Examples with DSSPSecondaryStructure de.bioforscher.jstructure.feature.sse.dssp.DSSPSecondaryStructure used on opensource projects

Example 1 with DSSPSecondaryStructure

use of de.bioforscher.jstructure.feature.sse.dssp.DSSPSecondaryStructure in project jstructure by JonStargaryen.

the class DictionaryOfProteinSecondaryStructureTest method getSecondaryStructureAnnotation.

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

Example 2 with DSSPSecondaryStructure

use of de.bioforscher.jstructure.feature.sse.dssp.DSSPSecondaryStructure in project jstructure by JonStargaryen.

the class DictionaryOfProteinSecondaryStructureTest method test1bta.

@Test
public void test1bta() {
    Structure structure = StructureParser.fromPdbId("1bta").parse();
    featureProvider.process(structure);
    structure.aminoAcids().forEach(aminoAcid -> {
        System.out.println(aminoAcid);
        DSSPSecondaryStructure sse = aminoAcid.getFeature(DSSPSecondaryStructure.class);
        System.out.println(sse.getSecondaryStructure().name());
    });
    System.out.println(structure.getFirstChain().aminoAcids().map(aminoAcid -> aminoAcid.getFeature(DSSPSecondaryStructure.class).getSecondaryStructure().getOneLetterRepresentation()).collect(Collectors.joining()));
}