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

/**
 * 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;
}
 

/**
 * Set up the configuration parameters for BioJava.
 * @param extraUrl the string describing the URL (or file path) from which
 * to get missing CCD entries.
 */
public static AtomCache setUpBioJava(String extraUrl) {
	// 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.serverBaseUrl = extraUrl;
	DownloadChemCompProvider.useDefaultUrlLayout = false;
	DownloadChemCompProvider cc = new DownloadChemCompProvider();
	ChemCompGroupFactory.setChemCompProvider(cc);
	cc.checkDoFirstInstall();
	cache.setFileParsingParams(params);
	StructureIO.setAtomCache(cache);
	return cache;
}
 

/**
 * Actually perform the test to see all alt locs are the same size as the main group
 * @throws StructureException
 * @throws IOException
 *
 */
private void doTestAllAltLocsSamAtomsMainGroup(String pdbId) throws IOException, StructureException {
	AtomCache cache = new AtomCache();
	FileParsingParameters params = new FileParsingParameters();
	params.setAlignSeqRes(true);
	params.setCreateAtomBonds(true);
	cache.setFileParsingParams(params);
	StructureIO.setAtomCache(cache);
	Structure structure = StructureIO.getStructure(pdbId);
	// Loop through the atoms
	for ( Chain c: structure.getChains()){
		for (Group g: c.getAtomGroups()){

			for (Group altLocGroup:g.getAltLocs()) {
				assertEquals(g.size(), altLocGroup.size());
			}
		}
	}
}
 

@BeforeClass
public static void setUp() throws IOException {
	InputStream inStream = StructureTest.class.getResourceAsStream("/5pti_old.pdb");
	assertNotNull(inStream);

	PDBFileParser pdbpars = new PDBFileParser();
	FileParsingParameters params = new FileParsingParameters();
	params.setAlignSeqRes(true);
	params.setCreateAtomBonds(true);
	pdbpars.setFileParsingParameters(params);

	structure = pdbpars.parsePDBFile(inStream) ;

	assertNotNull(structure);

	assertEquals("structure does not contain one chain ", 1 ,structure.size());
}
 

@Test @Ignore
public void test4v5aInternalChainIds() throws StructureException, IOException {
	AtomCache cache = new AtomCache();

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


	// this would throw an exception when making ss bonds from struct_conn because
	// chain id "AD" is both an author chain id and an asym chain id and the chains were
	// getting mixed
	StructureIO.getStructure("4v5a");

	//for (Chain c : s.getChains()) {
	//	System.out.println(c.getChainID()+" "+c.getInternalChainID()+" "+c.getAtomLength());
	//}


}
 

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

	final AtomCache cache = new AtomCache();
	cache.setUseMmCif(true);

	final FileParsingParameters params = cache.getFileParsingParams();
	params.setCreateAtomBonds(true);
	cache.setFileParsingParams(params);

	final Structure s = cache.getStructure("2I13");
	List<Bond> bonds = s.getNonPolyChain("G").getAtomGroup(0).getAtom(0).getBonds();
	assertNotNull(bonds);

	Structure s2 = s.clone();
	List<Bond> bonds2 = s2.getNonPolyChain("G").getAtomGroup(0).getAtom(0).getBonds();
	assertNotNull(bonds2);

	assertEquals(bonds.toString(), bonds2.toString());
	// But the objects should be different as the atoms are clones
	assertNotEquals(bonds.toArray(), bonds2.toArray());

	// Also test for polymeric chains
	bonds = s.getPolyChain("E").getAtomGroup(0).getAtom(0).getBonds();
	assertNotNull(bonds);

	s2 = s.clone();
	bonds2 = s2.getPolyChain("E").getAtomGroup(0).getAtom(0).getBonds();
	assertNotNull(bonds2);
}
 

@BeforeClass
public static void setUp() {

	// important: without this the tests can fail when running in maven (but not in IDE)
	// that's because it depends on the order on how tests were run - JD 2018-03-10
	ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());

	cache = new AtomCache();

	cache.setUseMmCif(true);

