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

Example 56 with Structure

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

the class A04_ComputeContactTypeFrequencies method handleLine.

private static void handleLine(String 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);
    List<AminoAcid> earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).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);
    }
    efr += earlyFoldingResidues.size();
    func += functionalResidues.size();
    efr_hb += earlyFoldingResidues.stream().filter(aminoAcid -> aminoAcid.getFeature(PLIPInteractionContainer.class).getHydrogenBonds().size() > 0).count();
    efr_hi += earlyFoldingResidues.stream().filter(aminoAcid -> aminoAcid.getFeature(PLIPInteractionContainer.class).getHydrophobicInteractions().size() > 0).count();
    func_hb += functionalResidues.stream().filter(aminoAcid -> aminoAcid.getFeature(PLIPInteractionContainer.class).getHydrogenBonds().size() > 0).count();
    func_hi += functionalResidues.stream().filter(aminoAcid -> aminoAcid.getFeature(PLIPInteractionContainer.class).getHydrophobicInteractions().size() > 0).count();
}

Example 57 with Structure

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

the class ConfoldServiceWorker method call.

@Override
public ReconstructionResult call() {
    long start = System.currentTimeMillis();
    Path sequencePath = null;
    Path mapPath = null;
    Path secondaryStructurePath = null;
    Path outputDirectory = null;
    try {
        sequencePath = Files.createTempFile("confoldworker-seq", ".fasta");
        mapPath = Files.createTempFile("confoldworker-map", ".rr");
        secondaryStructurePath = Files.createTempFile("confoldworker-sse", ".ss");
        outputDirectory = Files.createTempDirectory("confoldworker-output");
        Files.write(sequencePath, sequence.getBytes());
        Files.write(mapPath, contacts.getBytes());
        Files.write(secondaryStructurePath, secondaryStructure.getBytes());
        String[] arguments = new String[] { serviceLocation, "-rrtype", confoldRRType, "-seq", sequencePath.toFile().getAbsolutePath(), "-rr", mapPath.toFile().getAbsolutePath(), "-ss", secondaryStructurePath.toFile().getAbsolutePath(), "-o", outputDirectory.toFile().getAbsolutePath() };
        logger.debug("spawning confold process with arguments:{}{}", System.lineSeparator(), arguments);
        ProcessBuilder processBuilder = new ProcessBuilder(arguments);
        Process process = processBuilder.start();
        process.waitFor();
        List<Chain> chains = Files.list(outputDirectory.resolve("stage1")).filter(path -> path.toFile().getName().endsWith(".pdb")).filter(path -> path.toFile().getName().contains("_model")).map(path -> StructureParser.fromPath(path).parse()).map(Structure::getFirstChain).collect(Collectors.toList());
        long time = System.currentTimeMillis() - start;
        return new ReconstructionResult(chains, time);
    } catch (IOException | InterruptedException e) {
        throw new RuntimeException(e);
    } finally {
        // cleanup
        tryDeleteFile(sequencePath);
        tryDeleteFile(mapPath);
        tryDeleteFile(secondaryStructurePath);
        tryDeleteDirectory(outputDirectory);
    }
}

