Java Code Examples for org.biojava.nbio.structure.Structure#addChain()

/**
 * Adds a chain to the given structure to form a biological assembly,
 * adding the symmetry expanded chains as new models per transformId.
 * @param s
 * @param newChain
 * @param transformId
 */
private void addChainMultiModel(Structure s, Chain newChain, String transformId) {

	// multi-model bioassembly

	if ( modelIndex.size() == 0)
		modelIndex.add("PLACEHOLDER FOR ASYM UNIT");

	int modelCount = modelIndex.indexOf(transformId);
	if ( modelCount == -1)  {
		modelIndex.add(transformId);
		modelCount = modelIndex.indexOf(transformId);
	}

	if (modelCount == 0) {
		s.addChain(newChain);
	} else if (modelCount > s.nrModels()) {
		List<Chain> newModel = new ArrayList<>();
		newModel.add(newChain);
		s.addModel(newModel);
	} else {
		s.addChain(newChain, modelCount-1);
	}

}
 

/**
 * Test getting the number of groups from a structure.
 */
@Test
public void testGetNumGroups() {
	Structure structure = new StructureImpl();
	Chain chain = new ChainImpl();
	Group groupOne = new  AminoAcidImpl();
	Group groupTwo = new HetatomImpl();
	Group groupThree = new NucleotideImpl();
	structure.addChain(chain);
	chain.addGroup(groupOne);
	chain.addGroup(groupTwo);
	chain.addGroup(groupThree);
	assertEquals(3,MmtfUtils.getNumGroups(structure));
}
 

/**
 * Test that getting the structure data info works.
 */
@Test
public void testGetStructureInfo() {
	Structure structure = new StructureImpl();
	Chain chain = new ChainImpl();
	chain.setId("A");
	Map<String,Integer> testMap = new HashMap<>();
	testMap.put("A", 0);
	List<Chain> chainList = new ArrayList<>();
	chainList.add(chain);
	Group group = new AminoAcidImpl();
	chain.addGroup(group);
	Atom atomOne = new AtomImpl();
	Atom atomTwo = new AtomImpl();
	List<Atom> atomList = new ArrayList<>();
	atomList.add(atomOne);
	atomList.add(atomTwo);
	new BondImpl(atomOne, atomTwo, 1);
	structure.addChain(chain);
	group.addAtom(atomOne);
	group.addAtom(atomTwo);
	// Get the structure
	MmtfSummaryDataBean mmtfSummaryDataBean = MmtfUtils.getStructureInfo(structure);
	assertEquals(mmtfSummaryDataBean.getAllAtoms(), atomList);
	assertEquals(testMap, mmtfSummaryDataBean.getChainIdToIndexMap());
	assertEquals(chainList, mmtfSummaryDataBean.getAllChains());
	assertEquals(1, mmtfSummaryDataBean.getNumBonds());
}
 

/**
 * Create and set a new structure from a given atom array.
 * @param atoms
 */
public void setAtoms(Atom[] atoms){
	Structure s = new StructureImpl();
	Chain c = new ChainImpl();
	c.setId("A");
	for (Atom a: atoms){
		c.addGroup(a.getGroup());
	}
	s.addChain(c);
	setStructure(s);
}
 

/**
 * Create a mock structure with 2 entities 1 (chains A, B) and 2 (chain C).
 * @return a structure
 */
private Structure mockStructure() {
    Structure structure = new StructureImpl();
    EntityInfo entity1 = new EntityInfo();
    entity1.setMolId(1);
    EntityInfo entity2 = new EntityInfo();
    entity2.setMolId(2);
    structure.addEntityInfo(entity1);
    structure.addEntityInfo(entity2);

