Java StructureIO类代码示例

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
public static void main(String[] args) throws IOException,
		StructureException {

	// Align two trimeric DNA clamps
	Structure s1 = StructureIO.getStructure("1bcc");
	Structure s2 = StructureIO.getStructure("1kb9");

	// Select the parameters for clustering and alignment
	SubunitClustererParameters clusterParams = new SubunitClustererParameters();
	QsAlignParameters alignParams = new QsAlignParameters();

	QsAlignResult result = QsAlign
			.align(s1, s2, clusterParams, alignParams);

	System.out.println(result);

}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/**
 * Set up the configuration parameters for BioJava.
 */
public static AtomCache setUpBioJava() {
	// Set up the atom cache etc
	AtomCache cache = new AtomCache();
	cache.setUseMmCif(true);
	FileParsingParameters params = cache.getFileParsingParams();
	params.setCreateAtomBonds(true);
	params.setAlignSeqRes(true);
	params.setParseBioAssembly(true);
	DownloadChemCompProvider cc = new DownloadChemCompProvider();
	ChemCompGroupFactory.setChemCompProvider(cc);
	cc.checkDoFirstInstall();
	cache.setFileParsingParams(params);
	StructureIO.setAtomCache(cache);
	return cache;
}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/**
 * Test {@link SubunitCluster#divideInternally(SubunitClustererParameters)}
 * 
 * @throws StructureException
 * @throws IOException
 */
@Test
public void testDivideInternally() throws StructureException, IOException {

	Structure s = StructureIO.getStructure("4e3e");

	// Create a SubunitCluster for the chain
	SubunitCluster sc1 = new SubunitCluster(
			new Subunit(StructureTools.getRepresentativeAtomArray(s
					.getChainByIndex(0)), "chain 0", null, s));

	SubunitClustererParameters clustererParameters = new SubunitClustererParameters();
	clustererParameters.setStructureCoverageThreshold(0.8);
	clustererParameters.setRMSDThreshold(3.0);
	clustererParameters.setMinimumSequenceLength(20);

	// Clusters should be merged by identity
	boolean divided = sc1.divideInternally(clustererParameters);

	// Divided has to be true, and Subunit length shorter than half
	assertTrue(divided);
	assertEquals(sc1.size(), 2);
	assertTrue(sc1.length() < 178);
	assertEquals(sc1.getAlignedAtomsSubunit(0).length,
			sc1.getAlignedAtomsSubunit(1).length);
}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/**
 * Some collagen structures have very short Chains, so the minimum sequence
 * length is adjusted: 1A3I.
 * 
 * @see SubunitClustererParameters#getMinimumSequenceLengthFraction()
 */
@Test
public void testCollagen() throws StructureException, IOException {

	Structure s = StructureIO.getStructure("1A3I");

	List<Subunit> subunits = SubunitExtractor.extractSubunits(s, 5, 0.75, 20);

	// We expect all 3 subunits to be returned
	assertEquals(subunits.size(), 3);

	subunits = SubunitExtractor.extractSubunits(s, 8, 0.75, 9);

	// Now we expect only the long Subunit to be returned
	assertEquals(subunits.size(), 1);
	assertEquals(subunits.get(0).size(), 9);
}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/**
 * Test parsing dates from MMCIF file version 4.
 */
@Test
public void testDatesV4() throws IOException, StructureException, ParseException {
	
	ClassLoader classLoader = this.getClass().getClassLoader();
	String file4 = classLoader.getResource("org/biojava/nbio/structure/io/mmcif/1stp_v4.cif").getPath();
	Structure s = StructureIO.getStructure(file4);
	
	SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US);
	
	Date modDate = dateFormat.parse("2011-07-13");
	assertEquals(modDate, s.getPDBHeader().getModDate());

	Date releaseDate = dateFormat.parse("1992-10-15");
	assertEquals(releaseDate, s.getPDBHeader().getRelDate());
	
	Date depositionDate = dateFormat.parse("1992-03-12");
	assertEquals(depositionDate, s.getPDBHeader().getDepDate());
	
}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
@Test
public void testSites1a4w()throws IOException, StructureException {
	AtomCache cache = new AtomCache();

	StructureIO.setAtomCache(cache);

	cache.setUseMmCif(true);
	Structure sCif = StructureIO.getStructure("1A4W");

	assertNotNull(sCif);

	// After it has read the file, it should check that expected SITES are present.
	List<Site> sites = sCif.getSites();

	// 1a4w has 5 sites from ligands.
	assertEquals(5, sites.size());

	// Check for each site that it has parsed all residues.
	assertEquals(3, getGroupsInSite(sCif, "CAT"));
	assertEquals(6, getGroupsInSite(sCif, "AC1")); // Site has residue with insertion code.
	assertEquals(6, getGroupsInSite(sCif, "AC2"));
	assertEquals(14, getGroupsInSite(sCif, "AC3"));
	assertEquals(14, getGroupsInSite(sCif, "AC4"));

}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
private void checkPDB(String pdbId, String organismTaxId) throws IOException, StructureException {
	Structure s = StructureIO.getStructure(pdbId);

	assertNotNull(s.getEntityInfos());
	assertTrue(s.getEntityInfos().size() > 0);

	for ( EntityInfo c : s.getEntityInfos()) {
		if(EntityType.POLYMER.equals(c.getType())) { 
			assertNotNull(c.getOrganismTaxId());
			if(pdbId.equals("3zd6")){
				if(c.getMolId()==2) {
					assertEquals(c.getOrganismTaxId(), "32630");
					continue;
				}
			}
			assertEquals(c.getOrganismTaxId(), organismTaxId);
		
