Examples with Pisces edu.sdsc.mmtf.spark.webfilters.Pisces used on opensource projects

Example 6 with Pisces

use of edu.sdsc.mmtf.spark.webfilters.Pisces in project mmtf-spark by sbl-sdsc.

the class SecondaryStructureElementsWord2VecEncoder method main.

public static void main(String[] args) throws IOException {
    String path = MmtfReader.getMmtfReducedPath();
    if (args.length != 0 && args.length != 2) {
        System.err.println("Usage: " + SecondaryStructureElementsWord2VecEncoder.class.getSimpleName() + " [<outputFilePath> + <fileFormat>]");
        System.exit(1);
    }
    long start = System.nanoTime();
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(SecondaryStructureWord2VecEncoder.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    // read MMTF Hadoop sequence file and create a non-redundant Pisces
    // subset set (<=20% seq. identity) of L-protein chains
    int sequenceIdentity = 20;
    double resolution = 3.0;
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.readSequenceFile(path, sc).flatMapToPair(new StructureToPolymerChains()).filter(new Pisces(sequenceIdentity, resolution));
    int segmentLength = 11;
    // extract helical sequence segments
    Dataset<Row> data = SecondaryStructureElementExtractor.getDataset(pdb, "H", segmentLength);
    System.out.println(data.count());
    data.show(10, false);
    // add Word2Vec encoded feature vector
    ProteinSequenceEncoder encoder = new ProteinSequenceEncoder(data);
    int n = 2;
    int windowSize = (segmentLength - 1) / 2;
    int vectorSize = 50;
    data = encoder.overlappingNgramWord2VecEncode(n, windowSize, vectorSize);
    data.show(50, false);
    // optionally, save results
    if (args.length > 0) {
        if (args[1].equals("json")) {
            // coalesce data into a single file
            data = data.coalesce(1);
        }
        data.write().mode("overwrite").format(args[1]).save(args[0]);
    }
    long end = System.nanoTime();
    System.out.println(TimeUnit.NANOSECONDS.toSeconds(end - start) + " sec.");
}

Example 7 with Pisces

use of edu.sdsc.mmtf.spark.webfilters.Pisces in project mmtf-spark by sbl-sdsc.

the class SecondaryStructureShiftedWord2VecEncoder method main.

/**
 * @param args args[0] outputFilePath, args[1] outputFormat (json|parquet)
 * @throws IOException
 * @throws StructureException
 */
public static void main(String[] args) throws IOException {
    String path = MmtfReader.getMmtfReducedPath();
    if (args.length != 2) {
        System.err.println("Usage: " + SecondaryStructureShiftedWord2VecEncoder.class.getSimpleName() + " <outputFilePath> + <fileFormat>");
        System.exit(1);
    }
    long start = System.nanoTime();
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(SecondaryStructureShiftedWord2VecEncoder.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    // read MMTF Hadoop sequence file and create a non-redundant set (<=20% seq. identity)
    // of L-protein chains
    int sequenceIdentity = 20;
    double resolution = 3.0;
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.readSequenceFile(path, sc).flatMapToPair(new StructureToPolymerChains()).filter(new Pisces(sequenceIdentity, resolution));
    // get content
    int segmentLength = 11;
    Dataset<Row> data = SecondaryStructureSegmentExtractor.getDataset(pdb, segmentLength);
    // create a Word2Vector representation of the protein sequences
    ProteinSequenceEncoder encoder = new ProteinSequenceEncoder(data);
    int windowSize = (segmentLength - 1) / 2;
    // dimension of feature vector	(50)
    int vectorSize = 50;
    data = encoder.shifted3GramWord2VecEncode(windowSize, vectorSize).cache();
    data.printSchema();
    data.show(25, false);
    if (args[1].equals("json")) {
        // coalesce data into a single file
        data = data.coalesce(1);
    }
    data.write().mode("overwrite").format(args[1]).save(args[0]);
    long end = System.nanoTime();
    System.out.println(TimeUnit.NANOSECONDS.toSeconds(end - start) + " sec.");
}

Example 8 with Pisces

use of edu.sdsc.mmtf.spark.webfilters.Pisces in project mmtf-spark by sbl-sdsc.

the class CreateRepresentativeSet method main.

/**
 * @throws IOException
 */
public static void main(String[] args) throws IOException {
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(CreateRepresentativeSet.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    // filter by representative protein chains at 40% sequence identify
    // and  2.5 A resolution using the Pisces filter. Any pair of protein
    // chains in the representative set will have <= 40% sequence identity.
    int sequenceIdentity = 40;
    double resolution = 2.5;
    // read PDB, split entries into polymer chains, and filter by Pisces filter
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.readReducedSequenceFile(sc).flatMapToPair(new StructureToPolymerChains()).filter(new Pisces(sequenceIdentity, resolution));
    System.out.println("# representative chains: " + pdb.count());
    // coalesce partitions to avoid saving many small files
    pdb = pdb.coalesce(12);
    // save representative set
    String path = MmtfReader.getMmtfReducedPath();
    MmtfWriter.writeSequenceFile(path + "_representatives_i40_r2.5", sc, pdb);
    sc.close();
}

Example 9 with Pisces

use of edu.sdsc.mmtf.spark.webfilters.Pisces in project mmtf-spark by sbl-sdsc.

the class SecondaryStructureWord2VecModelEncoder method main.

/**
 * @param args args[0] outputFilePath, args[1] outputFormat (json|parquet), args[3] word2VecModelFile
 * @throws IOException
 * @throws StructureException
 */
public static void main(String[] args) throws IOException {
    String path = MmtfReader.getMmtfFullPath();
    if (args.length != 3) {
        System.err.println("Usage: " + SecondaryStructureWord2VecModelEncoder.class.getSimpleName() + " <outputFilePath> + <fileFormat> + <word2VecModelFile>");
        System.exit(1);
    }
    long start = System.nanoTime();
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(SecondaryStructureWord2VecModelEncoder.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    // read MMTF Hadoop sequence file and create a non-redundant Pisces
    // subset set (<=20% seq. identity) of L-protein chains
    int sequenceIdentity = 20;
    double resolution = 3.0;
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.readSequenceFile(path, sc).flatMapToPair(new StructureToPolymerChains()).filter(new Pisces(sequenceIdentity, resolution));
    // get content
    int segmentLength = 11;
    Dataset<Row> data = SecondaryStructureSegmentExtractor.getDataset(pdb, segmentLength);
    // add Word2Vec encoded feature vector using
    // a pre-trained Word2Vec model read from file
    ProteinSequenceEncoder encoder = new ProteinSequenceEncoder(data);
    int n = 2;
    String modelFileName = args[2];
    data = encoder.overlappingNgramWord2VecEncode(modelFileName, n).cache();
    data.printSchema();
    data.show(25, false);
    if (args[1].equals("json")) {
        // coalesce data into a single file
        data = data.coalesce(1);
    }
    data.write().mode("overwrite").format(args[1]).save(args[0]);
    long end = System.nanoTime();
    System.out.println(TimeUnit.NANOSECONDS.toSeconds(end - start) + " sec.");
}

Example 10 with Pisces

use of edu.sdsc.mmtf.spark.webfilters.Pisces 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();
}