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

Example 1 with SecStrucState

use of org.biojava.nbio.structure.secstruc.SecStrucState 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());
}

Example 2 with SecStrucState

use of org.biojava.nbio.structure.secstruc.SecStrucState in project mm-dev by sbl-sdsc.

the class BioJavaStructureToDssp2 method calculateSecStructure.

private String calculateSecStructure(Structure structure, SecStrucCalc calculator) {
    List<SecStrucState> states = Collections.emptyList();
    // calculate DSSP secondary structure
    try {
        states = calculator.calculate(structure, false);
    } catch (StructureException e) {
    // this happens if there are not at least 4 consecutive residues
    }
    // create a DSSP string
    StringBuilder dssp = new StringBuilder();
    for (SecStrucState state : states) {
        dssp.append(state.getType().type);
    }
    return dssp.toString();
}

Example 3 with SecStrucState

use of org.biojava.nbio.structure.secstruc.SecStrucState in project mm-dev by sbl-sdsc.

the class BioJavaStructureToDssp3 method calculateSecStructure.

private String calculateSecStructure(Structure structure, SecStrucCalc calculator) throws Exception {
    List<SecStrucState> states = Collections.emptyList();
    // calculate DSSP secondary structure
    try {
        states = calculator.calculate(structure, false);
    } catch (StructureException e) {
    // this happens if there are not at least 4 consecutive residues
    }
    // create a DSSP string
    StringBuilder dssp = new StringBuilder();
    for (SecStrucState state : states) {
        dssp.append(state.getType().type);
    }
    return dssp.toString();
}

Example 4 with SecStrucState

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

the class DictionaryOfProteinSecondaryStructureTest method getDSSPAnnotatedStructure.

private String getDSSPAnnotatedStructure(String id) throws IOException, StructureException {
    // load structure
    org.biojava.nbio.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());
}

Example 5 with SecStrucState

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

the class DictionaryOfProteinSecondaryStructureTest method test1btaBiojava.

@Test
public void test1btaBiojava() throws IOException, StructureException {
    org.biojava.nbio.structure.Structure structure = new PDBFileReader().getStructureById("1bta");
    new SecStrucCalc().calculate(structure, true);
    // return complete DSSP annotation string from BioJava
    System.out.println(structure.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)).map(type -> type.equals(" ") ? "-" : type).collect(Collectors.joining()));
}