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

Example 46 with Structure

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

the class DictionaryOfProteinSecondaryStructureTest method shouldClearPseudoAtomsAfterRun.

@Test
public void shouldClearPseudoAtomsAfterRun() {
    Structure protein = StructureParser.fromPdbId(ID).parse();
    featureProvider.process(protein);
    boolean containsPseudoHydrogenLine = protein.getPdbRepresentation().contains("ATOM      0  H");
    Assert.assertFalse("pseudo-atoms were not removed!", containsPseudoHydrogenLine);
}

Example 47 with Structure

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

the class DictionaryOfProteinSecondaryStructureTest method test1bta.

@Test
public void test1bta() {
    Structure structure = StructureParser.fromPdbId("1bta").parse();
    featureProvider.process(structure);
    structure.aminoAcids().forEach(aminoAcid -> {
        System.out.println(aminoAcid);
        DSSPSecondaryStructure sse = aminoAcid.getFeature(DSSPSecondaryStructure.class);
        System.out.println(sse.getSecondaryStructure().name());
    });
    System.out.println(structure.getFirstChain().aminoAcids().map(aminoAcid -> aminoAcid.getFeature(DSSPSecondaryStructure.class).getSecondaryStructure().getOneLetterRepresentation()).collect(Collectors.joining()));
}

Example 48 with Structure

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

the class A03_PrintStart2FoldDatasetTable method handleLine.

private static String handleLine(String line) {
    try {
        String[] split = line.split(";");
        String entryId = split[0];
        String pdbId = split[1];
        List<Integer> experimentIds = Pattern.compile(",").splitAsStream(split[2].replaceAll("\\[", "").replaceAll("]", "")).map(Integer::valueOf).collect(Collectors.toList());
        Structure structure = StructureParser.fromPdbId(pdbId).parse();
        Chain chain = structure.chains().findFirst().get();
        Start2FoldXmlParser.parseStability(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"));
        Start2FoldXmlParser.parseSpecificExperiment(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"), experimentIds);
        List<AminoAcid> earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).collect(Collectors.toList());
        List<AminoAcid> stableResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isStrong()).collect(Collectors.toList());
        List<Integer> functionalResidueNumbers = Start2FoldConstants.extractFunctionalResidueNumbers(split);
        List<AminoAcid> functionalResidues = new ArrayList<>();
        // do nothing if no annotation of functional residues exists
        if (!functionalResidueNumbers.isEmpty()) {
            FunctionalResidueParser.parse(chain, functionalResidueNumbers);
            chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(FunctionalResidueAnnotation.class).isFunctional()).forEach(functionalResidues::add);
        }
        List<AminoAcid> aminoAcids = chain.aminoAcids().collect(Collectors.toList());
        long intersection = earlyFoldingResidues.stream().filter(functionalResidues::contains).count();
        return entryId + "\t" + pdbId + "\t" + split[2] + "\t" + aminoAcids.size() + "\t" + earlyFoldingResidues.size() + "\t" + functionalResidues.size() + "\t" + intersection;
    } catch (Exception e) {
        e.printStackTrace();
        return "";
    }
}

Example 49 with Structure

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

the class A07_WriteCouplingRangeCsv method handleLine.