    Chain chainA = new ChainImpl();
    chainA.setId("A");
    chainA.setName("A");
    Chain chainB = new ChainImpl();
    chainB.setId("B");
    chainB.setName("B");
    entity1.addChain(chainA);
    entity1.addChain(chainB);
    Chain chainC = new ChainImpl();
    chainC.setId("C");
    chainC.setName("C");
    entity2.addChain(chainC);

    structure.addChain(chainA);
    structure.addChain(chainB);
    structure.addChain(chainC);

    // entity 1: chain A 10 observed residues, chain B 9 observed residues (first unobserved)
    List<Group> aGroups = getGroupList(10, "ALA", chainA, new Point3d(0,0,0));
    chainA.setAtomGroups(new ArrayList<>(aGroups));
    chainA.setSeqResGroups(aGroups);
    chainA.setEntityInfo(entity1);

    List<Group> bGroups = getGroupList(10, "ALA", chainB, new Point3d(4, 0, 0));
    chainB.setAtomGroups(new ArrayList<>(bGroups.subList(1,10)));
    chainB.setSeqResGroups(bGroups);
    chainB.setEntityInfo(entity1);

    List<Group> cGroups = getGroupList(20, "GLY", chainC, new Point3d(0, 4, 0));
    chainC.setAtomGroups(new ArrayList<>(cGroups));
    chainC.setSeqResGroups(cGroups);
    chainC.setEntityInfo(entity2);

    return structure;
}
 

/**
 * Create a mock structure with 2 entities 1 (chains A, B) and 2 (chain C).
 * @return a structure
 */
private Structure mockStructure() {
	Structure structure = new StructureImpl();
	EntityInfo entity1 = new EntityInfo();
	entity1.setMolId(1);
	EntityInfo entity2 = new EntityInfo();
	entity2.setMolId(2);
	structure.addEntityInfo(entity1);
	structure.addEntityInfo(entity2);

	Chain chainA = new ChainImpl();
	chainA.setId("A");
	Chain chainB = new ChainImpl();
	chainB.setId("B");
	entity1.addChain(chainA);
	entity1.addChain(chainB);
	Chain chainC = new ChainImpl();
	chainC.setId("C");
	entity2.addChain(chainC);

	structure.addChain(chainA);
	structure.addChain(chainB);
	structure.addChain(chainC);

	// entity 1: chain A 10 observed residues, chain B 9 observed residues (first unobserved)
	List<Group> aGroups = getGroupList(10, "ALA", chainA);
	chainA.setAtomGroups(new ArrayList<>(aGroups));
	chainA.setSeqResGroups(aGroups);
	chainA.setEntityInfo(entity1);

	List<Group> bGroups = getGroupList(10, "ALA", chainB);
	chainB.setAtomGroups(new ArrayList<>(bGroups.subList(1,10)));
	chainB.setSeqResGroups(bGroups);
	chainB.setEntityInfo(entity1);

	List<Group> cGroups = getGroupList(20, "GLY", chainC);
	chainC.setAtomGroups(new ArrayList<>(cGroups));
	chainC.setSeqResGroups(cGroups);
	chainC.setEntityInfo(entity2);

	return structure;
}
 

private static Structure createDummyStructure() {
	Group g = new AminoAcidImpl();
	Atom a = getAtom("CA", Element.C, 1, 1, 1, 1);
	g.addAtom(a);
	g.setResidueNumber(new ResidueNumber("A", 1, null));
	Group altLocG = new AminoAcidImpl();
	Atom a2 = getAtom("CA", Element.C, 2, 2, 2, 2);
	altLocG.addAtom(a2);
	altLocG.setResidueNumber(new ResidueNumber("A", 1, null));

	g.addAltLoc(altLocG);

	Chain c1 = new ChainImpl();
	c1.addGroup(g);
	c1.setId("A");
	EntityInfo entityInfo = new EntityInfo();
	entityInfo.setMolId(1);
	entityInfo.addChain(c1);
	c1.setEntityInfo(entityInfo);

