1.getAtomGroups(GroupType.NUCLEOTIDE);
	assertEquals(6,ngr1.size());


	ChemCompGroupFactory.setChemCompProvider(chemProv);


}