Examples with Experiment de.bioforscher.jstructure.efr.model.Experiment used on opensource projects

Example 1 with Experiment

use of de.bioforscher.jstructure.efr.model.Experiment 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.debug("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 Experiment

use of de.bioforscher.jstructure.efr.model.Experiment in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method parseSpecificExperiment.

public static void parseSpecificExperiment(Chain chain, InputStream inputStream, List<Integer> experimentIds) {
    logger.debug("ids: {}", experimentIds);
    try {
        // assign baseline resp. entry container for each residue if not already happened
        chain.aminoAcids().filter(aminoAcid -> !aminoAcid.getFeatureContainer().getFeatureOptional(Start2FoldResidueAnnotation.class).isPresent()).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());
        logger.debug("processing {} experiments", experiments.size());
        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 Experiment

use of de.bioforscher.jstructure.efr.model.Experiment in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method assignValues.

private static void assignValues(Experiment experiment, Chain chain) {
    String pdbSequence = chain.getAminoAcidSequence();
    String experimentSequence = experiment.getSequence();
    // align sequences to ensure correct mapping
    SequencePair<ProteinSequence, AminoAcidCompound> pair = null;
    try {
        pair = Alignments.getPairwiseAlignment(new ProteinSequence(experimentSequence), new ProteinSequence(pdbSequence), Alignments.PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), SubstitutionMatrixHelper.getBlosum62());
        logger.debug("alignment:{}{}", System.lineSeparator(), pair.toString());
        List<AminoAcid> aminoAcids = chain.aminoAcids().collect(Collectors.toList());
        for (Experiment.Residue residue : experiment.getResidues()) {
            int experimentIndex = residue.getIndex() - 1;
            try {
                int pdbIndex;
                if (residue.getCode().equals("P") && residue.getIndex() == 1) {
                    // super-russian fix for STF0017 where the alignment should match theoretically
                    pdbIndex = 0;
                } else {
                    pdbIndex = pair.getIndexInTargetForQueryAt(experimentIndex);
                }
                AminoAcid aminoAcid = aminoAcids.get(pdbIndex);
                logger.debug("mapped experiment {}-{} onto PDB {}-{}", residue.getCode(), residue.getIndex(), aminoAcid.getOneLetterCode(), aminoAcid.getResidueIdentifier());
                // if(!residue.getCode().equals(aminoAcid.getOneLetterCode())) {
                // logger.warn("alignment:{}{}",
                // System.lineSeparator(),
                // pair.toString());
                // logger.warn("could not map data correctly for {}-{} and {}-{}",
                // residue.getCode(),
                // residue.getIndex(),
                // aminoAcid.getOneLetterCode(),
                // aminoAcid.getResidueIdentifier());
                // }
                // ignore: STF0034 (cannot align)
                // assign experiment-specific protection level to residue
                aminoAcid.getFeature(Start2FoldResidueAnnotation.class).addProtectionLevelEntry(Stream.of(ProtectionLevel.values()).filter(pl -> pl == experiment.getProtectionLevel()).findFirst().get());
            } catch (Exception e) {
                // residue not present in structure - e.g. for STF0031 and STF0032
                logger.warn("alignment:{}{}", System.lineSeparator(), pair.toString());
                logger.warn("failed to map residue {}-{}", residue.getCode(), residue.getIndex(), e);
            }
        }
    } catch (CompoundNotFoundException e) {
        throw new IllegalArgumentException(e);
    }
}

Example 4 with Experiment

use of de.bioforscher.jstructure.efr.model.Experiment in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method assignValuesForStrong.

private static void assignValuesForStrong(Experiment experiment, Chain chain) {
    String pdbSequence = chain.getAminoAcidSequence();
    String experimentSequence = experiment.getSequence();
    // align sequences to ensure correct mapping
    SequencePair<ProteinSequence, AminoAcidCompound> pair = null;
    try {
        pair = Alignments.getPairwiseAlignment(new ProteinSequence(experimentSequence), new ProteinSequence(pdbSequence), Alignments.PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), SubstitutionMatrixHelper.getBlosum62());
        List<AminoAcid> aminoAcids = chain.aminoAcids().collect(Collectors.toList());
        for (Experiment.Residue residue : experiment.getResidues()) {
            int experimentIndex = residue.getIndex() - 1;
            try {
                int pdbIndex;
                if (residue.getCode().equals("P") && residue.getIndex() == 1) {
                    // super-russian fix for STF0017 where the alignment should match theoretically
                    pdbIndex = 0;
                } else {
                    pdbIndex = pair.getIndexInTargetForQueryAt(experimentIndex);
                }
                AminoAcid aminoAcid = aminoAcids.get(pdbIndex);
                // assign experiment-specific protection level to residue
                aminoAcid.getFeature(Start2FoldResidueAnnotation.class).addProtectionLevelEntry(ProtectionLevel.STRONG);
            } catch (Exception e) {
                // residue not present in structure - e.g. for STF0031 and STF0032
                logger.warn("alignment:{}{}", System.lineSeparator(), pair.toString());
                logger.warn("failed to map residue {}-{}", residue.getCode(), residue.getIndex(), e);
            }
        }
    } catch (CompoundNotFoundException e) {
        throw new IllegalArgumentException(e);
    }
}

Example 5 with Experiment

use of de.bioforscher.jstructure.efr.model.Experiment in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method parseStability.

public static void parseStability(Chain chain, InputStream inputStream) {
    try {
        // assign baseline resp. entry container for each residue if not already happened
        chain.aminoAcids().filter(aminoAcid -> !aminoAcid.getFeatureContainer().getFeatureOptional(Start2FoldResidueAnnotation.class).isPresent()).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 -> experiment.getMethod() == Method.STABILITY).collect(Collectors.toList());
        for (Experiment experiment : experiments) {
            assignValuesForStrong(experiment, chain);
        }
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}