Examples with Protein de.bioforscher.jstructure.model.structure.Protein used on opensource projects

Example 6 with Protein

use of de.bioforscher.jstructure.model.structure.Protein in project jstructure by JonStargaryen.

the class BindingSiteExtractor method handleLine.

private void handleLine(String line, String className, String modeName) {
    System.out.println(line);
    // map to amino acid family
    String aminoAcid = Stream.of(AminoAcid.Family.values()).filter(aminoAcidFamily -> aminoAcidFamily.name().equalsIgnoreCase(line.split(":")[0])).findFirst().map(AminoAcid.Family::getGroupPrototype).map(GroupPrototype::getThreeLetterCode).orElse("Pyr");
    int[] residueNumbers = Pattern.compile(", ").splitAsStream(line.split("\\[")[1].split("]")[0]).mapToInt(Integer::valueOf).toArray();
    AARSConstants.lines(Paths.get(AARSConstants.MAIN_TABLE_CATALYTIC_PATH)).filter(mainTableLine -> mainTableLine.split(",")[1].equalsIgnoreCase(aminoAcid)).filter(mainTableLine -> mainTableLine.endsWith("1")).forEach(mainTableLine -> {
        String[] split = mainTableLine.split(",");
        String pdbId = split[2];
        String chainId = split[13];
        Protein protein = ProteinParser.source(AARSConstants.RENUMBERED_STRUCTURES_PATH + className + "/renumbered_structures/" + pdbId + "_renum.pdb").parse();
        String output = "HEADER    LIGASE/RNA                              15-JUL-99   " + pdbId.toUpperCase() + "              " + System.lineSeparator() + protein.select().chainName(chainId).aminoAcids().residueNumber(residueNumbers).asGroupContainer().getPdbRepresentation();
        AARSConstants.write(Paths.get(AARSConstants.BINDING_SITE_PATH + className + "/ligand_based/per_type/" + modeName + "/" + aminoAcid.substring(0, 1).toUpperCase() + aminoAcid.substring(1, 3).toLowerCase() + "/" + pdbId + "_" + chainId + "_renum.pdb"), output.getBytes());
    });
}

Example 7 with Protein

use of de.bioforscher.jstructure.model.structure.Protein in project jstructure by JonStargaryen.

the class SimpleEnergyProfileRunnerTest method shouldPerformEnergyCalculationOnAARSDataset.

