Examples with InteractionFilter edu.sdsc.mmtf.spark.interactions.InteractionFilter used on opensource projects

Example 1 with InteractionFilter

use of edu.sdsc.mmtf.spark.interactions.InteractionFilter in project mmtf-spark by sbl-sdsc.

the class InteractionFilterTest method test3.

@Test
public void test3() {
    InteractionFilter filter = new InteractionFilter();
    filter.setTargetGroups(true, "HOH", "ZN");
    assertEquals(true, filter.isTargetGroup("ZN"));
    assertEquals(true, filter.isTargetGroup("HOH"));
    assertEquals(false, filter.isTargetGroup("MN"));
}

Example 2 with InteractionFilter

use of edu.sdsc.mmtf.spark.interactions.InteractionFilter in project mmtf-spark by sbl-sdsc.

the class InteractionFilterTest method test1.

@Test
public void test1() {
    InteractionFilter filter = new InteractionFilter();
    filter.setQueryGroups(true, "HOH", "ZN");
    assertEquals(true, filter.isQueryGroup("ZN"));
    assertEquals(true, filter.isQueryGroup("HOH"));
    assertEquals(false, filter.isQueryGroup("MN"));
}

Example 3 with InteractionFilter

use of edu.sdsc.mmtf.spark.interactions.InteractionFilter in project mmtf-spark by sbl-sdsc.

the class InteractionFilterTest method test4.

@Test
public void test4() {
    InteractionFilter filter = new InteractionFilter();
    filter.setTargetGroups(false, "HOH", "ZN");
    assertEquals(false, filter.isTargetGroup("ZN"));
    assertEquals(false, filter.isTargetGroup("HOH"));
    assertEquals(true, filter.isTargetGroup("MN"));
}

Example 4 with InteractionFilter

use of edu.sdsc.mmtf.spark.interactions.InteractionFilter in project mmtf-spark by sbl-sdsc.

the class Metalnteractions method main.

public static void main(String[] args) throws IOException {
    String path = MmtfReader.getMmtfFullPath();
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(Metalnteractions.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    // input parameters
    int sequenceIdentityCutoff = 30;
    double resolution = 2.5;
    int minInteractions = 4;
    int maxInteractions = 6;
    double distanceCutoff = 3.0;
    // chemical component codes of metals in different oxidation states
    String[] metals = { "V", "CR", "MN", "MN3", "FE", "FE2", "CO", "3CO", "NI", "3NI", "CU", "CU1", "CU3", "ZN", "MO", "4MO", "6MO" };
    // read PDB and create a non-redundant PISCES subset
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.readSequenceFile(path, sc).filter(new Pisces(sequenceIdentityCutoff, resolution));
    // Setup criteria for metal interactions
    InteractionFilter filter = new InteractionFilter();
    filter.setDistanceCutoff(distanceCutoff);
    filter.setMinInteractions(minInteractions);
    filter.setMaxInteractions(maxInteractions);
    filter.setQueryGroups(true, metals);
    // exclude non-polar interactions
    filter.setTargetElements(false, "H", "C", "P");
    // tabulate interactions in a dataframe
    Dataset<Row> interactions = GroupInteractionExtractor.getInteractions(pdb, filter).cache();
    System.out.println("Metal interactions: " + interactions.count());
    // select interacting atoms and orientational order parameters (q4 - q6)
    // see {@link CoordinationGeometry}
    interactions = interactions.select("pdbId", "q4", "q5", "q6", "element0", "groupNum0", "chain0", "element1", "groupNum1", "chain1", "distance1", "element2", "groupNum2", "chain2", "distance2", "element3", "groupNum3", "chain3", "distance3", "element4", "groupNum4", "chain4", "distance4", "element5", "groupNum5", "chain5", "distance5", "element6", "groupNum6", "chain6", "distance6").cache();
    // show some example interactions
    interactions.dropDuplicates("pdbId").show(10);
    System.out.println("Unique interactions by metal:");
    interactions.groupBy("element0").count().sort("count").show();
    sc.close();
}

Example 5 with InteractionFilter

use of edu.sdsc.mmtf.spark.interactions.InteractionFilter in project mmtf-spark by sbl-sdsc.

the class WaterInteractions method main.

public static void main(String[] args) throws IOException, ParseException {
    String timeStamp = new SimpleDateFormat("yyyyMMdd_HHmm").format(Calendar.getInstance().getTime());
    long start = System.nanoTime();
    // process command line options (defaults are provided)
    CommandLine cmd = getCommandLine(args);
    String outputPath = cmd.getOptionValue("output-path");
    System.out.println(outputPath);
    String resolution = cmd.getOptionValue("resolution", "2");
    String minInteractions = cmd.getOptionValue("min-interactions", "2");
    String maxInteractions = cmd.getOptionValue("max-interactions", "4");
    String distanceCutoff = cmd.getOptionValue("distance-cutoff", "3");
    String bFactorCutoff = cmd.getOptionValue("b-factor-cutoff", "1.645");
    boolean includeWaters = cmd.hasOption("include-waters");
    // get path to MMTF Hadoop Sequence file
    String path = MmtfReader.getMmtfFullPath();
    // initialize Spark
    SparkConf conf = new SparkConf().setMaster("local[*]").setAppName(WaterInteractions.class.getSimpleName());
    JavaSparkContext sc = new JavaSparkContext(conf);
    // read PDB structures and filter by resolution and only include proteins
    JavaPairRDD<String, StructureDataInterface> pdb = MmtfReader.readSequenceFile(path, sc).filter(new Resolution(0.0, Float.parseFloat(resolution))).filter(new ContainsLProteinChain(true));
    // setup interaction criteria
    InteractionFilter filter = new InteractionFilter();
    filter.setDistanceCutoff(Float.parseFloat(distanceCutoff));
    filter.setNormalizedbFactorCutoff(Float.parseFloat(bFactorCutoff));
    filter.setMinInteractions(Integer.parseInt(minInteractions));
    filter.setMaxInteractions(Integer.parseInt(maxInteractions));
    filter.setQueryGroups(true, "HOH");
    // only use water oxygen
    filter.setQueryElements(true, "O");
    filter.setTargetElements(true, "O", "N", "S");
    // exclude "uninteresting" ligands
    Set<String> prohibitedGroups = new HashSet<>();
    prohibitedGroups.addAll(ExcludedLigandSets.ALL_GROUPS);
    if (!includeWaters) {
        prohibitedGroups.add("HOH");
    }
    filter.setProhibitedTargetGroups(prohibitedGroups);
    // calculate interactions
    Dataset<Row> data = GroupInteractionExtractor.getInteractions(pdb, filter);
    // keep only interactions with at least one organic ligand and one protein interaction
    data = filterBridgingWaterInteractions(data, maxInteractions).cache();
    // show some results
    data.show(50);
    System.out.println("Hits(all): " + data.count());
    // save interactions to a .parquet file
    String waterTag = includeWaters ? "_w" : "";
    String filename = outputPath + "/water_pl" + "_r" + resolution + "_d" + distanceCutoff + "_b" + bFactorCutoff + "_i" + minInteractions + maxInteractions + waterTag + "_" + timeStamp + ".parquet";
    System.out.println("Saving results to: " + filename);
    data.coalesce(1).write().mode("overwrite").format("parquet").save(filename);
    // exit Spark
    sc.close();
    long end = System.nanoTime();
    System.out.println("Time: " + TimeUnit.NANOSECONDS.toSeconds(end - start) + " sec.");
}