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

Example 11 with Group

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

the class AbstractItemSetMinerDataSetComposer method handleLine.

private String handleLine(Protein protein, String line, boolean functional) {
    try {
        String[] sectionSplit = line.split("_");
        PLIPInteractionContainer container = protein.getFeatureContainer().getFeature(PLIPInteractionContainer.class);
        // extract peculiar residues
        List<Group> groups = Stream.of(sectionSplit).skip(1).map(residueSection -> extractResidue(protein, residueSection)).collect(Collectors.toList());
        return groups.stream().map(group -> mapToString(container, group)).collect(Collectors.joining(",", line + ",", "," + (functional ? "" : "non-") + "functional"));
    } catch (Exception e) {
        e.fillInStackTrace();
        // thrown upon missing backbone atoms during secondary structure assignment
        return "";
    }
}

Example 12 with Group

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

the class AbstractItemSetMinerDataSetComposer method extractResidue.

private Group extractResidue(Protein protein, String residueSection) {
    String[] split = residueSection.split("-");
    Group group = protein.select().chainName(split[0]).residueNumber(Integer.valueOf(split[1].substring(1))).asGroup();
    // check for integrity
    if (!group.getGroupPrototype().getOneLetterCode().get().equals(split[1].substring(0, 1))) {
        // happens for alternative positions
        throw new IllegalArgumentException("amino acid does not match expectation: " + residueSection + " found " + group.getGroupPrototype().getOneLetterCode());
    }
    return group;
}

Example 13 with Group

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

the class ProteinParserTest method shouldParseInsertedAminoAcids.

@Test
public void shouldParseInsertedAminoAcids() {
    Protein protein = ProteinParser.source("2w0l").parse();
    List<Group> groups = protein.select().chainName("A").residueNumber(95).asFilteredGroups().collect(Collectors.toList());
    Assert.assertEquals(2, groups.size());
    groups.forEach(System.out::println);
}