Examples with Pair de.bioforscher.jstructure.mathematics.Pair used on opensource projects

Example 1 with Pair

use of de.bioforscher.jstructure.mathematics.Pair in project jstructure by JonStargaryen.

the class StructuralInformationService method process.

public void process(Chain referenceChain, String jobName, Path confoldPath, Path tmalignPath, Path outputDirectory, int numberOfThreads, double baselineFrequency) {
    try {
        ExecutorService executorService = Executors.newFixedThreadPool(numberOfThreads);
        List<AminoAcid> aminoAcids = referenceChain.aminoAcids().collect(Collectors.toList());
        int numberOfAminoAcids = aminoAcids.size();
        ReconstructionContactMap fullMap = ReconstructionContactMap.createReconstructionContactMap(referenceChain, ContactDefinitionFactory.createAlphaCarbonContactDefinition(8.0));
        List<Pair<AminoAcid, AminoAcid>> contacts = fullMap.getLongRangeContacts();
        int numberOfLongRangeContacts = contacts.size();
        String sequence = fullMap.getSequence();
        String secondaryStructure = fullMap.getSecondaryStructureElements();
        // report general statistics
        logger.info("evaluating structural information of chain with {} residues and {} long-range contacts", numberOfAminoAcids, numberOfLongRangeContacts);
        logger.info("present long-range contacts:{}{}", System.lineSeparator(), composeConsoleOutput(fullMap.getLongRangeContacts()));
        logger.info("coverage per position:{}{}", System.lineSeparator(), aminoAcids.stream().map(fullMap::getNonLocalContactsOf).mapToInt(List::size).mapToObj(size -> {
            if (size < 10) {
                return String.valueOf(size);
            } else {
                return "*";
            }
        }).collect(Collectors.joining()));
        // write reference structure
        Path referenceChainStructurePath = Files.createTempFile("confoldservice-ref", ".pdb");
        Files.write(referenceChainStructurePath, referenceChain.getPdbRepresentation().getBytes());
        // create outputDirectory
        Path reconstructionDirectory = outputDirectory.resolve(jobName);
        if (!Files.exists(reconstructionDirectory)) {
            Files.createDirectory(reconstructionDirectory);
        }
        // create sampling containers
        List<Future<BaselineReconstruction>> baselineFutures = new ArrayList<>();
        for (int iteration = 0; iteration < COVERAGE; iteration++) {
            baselineFutures.add(executorService.submit(new BaselineReconstruction(iteration, referenceChainStructurePath, referenceChain, fullMap, sequence, secondaryStructure, baselineFrequency, confoldPath.toFile().getAbsolutePath(), tmalignPath.toFile().getAbsolutePath(), outputDirectory, jobName)));
        }
        List<BaselineReconstruction> baselineReconstructions = baselineFutures.stream().map(this::getBaselineFuture).collect(Collectors.toList());
        // create toggling reconstructions
        int numberOfCombinations = baselineReconstructions.size() * contacts.size();
        logger.info("reconstructing individual maps by contact toggling - evaluating {} combinations", numberOfCombinations);
        int counter = 1;
        List<Future<ContactTogglingReconstruction>> contactToggleFutures = new ArrayList<>();
        for (Pair<AminoAcid, AminoAcid> contact : contacts) {
            for (BaselineReconstruction baselineReconstruction : baselineReconstructions) {
                contactToggleFutures.add(executorService.submit(baselineReconstruction.createContactTogglingReconstruction(contact, counter, numberOfCombinations)));
                counter++;
            }
        }
        Path outputPath = outputDirectory.resolve(jobName + ".out");
        FileWriter outputWriter = new FileWriter(outputPath.toFile());
        contactToggleFutures.stream().map(this::getContactToggleFuture).filter(Optional::isPresent).map(Optional::get).map(contactTogglingReconstruction -> contactTogglingReconstruction.getContactToToggle() + "\t" + contactTogglingReconstruction.isContactWasRemoved() + "\t" + StandardFormat.format(contactTogglingReconstruction.getBaselineReconstruction().getAverageRmsd()) + "\t" + StandardFormat.format(contactTogglingReconstruction.getBaselineReconstruction().getAverageTmScore()) + "\t" + StandardFormat.format(contactTogglingReconstruction.getBaselineReconstruction().getAverageQ()) + "\t" + StandardFormat.format(contactTogglingReconstruction.getAverageRmsd()) + "\t" + StandardFormat.format(contactTogglingReconstruction.getAverageTmScore()) + "\t" + StandardFormat.format(contactTogglingReconstruction.getAverageQ()) + "\t" + StandardFormat.format(contactTogglingReconstruction.getDecreaseRmsd()) + "\t" + StandardFormat.format(contactTogglingReconstruction.getIncreaseTMScore()) + "\t" + StandardFormat.format(contactTogglingReconstruction.getIncreaseQ()) + System.lineSeparator()).forEach(line -> {
            try {
                outputWriter.write(line);
                outputWriter.flush();
            } catch (IOException e) {
                throw new UncheckedIOException(e);
            }
        });
        // clean up
        outputWriter.close();
        Files.delete(referenceChainStructurePath);
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}