Example 58 with Structure

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

the class A07_WriteStructuralInformationByContactCsv 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());
        // boolean sane = split[6].equalsIgnoreCase("true");
        Structure structure = StructureParser.fromPdbId(pdbId).parse();
        Chain chain = structure.chains().findFirst().get();
        LinearAlgebra.PrimitiveDoubleArrayLinearAlgebra centroid = chain.calculate().centroid();
        Path start2foldXml = Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml");
        Start2FoldXmlParser.parseStability(chain, start2foldXml);
        Start2FoldXmlParser.parseSpecificExperiment(chain, start2foldXml, experimentIds);
        List<AminoAcid> earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).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> strongResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isStrong()).collect(Collectors.toList());
        List<AminoAcid> orderedResidues = chain.aminoAcids().filter(aminoAcid -> !aminoAcid.getFeature(GenericSecondaryStructure.class).getSecondaryStructure().isCoilType()).collect(Collectors.toList());
        List<AminoAcid> buriedResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(AccessibleSurfaceArea.class).isBuried()).collect(Collectors.toList());
        List<AminoAcid> residuesInEarlyFoldingSecondaryStructureElements = chain.aminoAcids().filter(aminoAcid -> !aminoAcid.getFeature(GenericSecondaryStructure.class).getSecondaryStructure().isCoilType()).filter(aminoAcid -> {
            GenericSecondaryStructure.SecondaryStructureElement surroundingSecondaryStructureElement = aminoAcid.getFeature(GenericSecondaryStructure.class).getSurroundingSecondaryStructureElement(aminoAcid);
            List<AminoAcid> surroundingAminoAcids = chain.getAminoAcids().subList(surroundingSecondaryStructureElement.getStart(), surroundingSecondaryStructureElement.getEnd() + 1);
            return surroundingAminoAcids.stream().anyMatch(earlyFoldingResidues::contains);
        }).collect(Collectors.toList());
        List<AminoAcid> aromaticResidues = chain.aminoAcids().filter(AminoAcid.Filter.AROMATIC).collect(Collectors.toList());
        List<ContactStructuralInformation> contactStructuralInformation = StructuralInformationParserService.getInstance().parseContactStructuralInformation(Start2FoldConstants.DATA_DIRECTORY.resolve("si").resolve("raw").resolve(entryId.toUpperCase() + ".out"), chain, earlyFoldingResidues);
        ResidueGraph conventionalProteinGraph = ResidueGraph.createResidueGraph(chain, ContactDefinitionFactory.createAlphaCarbonContactDefinition(8.0));
        ResidueGraphCalculations residueGraphCalculations = new ResidueGraphCalculations(conventionalProteinGraph);
        try {
            EvolutionaryCouplingParser.parsePlmScore(contactStructuralInformation, Jsoup.parse(Start2FoldConstants.newInputStream(Start2FoldConstants.COUPLING_DIRECTORY.resolve(entryId + "_ec.html")), "UTF-8", ""), chain.getAminoAcids().size());
        } catch (Exception e) {
        }
        boolean ecAnnotation = contactStructuralInformation.stream().anyMatch(csi -> csi.getPlmScore() != 0.0);
        PLIPInteractionContainer plipInteractionContainer = chain.getFeature(PLIPInteractionContainer.class);
        System.out.println("efr: " + (earlyFoldingResidues.size() > 0) + " strong: " + (strongResidues.size() > 0) + " functional: " + (functionalResidues.size() > 0) + " couplings: " + ecAnnotation);
        return Optional.of(contactStructuralInformation.stream().map(contact -> {
            AminoAcid aminoAcid1 = chain.select().residueNumber(contact.getResidueIdentifier1()).asAminoAcid();
            AminoAcid aminoAcid2 = chain.select().residueNumber(contact.getResidueIdentifier2()).asAminoAcid();
            Pair<AminoAcid, AminoAcid> pair = new Pair<>(aminoAcid1, aminoAcid2);
            ResidueTopologicPropertiesContainer residueTopologicPropertiesContainer1 = aminoAcid1.getFeature(ResidueTopologicPropertiesContainer.class);
