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Java Structure.setPDBHeader方法代码示例

本文整理汇总了Java中org.biojava.nbio.structure.Structure.setPDBHeader方法的典型用法代码示例。如果您正苦于以下问题:Java Structure.setPDBHeader方法的具体用法?Java Structure.setPDBHeader怎么用?Java Structure.setPDBHeader使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在org.biojava.nbio.structure.Structure的用法示例。


在下文中一共展示了Structure.setPDBHeader方法的5个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Java代码示例。

示例1: getMetaModel

import org.biojava.nbio.structure.Structure; //导入方法依赖的package包/类
@Override
public Structure getMetaModel() throws InvalidParameterException, InvalidInputException {
    try {
        Structure structure = (Structure) getStructure();
        PDBHeader pdbHeader = new PDBHeader();
        pdbHeader.setTitle(inputParser.getTitleFromFile(getInputFile()));
        PDBCrystallographicInfo pdbCrystallographicInfo = new PDBCrystallographicInfo();
        List<Chain> modelFromFile = inputParser.getModelFromFile(getInputFile());
        structure.setModel(0, modelFromFile);

        pdbCrystallographicInfo.setSpaceGroup(new SpaceGroup(0, 1, 1, "P 1", "P 1", BravaisLattice.CUBIC));
        CrystalCell crystalCell = pdbCrystallographicInfo.getSpaceGroup().getBravLattice().getExampleUnitCell();
        //call always after getModelFromFile --> box calculation
        inputParser.getCrystlCell(getInputFile(), crystalCell);
        pdbCrystallographicInfo.setCrystalCell(crystalCell);
        pdbHeader.setCrystallographicInfo(pdbCrystallographicInfo);

        structure.setPDBHeader(pdbHeader);
        return structure;
    } catch (IOException e) {
        getConsoleHandler().printErrorln(e.getMessage());
        throw new InvalidInputException(getName() + " wasn't able to parse input file!");
    }
}
 
开发者ID:ccaleman,项目名称:MDConverter,代码行数:25,代码来源:GromacsReader.java

示例2: toMultimodelStructure

import org.biojava.nbio.structure.Structure; //导入方法依赖的package包/类
public static Structure toMultimodelStructure(MultipleAlignment multAln, List<Atom[]> transformedAtoms) throws StructureException {
	PDBHeader header = new PDBHeader();
	String title = multAln.getEnsemble().getAlgorithmName() + " V."
			+ multAln.getEnsemble().getVersion() + " : ";

	for (StructureIdentifier name : multAln.getEnsemble()
			.getStructureIdentifiers()) {
		title += name.getIdentifier() + " ";
	}
	Structure artificial = getAlignedStructure(transformedAtoms);

	artificial.setPDBHeader(header);
	header.setTitle(title);
	return artificial;
}
 
开发者ID:biojava,项目名称:biojava,代码行数:16,代码来源:MultipleAlignmentTools.java

示例3: testWrite

import org.biojava.nbio.structure.Structure; //导入方法依赖的package包/类
/**
 * Test the writing of Structure objects to a file.
 * @throws IOException 
 */
@Test
public void testWrite() throws IOException {
	Structure structure = new StructureImpl();
	PDBHeader pdbHeader = new PDBHeader();
	pdbHeader.setExperimentalTechnique("X-RAY DIFFRACTION");
	structure.setEntityInfos(new ArrayList<EntityInfo>());
	structure.setPDBHeader(pdbHeader);
	Chain chain = new ChainImpl();
	chain.setId("A");
	chain.setName("A");
	Group group = new AminoAcidImpl(); 
	group.setPDBName("FKF");
	ChemComp chemComp = new ChemComp();
	chemComp.setType("TYPfdl");
	chemComp.setOne_letter_code("A");
	group.setChemComp(chemComp);
	Atom atom = new AtomImpl();
	atom.setName("A");
	atom.setElement(Element.Ag);
	atom.setCoords(new double[] {1.0,2.0,3.0});
	chain.addGroup(group);
	group.addAtom(atom);
	ResidueNumber residueNumber = new ResidueNumber();
	residueNumber.setInsCode('A');
	residueNumber.setSeqNum(100);
	group.setResidueNumber(residueNumber);
	structure.addChain(chain);
	File tempFile = testFolder.newFile("tmpfile");
	MmtfActions.writeToFile(structure, tempFile.toPath());		
}
 
开发者ID:biojava,项目名称:biojava,代码行数:35,代码来源:TestBasicMmtf.java

示例4: fromPDB

import org.biojava.nbio.structure.Structure; //导入方法依赖的package包/类
private Structure fromPDB(JTextField f, JTextField c) throws StructureException{
	String pdb = f.getText();


	if ( pdb.length() < 4) {
		f.setText("!!!");
		return null;
	}

	String chain = c.getText();
	if ( debug )
		System.out.println("file :" + pdb + " " +  chain);
	/// prepare structures

	// load them from the file system

	PDBFileReader reader = new PDBFileReader();

	reader.setPath(".");

	Structure tmp1 = new StructureImpl();

	try {
		Structure structure1 = reader.getStructureById(pdb);

		// no chain has been specified
		// return whole structure
		if (( chain == null) || (chain.length()==0)){
			return structure1;
		}
		if ( debug)
			System.out.println("using chain " + chain +  " for structure " + structure1.getPDBCode());
		Chain c1 = structure1.findChain(chain);
		tmp1.setPDBCode(structure1.getPDBCode());
		tmp1.setPDBHeader(structure1.getPDBHeader());
		tmp1.setPDBCode(structure1.getPDBCode());
		tmp1.addChain(c1);
		System.out.println("ok");

	} catch (IOException e){
		logger.warn(e.getMessage());
		throw new StructureException(e);
	}
	return tmp1;
}
 
开发者ID:biojava,项目名称:biojava,代码行数:46,代码来源:PDBServerPanel.java

示例5: fromPDB

import org.biojava.nbio.structure.Structure; //导入方法依赖的package包/类
private Structure fromPDB(JTextField f, JTextField c) throws StructureException{
	String pdb = f.getText();


	if ( pdb.length() < 4) {
		f.setText("!!!");
		return null;
	}

	String chain = c.getText();
	if ( debug )
		System.out.println("file :" + pdb + " " +  chain);
	/// prepare structures

	// load them from the file system



	String dir = pdbDir.getText();
	PDBFileReader reader = new PDBFileReader(dir);

	if ( debug )
		System.out.println("dir: " + dir);

	Structure tmp1 = new StructureImpl();

	try {
		Structure structure1 = reader.getStructureById(pdb);

		// no chain has been specified
		// return whole structure
		if (( chain == null) || (chain.length()==0)){
			return structure1;
		}
		if ( debug)
			System.out.println("using chain " + chain +  " for structure " + structure1.getPDBCode());
		Chain c1 = structure1.findChain(chain);
		tmp1.setPDBCode(structure1.getPDBCode());
		tmp1.setPDBHeader(structure1.getPDBHeader());
		tmp1.setPDBCode(structure1.getPDBCode());
		tmp1.addChain(c1);
		System.out.println("ok");

	} catch (IOException e){
		logger.warn(e.getMessage());
		throw new StructureException(e);
	}
	return tmp1;
}
 
开发者ID:biojava,项目名称:biojava,代码行数:50,代码来源:PDBDirPanel.java


注:本文中的org.biojava.nbio.structure.Structure.setPDBHeader方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。