Examples with Start2FoldResidueAnnotation de.bioforscher.start2fold.model.Start2FoldResidueAnnotation used on opensource projects

Example 1 with Start2FoldResidueAnnotation

use of de.bioforscher.start2fold.model.Start2FoldResidueAnnotation in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method parse.

public static void parse(Chain chain, InputStream inputStream) {
    try {
        // assign baseline resp. entry container for each residue
        chain.aminoAcids().forEach(aminoAcid -> aminoAcid.getFeatureContainer().addFeature(new Start2FoldResidueAnnotation()));
        Document document = Jsoup.parse(inputStream, "UTF-8", "/");
        Elements experimentElements = document.getElementsByTag("experiment");
        // logger.info("found {} experiments",
        // experimentElements.size());
        List<Experiment> experiments = experimentElements.stream().map(Experiment::parse).collect(Collectors.toList());
        for (Experiment experiment : experiments) {
            assignValues(experiment, chain);
        }
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}

Example 2 with Start2FoldResidueAnnotation

use of de.bioforscher.start2fold.model.Start2FoldResidueAnnotation in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method parseSpecificExperiment.

public static void parseSpecificExperiment(Chain chain, InputStream inputStream, List<Integer> experimentIds) {
    // experimentIds);
    try {
        // assign baseline resp. entry container for each residue
        chain.aminoAcids().forEach(aminoAcid -> aminoAcid.getFeatureContainer().addFeature(new Start2FoldResidueAnnotation()));
        Document document = Jsoup.parse(inputStream, "UTF-8", "/");
        Elements experimentElements = document.getElementsByTag("experiment");
        List<Experiment> experiments = experimentElements.stream().map(Experiment::parse).filter(experiment -> experimentIds.contains(experiment.getExperimentId())).collect(Collectors.toList());
        if (experimentIds.size() != experiments.size()) {
            throw new IllegalArgumentException("did not find all referenced experiments");
        }
        for (Experiment experiment : experiments) {
            assignValuesForEarly(experiment, chain);
        }
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}

Example 3 with Start2FoldResidueAnnotation

use of de.bioforscher.start2fold.model.Start2FoldResidueAnnotation in project jstructure by JonStargaryen.

the class A01_ReportGeneralStatistics method handleStrongFile.

private static void handleStrongFile(Path path) {
    try {
        String pdbId = Jsoup.parse(path.toFile(), "UTF-8").getElementsByTag("protein").attr("pdb_id");
        Structure structure = StructureParser.fromPdbId(pdbId).parse();
        Chain chain = structure.chains().findFirst().get();
        Start2FoldXmlParser.parse(chain, path);
        boolean hasStabilityData = chain.aminoAcids().map(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class)).anyMatch(Start2FoldResidueAnnotation::isStrong);
        if (!hasStabilityData) {
            return;
        }
        long count = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isStrong()).count();
        strong.add((int) count);
        weak.add((int) (chain.aminoAcids().count() - count));
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}