Examples with StructureToProteinDimers edu.sdsc.mmtf.spark.mappers.StructureToProteinDimers used on opensource projects

Example 1 with StructureToProteinDimers

use of edu.sdsc.mmtf.spark.mappers.StructureToProteinDimers in project mmtf-spark by sbl-sdsc.

the class MapToProteinDimers method main.

public static void main(String[] args) {
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(MapToProteinDimers.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    // single protein chain 5IBZ
    List<String> pdbIds = Arrays.asList("5IBZ");
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.downloadFullMmtfFiles(pdbIds, sc);
    // if distance between C-beta atoms is less than the cutoff distance, two chains are considered in contact
    double cutoffDistance = 8;
    // minimum number of contacts to qualify as an interaction
    int minContacts = 20;
    pdb = // convert to bioassembly (homotetramer with D2 symmetry)
    pdb.flatMapToPair(new StructureToBioassembly()).flatMapToPair(// find all dimers with in bioassembly
    new StructureToProteinDimers(cutoffDistance, minContacts));
    System.out.println("Number of dimers in 5IBZ bioassembly: " + pdb.count());
    sc.close();
}