@Test
@Ignore("skipped due to long computation")
public void shouldPerformEnergyCalculationOnAARSDataset() {
    List<String> ids = Stream.of("1bs2", "1f7u", "1f7v", "3fnr", "4oby", "4q2t", "4q2x", "4q2y", "4r3z", "1li5", "1li7", "1u0b", "3c8z", "3sp1", "3tqo", "1euq", "1euy", "1exd", "1gsg", "1gtr", "1gts", "1nyl", "1o0b", "1qrs", "1qrt", "1qru", "1qtq", "1zjw", "2hz7", "2rd2", "2re8", "4h3s", "4jxx", "4jxz", "4jyz", "4p2b", "4r3z", "4ye6", "4ye8", "4ye9", "5bnz", "1g59", "1gln", "1j09", "1n75", "1n77", "1n78", "1nzj", "2cfo", "2cuz", "2cv0", "2cv1", "2cv2", "2dxi", "2ja2", "2o5r", "3afh", "3aii", "3akz", "3pnv", "3pny", "4gri", "1ile", "1jzq", "1jzs", "3zgz", "3ziu", "3zjt", "3zju", "3zjv", "4aq7", "4arc", "4ari", "4as1", "4cqn", "5ah5", "1a8h", "1f4l", "1p7p", "1pfv", "1pfw", "1pfy", "1pg0", "1pg2", "1qqt", "1woy", "2csx", "2ct8", "2d54", "2d5b", "2x1l", "2x1m", "3h97", "3h99", "3h9b", "3kfl", "3vu8", "4dlp", "4eg1", "4eg3", "4eg4", "4eg5", "4eg6", "4eg7", "4eg8", "4ega", "4mvw", "4mvx", "4mvy", "4mw0", "4mw1", "4mw2", "4mw4", "4mw5", "4mw6", "4mw7", "4mw9", "4mwb", "4mwc", "4mwd", "4mwe", "4py2", "1o5t", "1r6t", "1r6u", "1ulh", "1yi8", "1yia", "1yid", "2a4m", "2ake", "2azx", "2dr2", "2el7", "2g36", "2ip1", "2quh", "2qui", "2quj", "2quk", "2yy5", "3a04", "3a05", "3foc", "3hv0", "3i05", "3kt0", "3kt3", "3kt6", "3kt8", "3m5w", "3n9i", "3prh", "3sz3", "3tze", "3tzl", "4j75", "4j76", "4jfa", "1j1u", "1n3l", "1q11", "1u7d", "1u7x", "1vbm", "1vbn", "1wq3", "1wq4", "1x8x", "2cya", "2cyb", "2dlc", "2j5b", "2jan", "2pid", "2rkj", "2yxn", "2zp1", "3p0h", "3p0i", "3p0j", "3vgj", "3zxi", "4hjr", "4hjx", "4hk4", "4hpw", "4nd6", "4nd7", "4nda", "4ojm", "4q93", "4qbt", "1riq", "1yfr", "1yfs", "1yft", "1ygb", "2ztg", "3htz", "3hxu", "3hxv", "3hxw", "3hxx", "3hxy", "3hxz", "3hy0", "3hy1", "3wqy", "3wqz", "4xem", "4xeo", "1nnh", "3m4p", "3m4q", "1asy", "1asz", "1b8a", "1c0a", "1eov", "1eqr", "1il2", "1n9w", "1wyd", "3i7f", "3nel", "3nem", "3nen", "4ah6", "4j15", "4o2d", "4rmf", "1ati", "1b76", "1ggm", "2pme", "2pmf", "2q5h", "2q5i", "2zt5", "2zt6", "2zt7", "2zt8", "2zxf", "3rgl", "3ufg", "4h2x", "4kqe", "4kr2", "4kr3", "4qei", "1htt", "1kmm", "1kmn", "2el9", "1bbu", "1bbw", "1e1o", "1e1t", "1e22", "1e24", "1lyl", "3a5y", "3a5z", "3bju", "3g1z", "4dpg", "4h02", "4pg3", "4up7", "4up8", "4up9", "4upa", "4ycu", "4ycv", "4ycw", "1eiy", "1jjc", "1pys", "3cmq", "3hfv", "3hfz", "3l4g", "3pco", "3teg", "3tup", "4p71", "4p72", "4p73", "4p74", "4p75", "4tva", "1h4q", "1h4s", "1h4t", "1hc7", "1nj1", "1nj2", "1nj5", "1nj6", "1nj8", "2i4l", "2i4m", "2i4n", "2i4o", "2j3l", "2j3m", "3ial", "4hvc", "4k86", "4k87", "4k88", "4ncx", "4olf", "4twa", "4ydq", "2e3c", "2q7e", "2q7g", "2q7h", "2zce", "2zim", "2zin", "2zio", "3qtc", "3vqv", "3vqw", "3vqx", "4bw9", "4bwa", "4ch3", "4ch4", "4ch5", "4ch6", "4cs2", "4cs3", "4cs4", "4q6g", "4tqd", "4tqf", "2du3", "2du4", "2du5", "2du6", "2du7", "2odr", "1wle", "2dq3", "3lsq", "3lss", "3mey", "3mf1", "3mf2", "3qne", "3qo5", "3qo7", "3qo8", "3vbb", "3w3s", "4l87", "4rqe", "4rqf", "1evk", "1evl", "1fyf", "1kog", "1qf6", "3a31", "3a32", "3ugq", "3ugt", "3uh0", "4eo4", "4hwo", "4hwp", "4hwr", "4hws", "4hwt", "4p3n", "4p3o", "4p3p", "4ttv", "4yye").collect(Collectors.toList());
    ids.forEach(id -> {
        System.out.println(id);
        Protein protein = ProteinParser.source(id).parse();
        try {
            String basePath = "/home/bittrich/energyprofiles/";
            Path pdbFile = Paths.get(basePath + id + ".pdb");
            Files.write(pdbFile, protein.getPdbRepresentation().getBytes());
            SimpleEnergyProfileRunner.main(pdbFile.toFile().getAbsolutePath(), basePath + id + ".ep");
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    });
}

