Examples with Rfree edu.sdsc.mmtf.spark.filters.Rfree used on opensource projects

Example 1 with Rfree

use of edu.sdsc.mmtf.spark.filters.Rfree in project mmtf-spark by sbl-sdsc.

the class WriteMmtfCustom method main.

/**
 * @param args
 * @throws FileNotFoundException
 */
public static void main(String[] args) throws FileNotFoundException {
    String path = MmtfReader.getMmtfFullPath();
    long start = System.nanoTime();
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(WriteMmtfCustom.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    // read a 20% random sample of the PDB
    double fraction = 0.2;
    long seed = 123;
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.readSequenceFile(path, fraction, seed, sc);
    // retain high resolution X-ray structures
    pdb = pdb.filter(new ExperimentalMethods(ExperimentalMethods.X_RAY_DIFFRACTION)).filter(new Resolution(0, 2.0)).filter(new Rfree(0, 0.2));
    // coalesce this into 8 partitions to avoid creating many small files
    pdb = pdb.coalesce(8);
    // save this subset in a Hadoop Sequence file
    MmtfWriter.writeSequenceFile(path + "_xray", sc, pdb);
    System.out.println("# structures in custom set: " + pdb.count());
    long end = System.nanoTime();
    System.out.println("Time: " + (end - start) / 1E9 + "sec.");
    sc.close();
}