Examples with SecStrucCalc org.biojava.nbio.structure.secstruc.SecStrucCalc used on opensource projects

Example 1 with SecStrucCalc

use of org.biojava.nbio.structure.secstruc.SecStrucCalc in project jstructure by JonStargaryen.

the class SecondaryStructureAnnotatorTest method getDSSPAnnotatedStructure.

private String getDSSPAnnotatedStructure(String id) throws IOException, StructureException {
    // load structure
    Structure protein = new PDBFileReader().getStructureById(id);
    // assign states
    new SecStrucCalc().calculate(protein, true);
    // return complete DSSP annotation string from BioJava
    return protein.getChains().stream().flatMap(chain -> chain.getAtomGroups(GroupType.AMINOACID).stream()).map(aminoAcid -> aminoAcid.getProperty(Group.SEC_STRUC)).map(SecStrucState.class::cast).map(SecStrucState::getType).map(type -> String.valueOf(type.type)).collect(Collectors.joining());
}