Example 2 with Pair

use of de.bioforscher.jstructure.mathematics.Pair in project jstructure by JonStargaryen.

the class BaselineReconstruction method call.

@Override
public BaselineReconstruction call() throws Exception {
    logger.info("submitting baseline reconstruction job with id {}", iteration);
    // create sampling of full map
    List<Pair<AminoAcid, AminoAcid>> fullContacts = fullMap.getLongRangeContacts();
    Collections.shuffle(fullContacts);
    int numberOfContactsToSelect = (int) (fullContacts.size() * baselineFrequency);
    List<Pair<AminoAcid, AminoAcid>> sampledContacts = fullContacts.subList(0, numberOfContactsToSelect);
    this.sampledMap = new ReconstructionContactMap(referenceChain.aminoAcids().collect(Collectors.toList()), sampledContacts, fullMap.getContactDefinition());
    // reconstruct sampled baseline map
    sampledReconstructions = new ConfoldServiceWorker(confoldPath, sequence, secondaryStructure, sampledMap.getCaspRRRepresentation(), fullMap.getConfoldRRType()).call().getChains();
    // write reconstruction files
    Path reconstructionDirectory = outputPath.resolve(jobname);
    for (int i = 1; i <= sampledReconstructions.size(); i++) {
        Files.write(reconstructionDirectory.resolve("baseline-reconstruction-" + iteration + "-" + i + ".pdb"), sampledReconstructions.get(i - 1).getPdbRepresentation().getBytes());
    }
    // score baseline models
    computeBaselinePerformance(sampledReconstructions);
    return this;
}

Example 3 with Pair

use of de.bioforscher.jstructure.mathematics.Pair in project jstructure by JonStargaryen.

the class A03_ReconstructByVariousStrategy method handleChain.

