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

Example 26 with Structure

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

the class ProteinLigandInteractionProfiler method parsePiStackingInteractions.

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

Example 27 with Structure

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

the class ProteinLigandInteractionProfiler method parseWaterBridges.

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

Example 28 with Structure

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

the class ProteinLigandInteractionProfiler method annotatePolymerInteractions.

private InteractionContainer annotatePolymerInteractions(Chain chain) {
    try {
        Path outputDirectoryPath = createTemporaryOutputDirectory();
        Structure structure = chain.getParentStructure();
        String[] commandLineCall = composePolymerCommandLineCall(structure, outputDirectoryPath, chain.getChainIdentifier().getChainId());
        // execute command
        executeCommandLineCall(commandLineCall);
        Path outputPath = outputDirectoryPath.resolve("report.xml");
        Document document = Jsoup.parse(outputPath.toFile(), "UTF-8");
        return parseDocument(structure, document);
    } catch (Exception e) {
        throw new ComputationException(e);
    }
}

Example 29 with Structure

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

the class ProteinLigandInteractionProfiler method parsePiCationInteractions.

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

Example 30 with Structure

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

the class ProteinLigandInteractionProfiler method parseSaltBridge.

private Optional<SaltBridge> parseSaltBridge(Structure structure, Element element) {
    // TODO: potentially half interaction
    Optional<Element> optionalCoordinateElement = element.getElementsByTag("protcoo").stream().findFirst();
    if (!optionalCoordinateElement.isPresent()) {
        return Optional.empty();
    }
    Element coordinateElement = optionalCoordinateElement.get();
    double[] coordinates = new double[] { Double.valueOf(coordinateElement.getElementsByTag("x").first().text()), Double.valueOf(coordinateElement.getElementsByTag("y").first().text()), Double.valueOf(coordinateElement.getElementsByTag("z").first().text()) };
    String chainId = element.getElementsByTag("reschain").first().text();
    int residueNumber = Integer.valueOf(element.getElementsByTag("resnr").first().text());
    Optional<Group> optionalGroup1 = structure.select().chainId(chainId).residueNumber(residueNumber).asOptionalGroup();
    if (!optionalGroup1.isPresent()) {
        return Optional.empty();
    }
    Group group1 = optionalGroup1.get();
    Optional<Atom> optionalAtom1 = group1.atoms().min(Comparator.comparingDouble(atom -> atom.calculate().distanceFast(coordinates)));
    if (!optionalAtom1.isPresent()) {
        return Optional.empty();
    }
    Atom atom1 = optionalAtom1.get();
    List<Atom> saltAtoms = element.getElementsByTag("idx").stream().map(Element::text).map(pdbSerial -> selectAtom(structure, pdbSerial)).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toList());
    if (saltAtoms.isEmpty()) {
        return Optional.empty();
    }
    Group saltGroup = saltAtoms.get(0).getParentGroup();
    return Optional.of(new SaltBridge(atom1, saltAtoms, group1, saltGroup));
}