Examples with Chain org.biojava.nbio.structure.Chain used on opensource projects

Example 1 with Chain

use of org.biojava.nbio.structure.Chain in project mmtf-spark by sbl-sdsc.

the class MmtfImporter method toStructureDataInterface.

/**
 * Parses PDB-formatted input stream and return structure data.
 *
 * @param inputStream PDB-formatted input stream
 * @param structureId id to be assigned to the structure
 * @return structure data
 * @throws IOException
 */
private static AdapterToStructureData toStructureDataInterface(InputStream inputStream, String structureId) throws IOException {
    // standardize PDB formatting
    InputStream pdbIs = standardizePdbInputStream(inputStream);
    // parse PDB and generate BioJava Structure object
    PDBFileParser parser = new PDBFileParser();
    parser.getFileParsingParameters().setCreateAtomBonds(true);
    Structure struct = parser.parsePDBFile(pdbIs);
    struct.setPDBCode(structureId);
    // where the entity info is null when there is only one polymer chain.
    for (EntityInfo info : struct.getEntityInfos()) {
        if (info.getType() == null) {
            for (String chainId : info.getChainIds()) {
                Chain c = struct.getChain(chainId);
                if (c.getAtomSequence().length() > 0) {
                    info.setType(EntityType.POLYMER);
                }
            }
        }
    }
    pdbIs.close();
    // convert to MMTF
    AdapterToStructureData writerToEncoder = new AdapterToStructureData();
    // TODO get version number
    writerToEncoder.setMmtfProducer("mmtf-spark 0.2.0");
    new MmtfStructureWriter(struct, writerToEncoder);
    return writerToEncoder;
}

Example 2 with Chain

use of org.biojava.nbio.structure.Chain in project mm-dev by sbl-sdsc.

the class BiojavaAligner method getCAAtoms.

/**
 * Converts an array of points representing C-alpha position to a minimal BioJava data structure.
 *
 * @param points coordinates of C-alpha atoms
 * @return BioJava atom array
 */
private static Atom[] getCAAtoms(Point3d[] points) {
    Chain c = new ChainImpl();
    c.setId("A");
    // create dummy BioJava atoms for each C-alpha coordinate
    Atom[] atoms = new Atom[points.length];
    for (int i = 0; i < points.length; i++) {
        atoms[i] = new AtomImpl();
        atoms[i].setName(CA_NAME);
        Group g = new AminoAcidImpl();
        g.setPDBName(GROUP_NAME);
        g.setResidueNumber("A", i, ' ');
        g.addAtom(atoms[i]);
        c.addGroup(g);
        atoms[i].setX(points[i].x);
        atoms[i].setY(points[i].y);
        atoms[i].setZ(points[i].z);
    }
    return atoms;
}