	FileParsingParameters params = cache.getFileParsingParams();

	params.setAlignSeqRes(true);
	params.setCreateAtomBonds(true);

	StructureIO.setAtomCache(cache);


}
 

/**
 * A test that adding bonds to atoms between groups - doesn't change the size of the groups
 * @throws StructureException
 * @throws IOException
 */
@Test
public void testAddBondsDoesntChangeGroups() throws IOException, StructureException {
	AtomCache cache = new AtomCache();
	FileParsingParameters params = new FileParsingParameters();
	params.setAlignSeqRes(true);
	params.setCreateAtomBonds(true);
	cache.setFileParsingParams(params);
	StructureIO.setAtomCache(cache);
	Structure structure = StructureIO.getStructure("4CUP");
	// Loop through and find
	for (Chain chain : structure.getChains()) {
		List<Group> groups = chain.getAtomGroups();

		for (Group mainGroup : groups) {
			// atoms with no residue number don't have atom information
			if (mainGroup.getResidueNumber() == null) {
				continue;
			}
			if (mainGroup.getAltLocs().isEmpty()) {
				continue;
			}
			int oldSize = mainGroup.size();
			// Now add support for altLocGroup
			List<Atom> atomsList = new ArrayList<>(mainGroup.getAtoms());
			for(Group altLocOne: mainGroup.getAltLocs()){
				for(Atom atomAltLocOne: altLocOne.getAtoms()){
					atomsList.add(atomAltLocOne);
				}
			}
			// Get the chem copm
			ChemComp aminoChemComp = ChemCompGroupFactory.getChemComp(mainGroup
					.getPDBName());
			// Now iterate through this list
			for(Atom atomA : atomsList){

				for (ChemCompBond chemCompBond : aminoChemComp.getBonds()) {

					//
					if(chemCompBond.getAtom_id_1().equals(atomA.getName())){
						// Get the other atom in the group
						for(Atom atomB : atomsList) {
							if(chemCompBond.getAtom_id_2().equals(atomB.getName())){
								int bondOrder = chemCompBond.getNumericalBondOrder();
								new BondImpl(atomA, atomB, bondOrder);
							}
						}
					}
				}
			}
			assertEquals(oldSize, mainGroup.size());
		}
	}
}
 

/**
 * Find all of the inter group bonds in a structure.
 *
 * @param pdbId the pdb id of the structure to determine
 * @return the number of inter group bonds (double counted) in a structure
 * @throws IOException
 * @throws StructureException
 */
public int getInterBonds(String pdbId) throws IOException, StructureException {

	// Download parameters
	AtomCache cache = new AtomCache();
	cache.setUseMmCif(true);
	cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
	FileParsingParameters params = cache.getFileParsingParams();
	params.setCreateAtomBonds(true);
	params.setAlignSeqRes(true);
	params.setParseBioAssembly(true);
	DownloadChemCompProvider dcc = new DownloadChemCompProvider();
	ChemCompGroupFactory.setChemCompProvider(dcc);
	dcc.checkDoFirstInstall();
	cache.setFileParsingParams(params);
	StructureIO.setAtomCache(cache);

	// Get the structure
	Structure newStruc = StructureIO.getStructure(pdbId);

	int counter =0;

	// Loop through the atoms and count the bonds
	for(Chain c: newStruc.getChains()){
		for(Group g: c.getAtomGroups()){
			List<Atom> theseAtoms = g.getAtoms();
			for(Atom a: theseAtoms){
				List<Bond> theseBonds = a.getBonds();
				if(theseBonds != null){
					for(Bond b: a.getBonds()){
						Atom other = b.getOther(a);
						int indexOther = theseAtoms.indexOf(other);
						// Check if the index is within the group
						if(indexOther<0 || indexOther >= theseAtoms.size()){
							counter++;
						}
					}
				}
			}
		}
	}
	return counter;
}
 

@Test @Ignore
public void test4v5a() throws StructureException, IOException {
	AtomCache cache = new AtomCache();

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

	StructureIO.getStructure("4v5a");


}