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

Example 1 with EntityInfo

use of org.biojava.nbio.structure.EntityInfo 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;
}