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

Example 26 with Protein

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

the class PLIPAnnotatorTest method shouldAnnotateSingleProtein.

@Test
public void shouldAnnotateSingleProtein() throws IOException {
    Protein protein = ProteinParser.source("4BPM").parse();
    plipAnnotator.process(protein);
    PLIPInteractionContainer plipInteractionContainer = protein.getFeatureContainer().getFeature(PLIPInteractionContainer.class);
    plipInteractionContainer.getInteractions().forEach(System.out::println);
}

Example 27 with Protein

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

the class SiftsMappingAnnotatorTest method shouldHandle5tgl.

@Test
public void shouldHandle5tgl() {
    Protein protein = ProteinParser.source("5tgl").parse();
    annotator.process(protein);
}

Example 28 with Protein

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

the class EnergyProfileCalculatorTest method shouldProcessStructureWithMPH.

@Test
public void shouldProcessStructureWithMPH() {
    Protein protein = ProteinParser.source("1P7P").parse();
    featureProvider.process(protein);
}

Example 29 with Protein

use of de.bioforscher.jstructure.model.structure.Protein 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 30 with Protein

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

the class LinkInteractionsToTopologyAndSequenceMotifs method handleLine.

private static void handleLine(String line) {
    System.out.println(line);
    // load protein, calculate features
    Protein protein = ProteinParser.source(line.split("_")[0]).parse();
    plipAnnotator.process(protein);
    sequenceMotifAnnotator.process(protein);
    topologyAnnotator.process(protein);
    // select wanted chain
    Chain chain = protein.select().chainName(line.split("_")[1]).asChain();
    System.out.println(chain.getAminoAcidSequence());
}