	Group gc2 = new AminoAcidImpl();
	Atom ac2 = getAtom("CA", Element.C, 3, 3, 3, 3);
	gc2.addAtom(ac2);
	gc2.setResidueNumber(new ResidueNumber("A_1", 1, null));

	Group altLocGc2 = new AminoAcidImpl();
	Atom ac22 = getAtom("CA", Element.C, 4, 4, 4, 4);
	altLocGc2.addAtom(ac22);
	altLocGc2.setResidueNumber(new ResidueNumber("A_1", 1, null));

	gc2.addAltLoc(altLocGc2);

	Chain c2 = new ChainImpl();
	c2.addGroup(gc2);
	c2.setId("A_1");
	c2.setEntityInfo(entityInfo);
	entityInfo.addChain(c2);

	Structure s = new StructureImpl();
	s.addChain(c1);
	s.addChain(c2);
	return s;
}
 

/**
 * Test the writing of Structure objects to a file.
 * @throws IOException
 */
@Test
public void testWrite() throws IOException {

	// Create a structure
	Structure structure = new StructureImpl();

	// Add some header information
	PDBHeader pdbHeader = new PDBHeader();
	pdbHeader.setExperimentalTechnique("X-RAY DIFFRACTION");
	structure.setPDBHeader(pdbHeader);

	// Create one chain
	structure.setEntityInfos(new ArrayList<EntityInfo>());
	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);

	// Create one Atom
	Atom atom = new AtomImpl();
	atom.setName("A");
	atom.setElement(Element.Ag);
	atom.setCoords(new double[] { 1.0, 2.0, 3.0 });

	// Link together the objects
	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());
}
 

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;
}
 

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;
}
 

private static Structure createDummyStructure() {
    Group g = new AminoAcidImpl();
    Atom a = getAtom("CA", Element.C, 1, 1, 1, 1);
    g.addAtom(a);
    g.setResidueNumber(new ResidueNumber("A", 1, null));
    Group altLocG = new AminoAcidImpl();
    Atom a2 = getAtom("CA", Element.C, 2, 2, 2, 2);
    altLocG.addAtom(a2);
    altLocG.setResidueNumber(new ResidueNumber("A", 1, null));

    g.addAltLoc(altLocG);

    Chain c1 = new ChainImpl();
    c1.addGroup(g);
    c1.setId("A");
    EntityInfo entityInfo = new EntityInfo();
    entityInfo.setMolId(1);
    entityInfo.addChain(c1);
    c1.setEntityInfo(entityInfo);

    Group gc2 = new AminoAcidImpl();
    Atom ac2 = getAtom("CA", Element.C, 3, 3, 3, 3);
    gc2.addAtom(ac2);
    gc2.setResidueNumber(new ResidueNumber("A_1", 1, null));

    Group altLocGc2 = new AminoAcidImpl();
    Atom ac22 = getAtom("CA", Element.C, 4, 4, 4, 4);
    altLocGc2.addAtom(ac22);
    altLocGc2.setResidueNumber(new ResidueNumber("A_1", 1, null));

    gc2.addAltLoc(altLocGc2);

    Chain c2 = new ChainImpl();
    c2.addGroup(gc2);
    c2.setId("A_1");
    c2.setEntityInfo(entityInfo);
    entityInfo.addChain(c2);

    Structure s = new StructureImpl();
    s.addChain(c1);
    s.addChain(c2);
    return s;
}
 

/**
 * Adds a chain to the given structure to form a biological assembly,
 * adding the symmetry-expanded chains as new chains with renamed
 * chain ids and names (in the form originalAsymId_transformId and originalAuthId_transformId).
 * @param s
 * @param newChain
 * @param transformId
 */
private void addChainFlattened(Structure s, Chain newChain, String transformId) {
	newChain.setId(newChain.getId()+SYM_CHAIN_ID_SEPARATOR+transformId);
	newChain.setName(newChain.getName()+SYM_CHAIN_ID_SEPARATOR+transformId);
	s.addChain(newChain);
}