            ResidueTopologicPropertiesContainer residueTopologicPropertiesContainer2 = aminoAcid1.getFeature(ResidueTopologicPropertiesContainer.class);
            LinearAlgebra.PrimitiveDoubleArrayLinearAlgebra contactCentroid = aminoAcid1.calculate().centroid().add(aminoAcid2.calculate().centroid()).divide(2);
            return pdbId + "," + "A" + "," + contact.getResidueIdentifier1() + "," + contact.getAa1() + "," + contact.getResidueIdentifier2() + "," + contact.getAa2() + "," + contact.getContactDistanceBin() + "," + (contact.getContactDistanceBin() == ContactDistanceBin.LONG) + "," + (contact.getContactDistanceBin() == ContactDistanceBin.MEDIUM) + "," + (contact.getContactDistanceBin() == ContactDistanceBin.SHORT) + "," + StandardFormat.format(contactCentroid.distance(centroid)) + "," + StandardFormat.format(contact.getAverageRmsdIncrease()) + "," + StandardFormat.format(contact.getAverageTmScoreIncrease()) + "," + StandardFormat.format(contact.getAverageQIncrease()) + "," + StandardFormat.format(contact.getMaximumRmsdIncrease()) + "," + StandardFormat.format(contact.getMaximumTmScoreIncrease()) + "," + StandardFormat.format(contact.getMaximumQIncrease()) + "," + StandardFormat.format(contact.getAverageRmsdIncreaseZScore()) + "," + contact.getFractionOfTopScoringContacts() + "," + StandardFormat.format(contact.getPlmScore()) + "," + contact.getCouplingRank() + "," + contact.istop02() + "," + contact.isTop04() + "," + contact.isTop06() + "," + contact.isTop08() + "," + contact.isTop10() + "," + contact.isTop12() + "," + contact.isTop14() + "," + contact.isTop16() + "," + StandardFormat.format(residueGraphCalculations.betweenness(pair)) + "," + StandardFormat.format(0.5 * residueTopologicPropertiesContainer1.getConventional().getBetweenness() + 0.5 * residueTopologicPropertiesContainer2.getConventional().getBetweenness()) + "," + StandardFormat.format(0.5 * residueTopologicPropertiesContainer1.getConventional().getCloseness() + 0.5 * residueTopologicPropertiesContainer2.getConventional().getCloseness()) + "," + StandardFormat.format(0.5 * residueTopologicPropertiesContainer1.getConventional().getClusteringCoefficient() + 0.5 * residueTopologicPropertiesContainer2.getConventional().getClusteringCoefficient()) + "," + plipInteractionContainer.getHydrogenBonds().stream().anyMatch(hydrogenBond -> isContact(hydrogenBond, aminoAcid1, aminoAcid2)) + "," + plipInteractionContainer.getHydrophobicInteractions().stream().anyMatch(hydrophobicInteraction -> isContact(hydrophobicInteraction, aminoAcid1, aminoAcid2)) + "," + contact.isEarlyFoldingResidue() + "," + contact.isEarlyFoldingContact() + "," + residueIsInCollection(functionalResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + contactIsInCollection(functionalResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + residueIsInCollection(strongResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + contactIsInCollection(strongResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + residueIsInCollection(buriedResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + contactIsInCollection(buriedResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + residueIsInCollection(orderedResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + contactIsInCollection(orderedResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + residueIsInCollection(residuesInEarlyFoldingSecondaryStructureElements, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + contactIsInCollection(residuesInEarlyFoldingSecondaryStructureElements, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + residueIsInCollection(aromaticResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + contactIsInCollection(aromaticResidues, contact.getResidueIdentifier1(), contact.getResidueIdentifier2()) + "," + (earlyFoldingResidues.size() > 0) + "," + (strongResidues.size() > 0) + "," + (functionalResidues.size() > 0) + "," + ecAnnotation;
        }).collect(Collectors.joining(System.lineSeparator())));
    } catch (Exception e) {
        logger.info("calculation failed for {}\nby: {}", line, e.getMessage());
        return Optional.empty();
    }
}

