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

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();
		}
	}

}
 

@Test
public void test2JA5() throws IOException, StructureException {

	FileParsingParameters fileParsingParameters = new FileParsingParameters();
	fileParsingParameters.setAlignSeqRes(true); // Need to align seqres to match chains.
	fileParsingParameters.setHeaderOnly(false); // Need header only off to have chains to match.

	AtomCache cache = new AtomCache();
	cache.setUseMmCif(false);
	cache.setFileParsingParams(fileParsingParameters);

	StructureIO.setAtomCache(cache);

	Structure s1 = StructureIO.getStructure("2ja5");

	// This is not applicable anymore, we need to parse atoms to have chains to match.
	// assertTrue(StructureTools.getNrAtoms(s1) == 0);

	// SeqRes contains 14 chains, but since we cannot align Chain N to AtomGroups => 14.
	// 2ja5 has been remediated on March 2017, now it has 14 chains in seqres matching the 14 chains in atoms (chain N has been removed)
	assertEquals(14, s1.getPolyChains().size());

	Chain nChain = s1.getPolyChain("N");

	assertNotNull(nChain);

	Chain chain = s1.getPolyChainByPDB("N");
	assertNull(chain);
}
 

@Test
public void test2JA5noHeader() throws IOException, StructureException {

	FileParsingParameters fileParsingParameters = new FileParsingParameters();
	fileParsingParameters.setHeaderOnly(true);

	AtomCache cache = new AtomCache();
	cache.setUseMmCif(false);
	cache.setFileParsingParams(fileParsingParameters);

	StructureIO.setAtomCache(cache);


	Structure s1 = StructureIO.getStructure("2ja5");

	// This is not applicable anymore, we need to parse atoms to have chains to match.
	assertEquals(0, StructureTools.getNrAtoms(s1));

	// 2ja5 has been remediated on March 2017, now it has 14 chains in seqres matching the 14 chains in atoms (chain N has been removed)
	assertEquals(14, s1.getPolyChains().size());

	Chain nChain = s1.getPolyChainByPDB("N");

	assertNull(nChain);
}
 

private void comparePDB2cif(String id, String chainId) throws IOException {
    String fileName = binary ? "/" + id + ".bcif" : "/" + id + ".cif";
    System.out.println(fileName);
    InputStream inStream = getClass().getResourceAsStream(fileName);
    assertNotNull("Could not find file " + fileName + ". Config problem?", inStream);

    LocalPDBDirectory reader = binary ? new BcifFileReader() : new CifFileReader();

    FileParsingParameters params = new FileParsingParameters();
    params.setHeaderOnly(headerOnly);
    reader.setFileParsingParameters(params);

    Structure cifStructure = reader.getStructure(inStream);
    assertNotNull(cifStructure);

    // load the PDB file via the PDB parser
    Structure pdbStructure;
    InputStream pinStream = this.getClass().getResourceAsStream("/" + id + ".pdb");
    assertNotNull(inStream);

    PDBFileParser pdbParser = new PDBFileParser();
    pdbParser.setFileParsingParameters(params);

    pdbStructure = pdbParser.parsePDBFile(pinStream);

    assertNotNull(pdbStructure);

    // check NMR data
    assertEquals(id + ": the isNMR flag is not the same!",
            pdbStructure.isNmr(),
            cifStructure.isNmr());

    if (pdbStructure.isNmr()) {
        assertEquals(id + ": the nr of NMR models is not the same!",
                pdbStructure.nrModels(),
                pdbStructure.nrModels());
        checkNMR(pdbStructure);
        checkNMR(cifStructure);
    }

    Chain a_pdb = pdbStructure.getPolyChainByPDB(chainId);
    Chain a_cif = cifStructure.getPolyChainByPDB(chainId);

    String pdb_SEQseq = a_pdb.getSeqResSequence();
    String cif_SEQseq = a_cif.getSeqResSequence();

    assertEquals(id + ": the SEQRES sequences don't match!",
            pdb_SEQseq,
            cif_SEQseq);

    assertEquals(id + ":  The nr of ATOM groups does not match!",
            a_pdb.getAtomGroups(GroupType.AMINOACID).size(),
            a_cif.getAtomGroups(GroupType.AMINOACID).size());

    // actually this check not necessarily works, since there can be waters in PDB that we don;t deal with yet in cif...
    for (int i = 0; i < a_pdb.getAtomGroups(GroupType.AMINOACID).size(); i++) {
        Group gp = a_pdb.getAtomGroups(GroupType.AMINOACID).get(i);
        List<Group> cifGroups = a_cif.getAtomGroups(GroupType.AMINOACID);
        Group gc = cifGroups.get(i);
        checkGroups(gp, gc);
    }

    String pdb_seq = a_pdb.getAtomSequence();
    String cif_seq = a_cif.getAtomSequence();

    assertEquals("the sequences obtained from PDB and mmCif don't match!", pdb_seq, cif_seq);

    List<DBRef> pdb_dbrefs = pdbStructure.getDBRefs();
    List<DBRef> cif_dbrefs = cifStructure.getDBRefs();

    assertEquals("nr of DBrefs found does not match!", pdb_dbrefs.size(), cif_dbrefs.size());

    DBRef p = pdb_dbrefs.get(0);
    DBRef c = cif_dbrefs.get(0);

    String pdb_dbref = p.toPDB();
    String cif_dbref = c.toPDB();
    assertEquals("DBRef is not equal", pdb_dbref, cif_dbref);

    PDBHeader h1 = pdbStructure.getPDBHeader();
    PDBHeader h2 = cifStructure.getPDBHeader();

    if (!h1.toPDB().toUpperCase().equals(h2.toPDB().toUpperCase())) {
        System.err.println(h1.toPDB());
        System.err.println(h2.toPDB());
        assertEquals(h1.toPDB(), h2.toPDB());
    }
    assertEquals("the PDBHeader.toPDB representation is not equivalent",
            h1.toPDB().toUpperCase(),
            h2.toPDB().toUpperCase());
}