Example 8 with Protein

use of de.bioforscher.jstructure.model.structure.Protein in project jstructure by JonStargaryen.

the class AbstractItemSetMinerDataSetComposer method handleLineGroup.

private void handleLineGroup(List<String> lines, boolean functional) {
    // skip filtered lines
    if (!filterFunctionalProteins(lines.get(0), functional)) {
        return;
    }
    //TODO remove - skip already processed entries
    if (lines.contains(lastProcessedEntry)) {
        passedLastProcessedEntry = true;
        System.out.println("skipping already processed entries: " + lines);
        return;
    }
    if (!passedLastProcessedEntry) {
        System.out.println("skipping already processed entries: " + lines);
        return;
    }
    try {
        System.out.println(lines);
        Protein protein = ProteinParser.source(lines.get(0).split("_")[0]).parse();
        // calculate features
        featureProviders.forEach(featureProvider -> featureProvider.process(protein));
        for (String line : lines) {
            String outputLine = handleLine(protein, line, functional);
            if (outputLine.isEmpty()) {
                continue;
            }
            System.out.println(outputLine);
            output.write(outputLine + System.lineSeparator());
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 9 with Protein

use of de.bioforscher.jstructure.model.structure.Protein in project jstructure by JonStargaryen.

the class SimpleEnergyProfileRunner method main.

public static void main(String... args) {
    if (args.length != 1 && args.length != 2) {
        // print usage
        System.err.println("usage: java -jar energy.jar /path/to/file.pdb [/path/to/output/file/if/desired.ep]");
        throw new IllegalArgumentException("too " + (args.length < 1 ? "few" : "many") + " arguments provided");
    }
    String inputPath = args[0];
    boolean outputRequested = false;
    String outputPath = null;
    if (args.length == 2) {
        outputRequested = true;
        outputPath = args[1];
    }
    logger.info("computing energy profile for {}", inputPath);
    logger.info("writing output to {}", outputRequested ? outputPath : "console");
    try {
        // read and parse protein
        Protein protein = ProteinParser.source(Paths.get(inputPath)).parse();
        // calculate energy profile
        featureProvider.process(protein);
        // compose output
        String output = AdvancedEnergyProfileRunner.composeOutput(protein);
        if (outputRequested) {
            Files.write(Paths.get(outputPath), output.getBytes());
        } else {
            System.out.println(output);
        }
    } catch (UncheckedIOException e) {
        System.err.println("failed to parse PDB file located at " + inputPath);
        throw e;
    } catch (IOException e) {
        System.err.println("writing the output file failed - destination " + outputPath);
        throw new UncheckedIOException(e);
    }
}

Example 10 with Protein

use of de.bioforscher.jstructure.model.structure.Protein in project jstructure by JonStargaryen.

the class SelectionTest method shouldFindSimilarNeighbors.

@Test
public void shouldFindSimilarNeighbors() {
    Protein protein = ProteinParser.source("1acj").parse();
    Atom atom = protein.getAtoms().get(100);
    double probeDistance = 4;
    List<Atom> neighboringGroupCountSelectionAPI = protein.select().atomSelection().distance(atom, probeDistance).asFilteredAtoms().collect(Collectors.toList());
    List<Atom> neighboringGroupCountNaive = protein.atoms().filter(a -> a.calculate().distance(atom.getCoordinates()) < probeDistance).collect(Collectors.toList());
    Assert.assertTrue(neighboringGroupCountSelectionAPI.containsAll(neighboringGroupCountNaive));
    Assert.assertTrue(neighboringGroupCountNaive.containsAll(neighboringGroupCountSelectionAPI));
}