private static Optional<String> handleLine(String line) {
    try {
        System.out.println(line);
        String[] split = line.split(";");
        String entryId = split[0];
        String pdbId = split[1];
        List<Integer> experimentIds = Pattern.compile(",").splitAsStream(split[2].replaceAll("\\[", "").replaceAll("]", "")).map(Integer::valueOf).collect(Collectors.toList());
        Structure structure = StructureParser.fromPdbId(pdbId).parse();
        Chain chain = structure.chains().findFirst().get();
        Start2FoldXmlParser.parseSpecificExperiment(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"), experimentIds);
        EvolutionaryCouplingParser.parseHotSpotFile(chain, Start2FoldConstants.COUPLING_DIRECTORY.resolve(entryId.toUpperCase() + "_hs.html"));
        List<AminoAcid> earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).collect(Collectors.toList());
        Map<Integer, List<Double>> localPlmScores = new HashMap<>();
        Map<Integer, List<Double>> longRangePlmScores = new HashMap<>();
        Document hotSpotDocument = Jsoup.parse(Files.readAllLines(Paths.get("/home/bittrich/git/phd_sb_repo/data/start2fold/coupling/" + entryId + "_ec.html")).stream().collect(Collectors.joining(System.lineSeparator())));
        List<AminoAcid> aminoAcids = chain.aminoAcids().collect(Collectors.toList());
        for (int i = 0; i < aminoAcids.size(); i++) {
            localPlmScores.put(i, new ArrayList<>());
            longRangePlmScores.put(i, new ArrayList<>());
        }
        hotSpotDocument.getElementsByTag("tr").stream().skip(1).forEach(element -> {
            Elements tds = element.getElementsByTag("td");
            int residueNumber1 = Integer.valueOf(tds.get(2).text()) - 1;
            int residueNumber2 = Integer.valueOf(tds.get(4).text()) - 1;
            double plmScore = Double.valueOf(tds.get(6).text());
            boolean localContact = Math.abs(residueNumber1 - residueNumber2) < 6;
            if (localContact) {
                System.out.println("local contact: " + element.text());
                localPlmScores.get(residueNumber1).add(plmScore);
                localPlmScores.get(residueNumber2).add(plmScore);
            } else {
                System.out.println("long-range contact: " + element.text());
                longRangePlmScores.get(residueNumber1).add(plmScore);
                longRangePlmScores.get(residueNumber2).add(plmScore);
            }
        });
        return Optional.of(aminoAcids.stream().map(aminoAcid -> pdbId + ",A," + aminoAcid.getOneLetterCode() + "," + aminoAcid.getResidueIdentifier().getResidueNumber() + "," + (earlyFoldingResidues.contains(aminoAcid) ? "early" : "late") + "," + "local," + StandardFormat.format(localPlmScores.get(aminoAcid.getResidueIndex()).stream().mapToDouble(Double::valueOf).average().orElse(0.0)) + System.lineSeparator() + pdbId + ",A," + aminoAcid.getOneLetterCode() + "," + aminoAcid.getResidueIdentifier().getResidueNumber() + "," + (earlyFoldingResidues.contains(aminoAcid) ? "early" : "late") + "," + "long-range," + StandardFormat.format(longRangePlmScores.get(aminoAcid.getResidueIndex()).stream().mapToDouble(Double::valueOf).average().orElse(0.0))).collect(Collectors.joining(System.lineSeparator())));
    } catch (Exception e) {
        e.printStackTrace();
        return Optional.empty();
    }
}

Example 50 with Structure

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

the class A03_WriteDatasetCsv method handleLine.