Example 59 with Structure

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

the class A01_CreateContactMaps method handleFile.

private static void handleFile(String line) {
    String[] split = line.split(";");
    String stfId = 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.fromPath(BASE_PATH.resolve("pdb").resolve(stfId + ".pdb")).parse();
    Chain chain = structure.chainsWithAminoAcids().findFirst().get();
    String sequence = chain.getAminoAcidSequence();
    String secondaryStructureString = chain.aminoAcids().map(aminoAcid -> aminoAcid.getFeature(GenericSecondaryStructure.class)).map(GenericSecondaryStructure::getSecondaryStructure).map(SecondaryStructureType::getReducedRepresentation).collect(Collectors.joining()).toUpperCase();
    Start2FoldConstants.write(BASE_PATH.resolve("reconstruction").resolve("fasta").resolve(stfId + ".fasta"), ">" + stfId + System.lineSeparator() + sequence);
    Start2FoldConstants.write(BASE_PATH.resolve("reconstruction").resolve("sse").resolve(stfId + ".sse"), ">" + stfId + System.lineSeparator() + secondaryStructureString);
    Start2FoldXmlParser.parseSpecificExperiment(chain, Start2FoldConstants.XML_DIRECTORY.resolve(stfId + ".xml"), experimentIds);
    List<AminoAcid> aminoAcids = chain.aminoAcids().collect(Collectors.toList());
    List<AminoAcid> earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).collect(Collectors.toList());
    List<Pair<AminoAcid, AminoAcid>> contacts = SetOperations.unorderedPairsOf(aminoAcids).filter(pair -> areNonCovalentGroups(pair.getLeft(), pair.getRight())).filter(pair -> ProteinGraphFactory.InteractionScheme.CALPHA8.areInContact(pair.getLeft(), pair.getRight())).collect(Collectors.toList());
    List<Pair<AminoAcid, AminoAcid>> earlyFoldingContacts = contacts.stream().filter(pair -> earlyFoldingResidues.contains(pair.getLeft()) && earlyFoldingResidues.contains(pair.getRight())).collect(Collectors.toList());
    String percentage = StandardFormat.formatToInteger(100 * earlyFoldingContacts.size() / (double) contacts.size());
    System.out.println("fraction of EFR contacts is " + percentage + "%: " + earlyFoldingContacts.size() + " " + contacts.size());
    Start2FoldConstants.write(MAP_PATH.resolve(stfId + "-sampled-100-1.rr"), composeRRString(contacts, sequence));
    Start2FoldConstants.write(MAP_PATH.resolve(stfId + "-efr-" + percentage + "-1.rr"), composeRRString(earlyFoldingContacts, sequence));
    for (int i = 5; i < 100; i = i + 5) {
        int numberOfContactsToSelect = (int) (i / (double) 100 * contacts.size());
        for (int j = 1; j < 6; j++) {
            Collections.shuffle(contacts);
            List<Pair<AminoAcid, AminoAcid>> selectedContacts = contacts.subList(0, numberOfContactsToSelect);
            Start2FoldConstants.write(MAP_PATH.resolve(stfId + "-random-" + i + "-" + j + ".rr"), composeRRString(selectedContacts, sequence));
        }
    }
    // create samplings of random residues
    for (int i = 5; i < 100; i = i + 5) {
        int numberOfResiduesToSelect = (int) (i / (double) 100 * aminoAcids.size());
        for (int j = 1; j < 6; j++) {
            Collections.shuffle(aminoAcids);
            List<AminoAcid> selectedAminoAcids = aminoAcids.subList(0, numberOfResiduesToSelect);
            Start2FoldConstants.write(MAP_PATH.resolve(stfId + "-residues-" + i + "-" + j + ".rr"), composeRRString(contacts.stream().filter(contact -> selectedAminoAcids.contains(contact.getLeft()) && selectedAminoAcids.contains(contact.getRight())).collect(Collectors.toList()), sequence));
        }
    }
    // create samplings of comparable nature of EFR contacts
    for (int j = 1; j < 6; j++) {
        int numberOfResiduesToSelect = earlyFoldingResidues.size();
        List<AminoAcid> interactingResidues = getInteractingResidues(aminoAcids, contacts, numberOfResiduesToSelect);
        Start2FoldConstants.write(MAP_PATH.resolve(stfId + "-interacting-" + percentage + "-" + j + ".rr"), composeRRString(contacts.stream().filter(contact -> interactingResidues.contains(contact.getLeft()) && interactingResidues.contains(contact.getRight())).collect(Collectors.toList()), sequence));
    }
    // create bin samplings of comparable nature of EFR contacts
    for (int i = 5; i < 100; i = i + 5) {
        int numberOfResiduesToSelect = (int) (i / (double) 100 * aminoAcids.size());
        for (int j = 1; j < 6; j++) {
            List<AminoAcid> interactingResidues = getInteractingResidues(aminoAcids, contacts, numberOfResiduesToSelect);
            Start2FoldConstants.write(MAP_PATH.resolve(stfId + "-interacting2-" + percentage + "-" + j + ".rr"), composeRRString(contacts.stream().filter(contact -> interactingResidues.contains(contact.getLeft()) && interactingResidues.contains(contact.getRight())).collect(Collectors.toList()), sequence));
        }
    }
}

Example 60 with Structure

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

the class A02_CreatePyMolRenderJobsForStrongResidues method composePyMolCommand.

private static Optional<String> composePyMolCommand(Path path) {
    try {
        String entryId = path.toFile().getName().split("\\.")[0];
        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, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"));
        List<Integer> strongResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isStrong()).map(AminoAcid::getResidueIdentifier).map(ResidueIdentifier::getResidueNumber).collect(Collectors.toList());
        if (strongResidues.isEmpty()) {
            return Optional.empty();
        }
        return Optional.of("delete all" + System.lineSeparator() + "fetch " + pdbId + ", async=0" + System.lineSeparator() + // hide non-relevant stuff
        "hide everything" + System.lineSeparator() + "show cartoon, chain A" + System.lineSeparator() + // decolor everything
        "color grey80" + System.lineSeparator() + "zoom (chain A)" + System.lineSeparator() + strongResidues.stream().map(res -> "color efr, resi " + res).collect(Collectors.joining(System.lineSeparator())) + System.lineSeparator() + "ray" + System.lineSeparator() + "png " + Start2FoldConstants.PYMOL_DIRECTORY.resolve(entryId + "-strong.png") + System.lineSeparator());
    } catch (IOException e) {
        return Optional.empty();
    }
}