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

Example 21 with Protein

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

the class SecondaryStructureAnnotatorTest method getSecondaryStructureAnnotation.

private String getSecondaryStructureAnnotation(String id) {
    // load structure
    Protein protein = ProteinParser.source(id).parse();
    // assign states
    featureProvider.process(protein);
    // return complete DSSP annotation string from jstructrue
    return protein.aminoAcids().map(residue -> residue.getFeatureContainer().getFeature(SecondaryStructure.class)).map(SecondaryStructure::getSecondaryStructure).map(SecondaryStructureElement::getOneLetterRepresentation).map(character -> character.equals("c") ? " " : character).collect(Collectors.joining());
}

Example 22 with Protein

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

the class AccessibleSurfaceAreaCalculatorTest method getJStructureASA.

private static List<Double> getJStructureASA(String id) {
    // load structure
    Protein protein = ProteinParser.source(id).parse();
    // assign states
    FeatureProviderRegistry.resolve(AccessibleSurfaceArea.class).process(protein);
    // return complete DSSP annotation string from jstructrue
    return protein.aminoAcids().map(residue -> residue.getFeatureContainer().getFeature(AccessibleSurfaceArea.class).getAccessibleSurfaceArea()).collect(Collectors.toList());
}

Example 23 with Protein

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

the class PLIPAnnotatorTest method shouldProteinWithIllReference.

@Test
public void shouldProteinWithIllReference() {
    Protein protein = ProteinParser.source("3AOU").parse();
    plipAnnotator.process(protein);
}

Example 24 with Protein

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

the class UniProtAnnotatorTest method shouldAnnotate4lg6.

@Test
public void shouldAnnotate4lg6() {
    Protein protein = ProteinParser.source("4lg6").parse();
    uniProtAnnotator.process(protein);
    protein.select().chainName("A").asFilteredChains().forEach(chain -> {
        UniProtAnnotationContainer container = chain.getFeatureContainer().getFeature(UniProtAnnotationContainer.class);
        Assert.assertTrue(container.getReferences().size() == 6);
        Assert.assertTrue(container.getMutagenesisSites().size() == 3);
        Assert.assertTrue(container.getNaturalVariants().size() == 0);
    });
}

Example 25 with Protein

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

the class EnergyProfileCalculatorTest method shouldProcessStructure.

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