Examples with StructureDataInterface org.rcsb.mmtf.api.StructureDataInterface used on opensource projects

Example 1 with StructureDataInterface

use of org.rcsb.mmtf.api.StructureDataInterface in project mm-dev by sbl-sdsc.

the class DemoAllVsAll_cluster method main.

public static void main(String[] args) throws IOException {
    String path = MmtfReader.getMmtfReducedPath();
    long start = System.nanoTime();
    SparkConf conf = new SparkConf();
    JavaSparkContext sc = new JavaSparkContext(conf);
    // Read PDB and create a Pisces non-redundant set at 20% sequence identity and a resolution better than 1.6 A.
    // Then take a 1% random sample.
    double fraction = 0.01;
    // optional command line argument
    if (args.length == 1) {
        fraction = Double.parseDouble(args[0]);
    }
    long seed = 123;
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.readSequenceFile(path, sc).flatMapToPair(new StructureToPolymerChains()).filter(new Pisces(20, 1.6)).sample(false, fraction, seed);
    System.out.println(pdb.count());
    // run the structural alignment
    String algorithmName = FatCatRigid.algorithmName;
    Dataset<Row> alignments = StructureAligner.getAllVsAllAlignments(pdb, algorithmName).cache();
    // show results
    int count = (int) alignments.count();
    alignments.show(count);
    System.out.println("Pairs: " + count);
    long end = System.nanoTime();
    System.out.println("Time per alignment: " + TimeUnit.NANOSECONDS.toMillis((end - start) / count) + " msec.");
    System.out.println("Time: " + TimeUnit.NANOSECONDS.toSeconds(end - start) + " sec.");
    sc.close();
}

Example 2 with StructureDataInterface

use of org.rcsb.mmtf.api.StructureDataInterface in project mm-dev by sbl-sdsc.

the class DemoQueryVsAll method main.

public static void main(String[] args) throws IOException {
    String path = MmtfReader.getMmtfReducedPath();
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(DemoQueryVsAll.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    long start = System.nanoTime();
    // download query structure
    List<String> queryId = Arrays.asList("2W47");
    JavaPairRDD<String, StructureDataInterface> query = MmtfReader.downloadFullMmtfFiles(queryId, sc).flatMapToPair(new StructureToPolymerChains());
    // use a 1 % sample of the PDB and then filter by the Pisces
    // non-redundant set
    // at 20% sequence identity and a resolution better than 1.6 A.
    double fraction = 1.0;
    long seed = 123;
    JavaPairRDD<String, StructureDataInterface> target = MmtfReader.readSequenceFile(path, fraction, seed, sc).flatMapToPair(new StructureToPolymerChains()).filter(new Pisces(20, 1.6)).sample(false, 0.08, seed);
    // specialized algorithms
    // String alignmentAlgorithm = CeMain.algorithmName;
    // String alignmentAlgorithm = CeCPMain.algorithmName;
    // String alignmentAlgorithm = FatCatFlexible.algorithmName;
    // two standard algorithms
    // String alignmentAlgorithm = CeMain.algorithmName;
    String alignmentAlgorithm = FatCatRigid.algorithmName;
    // String alignmentAlgorithm = ExhaustiveAligner.alignmentAlgorithm;
    // calculate alignments
    Dataset<Row> alignments = StructureAligner.getQueryVsAllAlignments(query, target, alignmentAlgorithm).cache();
    // show results
    int count = (int) alignments.count();
    alignments.sort(col("tm").desc()).show(count);
    System.out.println("Pairs: " + count);
    long end = System.nanoTime();
    System.out.println("Time per alignment: " + TimeUnit.NANOSECONDS.toMillis((end - start) / count) + " msec.");
    System.out.println("Time: " + TimeUnit.NANOSECONDS.toSeconds(end - start) + " sec.");
    sc.close();
}

Example 3 with StructureDataInterface

use of org.rcsb.mmtf.api.StructureDataInterface in project mm-dev by sbl-sdsc.

the class StructureAligner method getAllVsAllAlignments.

/**
 * Calculates all vs. all structural alignments of protein chains using the
 * specified alignment algorithm. The input structures must contain single
 * protein chains.
 *
 * @param targets structures containing single protein chains
 * @param alignmentAlgorithm name of the algorithm
 * @return dataset with alignment metrics
 */
public static Dataset<Row> getAllVsAllAlignments(JavaPairRDD<String, StructureDataInterface> targets, String alignmentAlgorithm) {
    SparkSession session = SparkSession.builder().getOrCreate();
    JavaSparkContext sc = new JavaSparkContext(session.sparkContext());
    // create a list of chainName/ C Alpha coordinates
    List<Tuple2<String, Point3d[]>> chains = targets.mapValues(s -> new ColumnarStructureX(s, true).getcAlphaCoordinates()).collect();
    // create an RDD of all pair indices (0,1), (0,2), ..., (1,2), (1,3), ...
    JavaRDD<Tuple2<Integer, Integer>> pairs = getPairs(sc, chains.size());
    // calculate structural alignments for all pairs.
    // broadcast (copy) chains to all worker nodes for efficient processing.
    // for each pair there can be zero or more solutions, therefore we flatmap the pairs.
    JavaRDD<Row> rows = pairs.flatMap(new StructuralAlignmentMapper(sc.broadcast(chains), alignmentAlgorithm));
    // convert rows to a dataset
    return session.createDataFrame(rows, getSchema());
}

Example 4 with StructureDataInterface

use of org.rcsb.mmtf.api.StructureDataInterface in project mm-dev by sbl-sdsc.

the class MergeMmtf method addEntityInfo.

private static void addEntityInfo(StructureDataInterface[] structures, AdapterToStructureData complex) {
    int currentOffset = 0;
    int offset = 0;
    for (StructureDataInterface structure : structures) {
        for (int i = 0; i < structure.getNumEntities(); i++) {
            int[] indices = structure.getEntityChainIndexList(i).clone();
            // System.out.println("offset: " + offset);
            for (int j = 0; j < indices.length; j++) {
                indices[j] += offset;
                currentOffset = Math.max(currentOffset, indices[j]);
            }
            complex.setEntityInfo(indices, structure.getEntitySequence(i), structure.getEntityDescription(i), structure.getEntityType(i));
        }
        offset = currentOffset + 1;
    }
}

Example 5 with StructureDataInterface

use of org.rcsb.mmtf.api.StructureDataInterface in project mm-dev by sbl-sdsc.

the class MergeMmtf method initStructure.

private static void initStructure(String structureId, StructureDataInterface[] structures, AdapterToStructureData complex) {
    int nBonds = 0;
    int nAtoms = 0;
    int nGroups = 0;
    int nChains = 0;
    int nModels = 1;
    float resolution = -1;
    float rFree = -1;
    float rWork = -1;
    String title = "";
    for (StructureDataInterface s : structures) {
        nBonds += s.getNumBonds();
        nAtoms += s.getNumAtoms();
        nGroups += s.getNumGroups();
        nChains += s.getNumChains();
        resolution = Math.max(resolution, s.getResolution());
        rFree = Math.max(rFree, s.getRfree());
        rWork = Math.max(rFree, s.getRwork());
        title += s.getTitle();
    }
    String[] experimentalMethods = { "THEORETICAL MODEL" };
    complex.setMmtfProducer("mmtf-spark");
    complex.initStructure(nBonds, nAtoms, nGroups, nChains, nModels, structureId);
    complex.setHeaderInfo(rFree, rWork, resolution, title, "20180101", "20180101", experimentalMethods);
    complex.setModelInfo(0, nChains);
}