private static Optional<String> handleLine(String line) {
    try {
        System.out.println(line);
        String[] split = line.split(";");
        String entryId = split[0];
        String pdbId = split[1];
        List<Integer> experimentIds = Pattern.compile(",").splitAsStream(split[2].replaceAll("\\[", "").replaceAll("]", "")).map(Integer::valueOf).collect(Collectors.toList());
        Structure structure = StructureParser.fromPdbId(pdbId).parse();
        Chain chain = structure.chains().findFirst().get();
        Start2FoldXmlParser.parseSpecificExperiment(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"), experimentIds);
        EvolutionaryCouplingParser.parseHotSpotFile(chain, Start2FoldConstants.COUPLING_DIRECTORY.resolve(entryId.toUpperCase() + "_hs.html"));
        EQuantParser.parseEQuantFile(chain, Start2FoldConstants.EQUANT_DIRECTORY.resolve(entryId.toLowerCase() + ".equant-small.txt"));
        List<AminoAcid> earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).collect(Collectors.toList());
        List<Integer> functionalResidueNumbers = Start2FoldConstants.extractFunctioanlResidueNumbers(split);
        List<AminoAcid> functionalResidues = new ArrayList<>();
        // do nothing if no annotation of functional residues exists
        if (!functionalResidueNumbers.isEmpty()) {
            FunctionalResidueParser.parse(chain, functionalResidueNumbers);
            chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(FunctionalResidueAnnotation.class).isFunctional()).forEach(functionalResidues::add);
        }
        List<AminoAcid> aminoAcids = chain.aminoAcids().collect(Collectors.toList());
        ProteinGraph conventionalProteinGraph = ProteinGraphFactory.createProteinGraph(chain, ProteinGraphFactory.InteractionScheme.CALPHA8);
        return Optional.of(chain.aminoAcids().map(aminoAcid -> {
            GenericSecondaryStructure sse = aminoAcid.getFeature(GenericSecondaryStructure.class);
            HotSpotScoring hotSpotScoring = aminoAcid.getFeature(HotSpotScoring.class);
            PLIPInteractionContainer plipInteractionContainer = aminoAcid.getFeature(PLIPInteractionContainer.class);
            PLIPInteractionContainer nonLocalPlipInteractionContainer = new PLIPInteractionContainer(null, plipInteractionContainer.getInteractions().stream().filter(inter -> Math.abs(inter.getPartner1().getResidueIndex() - inter.getPartner2().getResidueIndex()) > 5).collect(Collectors.toList()));
            PLIPInteractionContainer localPlipInteractionContainer = new PLIPInteractionContainer(null, plipInteractionContainer.getInteractions().stream().filter(inter -> !nonLocalPlipInteractionContainer.getInteractions().contains(inter)).collect(Collectors.toList()));
            String equantScore = "NA";
            try {
                equantScore = StandardFormat.format(aminoAcid.getFeature(EQuantScore.class).getEvaluation());
            } catch (ComputationException e) {
                logger.warn("missing equant scoring for {}", aminoAcid);
            }
            String functionalAnnotation = "NA";
            if (functionalResidues.size() > 0) {
                functionalAnnotation = functionalResidues.contains(aminoAcid) ? "functional" : "non-functional";
            }
            ResidueTopologicPropertiesContainer residueTopologicPropertiesContainer = aminoAcid.getFeature(ResidueTopologicPropertiesContainer.class);
            double terminusDistance = aminoAcids.indexOf(aminoAcid);
            terminusDistance = Math.min(terminusDistance, aminoAcids.size() - terminusDistance);
            terminusDistance /= (double) aminoAcids.size();
            return pdbId + "," + "A" + "," + aminoAcid.getResidueIdentifier() + "," + aminoAcid.getOneLetterCode() + "," + sse.getSecondaryStructure().getReducedRepresentation() + "," + sse.getSecondaryStructure().getOneLetterRepresentation() + "," + sse.getSurroundingSecondaryStructureElement(aminoAcid).getSize() + "," + (aminoAcid.getFeature(AccessibleSurfaceArea.class).isExposed() ? "exposed" : "buried") + "," + StandardFormat.format(aminoAcid.getFeature(GeometricProperties.class).getDistanceToCentroid()) + "," + StandardFormat.format(terminusDistance) + "," + plipInteractionContainer.getHydrogenBonds().size() + "," + plipInteractionContainer.getHydrophobicInteractions().size() + "," + plipInteractionContainer.getBackboneInteractions().size() + "," + plipInteractionContainer.getInteractions().size() + "," + localPlipInteractionContainer.getHydrogenBonds().size() + "," + localPlipInteractionContainer.getHydrophobicInteractions().size() + "," + localPlipInteractionContainer.getBackboneInteractions().size() + "," + localPlipInteractionContainer.getInteractions().size() + "," + nonLocalPlipInteractionContainer.getHydrogenBonds().size() + "," + nonLocalPlipInteractionContainer.getHydrophobicInteractions().size() + "," + nonLocalPlipInteractionContainer.getBackboneInteractions().size() + "," + nonLocalPlipInteractionContainer.getInteractions().size() + "," + StandardFormat.format(aminoAcid.getFeature(EnergyProfile.class).getSolvationEnergy()) + "," + StandardFormat.format(aminoAcid.getFeature(EgorAgreement.class).getEgorPrediction()) + "," + equantScore + "," + StandardFormat.format(aminoAcid.getFeature(AccessibleSurfaceArea.class).getRelativeAccessibleSurfaceArea()) + "," + StandardFormat.format(aminoAcid.getFeature(LoopFraction.class).getLoopFraction()) + "," + hotSpotScoring.getEcCount() + "," + StandardFormat.format(hotSpotScoring.getCumStrength()) + "," + StandardFormat.format(hotSpotScoring.getEcStrength()) + "," + hotSpotScoring.getConservation() + "," + StandardFormat.format(residueTopologicPropertiesContainer.getFullPlip().getBetweenness()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getFullPlip().getCloseness()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getFullPlip().getClusteringCoefficient()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getHydrogenPlip().getBetweenness()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getHydrogenPlip().getCloseness()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getHydrogenPlip().getClusteringCoefficient()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getHydrophobicPlip().getBetweenness()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getHydrophobicPlip().getCloseness()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getHydrophobicPlip().getClusteringCoefficient()) + "," + conventionalProteinGraph.getContactsOf(aminoAcid).size() + "," + conventionalProteinGraph.getLocalContactsOf(aminoAcid).size() + "," + conventionalProteinGraph.getNonLocalContactsOf(aminoAcid).size() + "," + StandardFormat.format(residueTopologicPropertiesContainer.getConventional().getBetweenness()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getConventional().getCloseness()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getConventional().getClusteringCoefficient()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getFullPlip().getDistinctNeighborhoodCount()) + "," + StandardFormat.format(residueTopologicPropertiesContainer.getConventional().getDistinctNeighborhoodCount()) + "," + (earlyFoldingResidues.contains(aminoAcid) ? "early" : "late") + "," + functionalAnnotation;
        }).collect(Collectors.joining(System.lineSeparator())));
    } catch (Exception e) {
        logger.info("calculation failed for {}", line, e);
        return Optional.empty();
    }
}