		}
	}

}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/**
 * Test that we can round trip a simple structure.
 * @throws IOException an error reading the file
 * @throws StructureException an error parsing the structure
 */
@Test
public void testRoundTrip() throws IOException, StructureException {
	AtomCache cache = new AtomCache();
	cache.setUseMmCif(true);
	ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());
	
	
	StructureIO.setAtomCache(cache);
	Structure structure = StructureIO.getStructure("4CUP");
	AdapterToStructureData writerToEncoder = new AdapterToStructureData();
	new MmtfStructureWriter(structure, writerToEncoder);
	MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
	new StructureDataToAdapter(writerToEncoder, mmtfStructureReader);
	assertTrue(checkIfAtomsSame(structure,mmtfStructureReader.getStructure()));
}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
@Test
public void testLigandConnections()throws IOException, StructureException {
	AtomCache cache = new AtomCache();
	// This needs MMCIF
	cache.setUseMmCif(true);
	StructureIO.setAtomCache(cache);

	cache.setUseMmCif(true);
	ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());

	FileParsingParameters params = cache.getFileParsingParams();
	params.setCreateAtomBonds(true);
	StructureIO.setAtomCache(cache);

	Structure sCif = StructureIO.getStructure("4HHB");

	//Verify that we have all HEM atoms from the CIF file.
	assertEquals( HEM_COUNT_4HHB, countBondedAtomsInLigandGroups(sCif) );

}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
@Test
public void testMultipleConformations()throws IOException, StructureException {
	AtomCache cache = new AtomCache();
	// This needs MMCIF
	cache.setUseMmCif(true);
	StructureIO.setAtomCache(cache);

	cache.setUseMmCif(true);
	ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());

	FileParsingParameters params = cache.getFileParsingParams();
	params.setCreateAtomBonds(true);
	StructureIO.setAtomCache(cache);

	Structure sCif = StructureIO.getStructure("3UCB");


	//Verify that we have all atoms from all conformations of the ligands

	assertEquals(ATOM_COUNT_3UCB, countBondedAtomsInLigandGroups(sCif));
}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
public static void main(String[] args){
	try {

		Structure struc = StructureIO.getStructure("1aoi");

		StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();

		jmolPanel.setStructure(struc);

		// send some RASMOL style commands to Jmol
		jmolPanel.evalString("select * ; color chain;");
		jmolPanel.evalString("select nucleic; cartoon on;");
		jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on;  ");
	} catch (Exception e){
		e.printStackTrace();
	}
}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/**
 * An NMR multi-model entry: 1B4C
 * 
 * @throws StructureException
 * @throws IOException
 */
@Test
public void testNMR() throws IOException, StructureException {

	// as of mmCIF v5 there's no bioassemblies for NMR entries, so now we use the AU (bioassembly 0) - JD 2017-08-02
	Structure pdb = StructureIO.getStructure("BIO:1b4c:0");

	SubunitClustererParameters clusterParams = new SubunitClustererParameters();
	QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
	QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
			pdb, symmParams, clusterParams);

	// C2 symmetry non pseudosymmetric
	assertEquals("C2", symmetry.getSymmetry());
	assertEquals("A2", symmetry.getStoichiometry());
	assertFalse(symmetry.isPseudoStoichiometric());

}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/** 
 * Test a dihedral symmetry: 2VML 
 */
@Test
public void testDihedral() throws IOException, StructureException {

	Structure pdb = StructureIO.getStructure("BIO:2vml:1");

	SubunitClustererParameters clusterParams = new SubunitClustererParameters();
	clusterParams.setClustererMethod(SubunitClustererMethod.SEQUENCE);
	QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
	QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
			pdb, symmParams, clusterParams);

	// D3 symmetry non pseudosymmetric
	assertEquals("D3", symmetry.getSymmetry());
	assertEquals("A6B6", symmetry.getStoichiometry());
	assertFalse(symmetry.isPseudoStoichiometric());


}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/**
 * A structure with combined internal and quaternary symmetry: 4E3E
 * 
 * @throws IOException
 * @throws StructureException
 */
@Test
public void testInternalSymmetry() throws IOException, StructureException {

	Structure pdb = StructureIO.getStructure("BIO:4e3e:1");

	// Internal symmetry analysis, use structural clustering
	SubunitClustererParameters cp = new SubunitClustererParameters();
	cp.setClustererMethod(SubunitClustererMethod.STRUCTURE);
	cp.setInternalSymmetry(true);
	cp.setStructureCoverageThreshold(0.75); // Lower coverage for internal symm

	QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
	QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
			pdb, symmParams, cp);

	// D2 combined internal and quaternary symmetry
	assertEquals("D3", symmetry.getSymmetry());
	assertEquals("A6", symmetry.getStoichiometry());

}
 

import org.biojava.nbio.structure.StructureIO; //导入依赖的package包/类
/**
 * A structure with helical symmetry: 1B47
 * 
 * @throws IOException
 * @throws StructureException
 */
@Test
public void testHelical() throws IOException, StructureException {

	Structure pdb = StructureIO.getStructure("BIO:1B47:1");

	SubunitClustererParameters cp = new SubunitClustererParameters();
	QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
	QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
			pdb, symmParams, cp);

	// H symmetry A3 stoichiometry
	assertEquals("H", symmetry.getSymmetry());
	assertEquals("A3", symmetry.getStoichiometry());

}