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

Example 11 with Structure

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

the class ProteinLigandInteractionProfiler method writePolymerInteractions.

public void writePolymerInteractions(Chain chain, Path outputPath) {
    try {
        Path outputDirectoryPath = createTemporaryOutputDirectory();
        Structure structure = chain.getParentStructure();
        String[] commandLineCall = composePolymerCommandLineCall(structure, outputDirectoryPath, chain.getChainIdentifier().getChainId());
        // execute command
        executeCommandLineCall(commandLineCall);
        Path output = outputDirectoryPath.resolve("report.xml");
        Files.copy(output, outputPath);
    } catch (Exception e) {
        throw new ComputationException(e);
    }
}

Example 12 with Structure

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

the class ProteinLigandInteractionProfiler method parseMetalComplexes.

private void parseMetalComplexes(Structure structure, Element interactionElement, List<Interaction> interactions) {
    Elements metalComplexes = interactionElement.getElementsByTag("metal_complex");
    metalComplexes.stream().map(element -> parseMetalComplex(structure, element)).filter(Optional::isPresent).map(Optional::get).forEach(interactions::add);
}

Example 13 with Structure

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

the class ProteinLigandInteractionProfiler method parsePiCationInteraction.

private Optional<PiCationInteraction> parsePiCationInteraction(Structure structure, Element element) {
    // TODO check if direction can be reversed: protein is pi system, ligand is cation
    // TODO: potentially half interaction
    Optional<Element> optionalCationCoordinateElement = element.getElementsByTag("protcoo").stream().findFirst();
    if (!optionalCationCoordinateElement.isPresent()) {
        return Optional.empty();
    }
    Element cationCoordinateElement = optionalCationCoordinateElement.get();
    double[] cationCoordinates = new double[] { Double.valueOf(cationCoordinateElement.getElementsByTag("x").first().text()), Double.valueOf(cationCoordinateElement.getElementsByTag("y").first().text()), Double.valueOf(cationCoordinateElement.getElementsByTag("z").first().text()) };
    String chainId = element.getElementsByTag("reschain").first().text();
    int residueNumber = Integer.valueOf(element.getElementsByTag("resnr").first().text());
    Optional<Group> optionalCationGroup = structure.select().chainId(chainId).residueNumber(residueNumber).asOptionalGroup();
    if (!optionalCationGroup.isPresent()) {
        return Optional.empty();
    }
    Group cationGroup = optionalCationGroup.get();
    Optional<Atom> optionalCation = cationGroup.atoms().min(Comparator.comparingDouble(atom -> atom.calculate().distanceFast(cationCoordinates)));
    if (!optionalCation.isPresent()) {
        return Optional.empty();
    }
    Atom cation = optionalCation.get();
    List<Atom> piAtoms = element.getElementsByTag("idx").stream().map(Element::text).map(pdbSerial -> selectAtom(structure, pdbSerial)).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toList());
    if (piAtoms.isEmpty()) {
        return Optional.empty();
    }
    Group piGroup = piAtoms.get(0).getParentGroup();
    return Optional.of(new PiCationInteraction(cation, piAtoms, cationGroup, piGroup));
}

Example 14 with Structure

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

the class ProteinLigandInteractionProfiler method parseHydrogenBonds.

private void parseHydrogenBonds(Structure structure, Element interactionElement, List<Interaction> interactions) {
    Elements hydrogenBonds = interactionElement.getElementsByTag("hydrogen_bond");
    hydrogenBonds.stream().map(element -> parseHydrogenBond(structure, element)).filter(Optional::isPresent).map(Optional::get).forEach(interactions::add);
}

Example 15 with Structure

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

the class ProteinLigandInteractionProfiler method parseSaltBridges.

private void parseSaltBridges(Structure structure, Element interactionElement, List<Interaction> interactions) {
    Elements saltBridges = interactionElement.getElementsByTag("salt_bridge");
    saltBridges.stream().map(element -> parseSaltBridge(structure, element)).filter(Optional::isPresent).map(Optional::get).forEach(interactions::add);
}