private static void handleChain(ExplorerChain explorerChain) {
    logger.info("[{}] starting job", explorerChain.getStfId());
    try {
        Chain nativeChain = explorerChain.getChain();
        Path nativeChainPath = Files.createTempFile("nativechain-", ".pdb");
        Files.write(nativeChainPath, nativeChain.getPdbRepresentation().getBytes());
        List<ContactStructuralInformation> contactStructuralInformation = explorerChain.getContacts();
        // annotate with PLIP data
        PLIPInteractionContainer plipInteractionContainer = nativeChain.getFeature(PLIPInteractionContainer.class);
        for (ContactStructuralInformation csi : contactStructuralInformation) {
            AminoAcid aminoAcid1 = nativeChain.select().residueNumber(csi.getResidueIdentifier1()).asAminoAcid();
            AminoAcid aminoAcid2 = nativeChain.select().residueNumber(csi.getResidueIdentifier2()).asAminoAcid();
            if (plipInteractionContainer.getHydrogenBonds().stream().anyMatch(hydrogenBond -> isContact(hydrogenBond, aminoAcid1, aminoAcid2))) {
                csi.markAsHydrogenBond();
            }
            if (plipInteractionContainer.getHydrophobicInteractions().stream().anyMatch(hydrophobicInteraction -> isContact(hydrophobicInteraction, aminoAcid1, aminoAcid2))) {
                csi.markAsHydrophobicInteraction();
            }
        }
        int numberOfNativeContacts = contactStructuralInformation.size();
        int numberOfContactsToSelect = (int) (numberOfNativeContacts * DEFAULT_COVERAGE);
        List<ReconstructionContactMap> contactMaps = Stream.of(ReconstructionStrategyDefinition.values()).map(ReconstructionStrategyDefinition::getReconstructionStrategy).flatMap(reconstructionStrategy -> IntStream.range(0, REDUNDANCY).boxed().flatMap(i -> {
            if (!reconstructionStrategy.isNegatable()) {
                ReconstructionContactMap contactMap = reconstructionStrategy.composeReconstructionContactMap(nativeChain, contactStructuralInformation, numberOfContactsToSelect);
                contactMap.setName(reconstructionStrategy.getName() + "-" + (i + 1));
                return Stream.of(contactMap);
            } else {
                // short, long, hydrogen, and hydrophobic bins have to be negated explicitly to get comparable results
                Pair<ReconstructionContactMap, ReconstructionContactMap> contactMapPair = reconstructionStrategy.composeReconstructionAndNegatedReconstructionContactMap(nativeChain, contactStructuralInformation, numberOfContactsToSelect);
                contactMapPair.getLeft().setName(reconstructionStrategy.getName() + "-" + (i + 1));
                contactMapPair.getRight().setName(reconstructionStrategy.getNegatedName() + "-" + (i + 1));
                return Stream.of(contactMapPair.getLeft(), contactMapPair.getRight());
            }
        })).filter(reconstructionContactMap -> reconstructionContactMap.getNumberOfContacts() > 0).collect(Collectors.toList());
        Map<String, List<Future<ReconstructionResult>>> reconstructionFutures = new HashMap<>();
        for (ReconstructionContactMap contactMap : contactMaps) {
            String name = contactMap.getName().split("-")[0];
            logger.info("[{}] handling contact map definition {}", explorerChain.getStfId(), name);
            if (!reconstructionFutures.containsKey(name)) {
                reconstructionFutures.put(name, new ArrayList<>());
            }
            List<Future<ReconstructionResult>> bin = reconstructionFutures.get(name);
            bin.add(executorService.submit(new ConfoldServiceWorker("/home/sb/programs/confold_v1.0/confold.pl", contactMap.getSequence(), contactMap.getSecondaryStructureElements(), contactMap.getCaspRRRepresentation(), contactMap.getConfoldRRType())));
        }
        for (Map.Entry<String, List<Future<ReconstructionResult>>> reconstructionFuture : reconstructionFutures.entrySet()) {
            try {
                String name = reconstructionFuture.getKey();
                List<Chain> reconstructions = reconstructionFuture.getValue().stream().map(future -> {
                    try {
                        return future.get();
                    } catch (Exception e) {
                        throw new ComputationException(e);
                    }
                }).map(ReconstructionResult::getChains).flatMap(Collection::stream).collect(Collectors.toList());
                logger.info("[{}][{}] {} reconstructs in bin", explorerChain.getStfId(), name, reconstructions.size());
                List<TMAlignAlignmentResult> alignmentResults = new ArrayList<>();
                List<Path> tmpFiles = new ArrayList<>();
                if (reconstructions.isEmpty()) {
                    throw new ComputationException("reconstruction did not yield any reconstructs");
                }
                for (Chain reconstructedChain : reconstructions) {
                    Path reconstructPath = Files.createTempFile("confoldservice-recon", ".pdb");
                    tmpFiles.add(reconstructPath);
                    Files.write(reconstructPath, reconstructedChain.getPdbRepresentation().getBytes());
                    alignmentResults.add(TM_ALIGN_SERVICE.process(new String[] { "/home/sb/programs/tmalign", nativeChainPath.toFile().getAbsolutePath(), reconstructPath.toFile().getAbsolutePath() }));
                }
                logger.info("[{}][{}] {} alignments in bin", explorerChain.getStfId(), name, alignmentResults.size());
                if (alignmentResults.isEmpty()) {
                    throw new ComputationException("tmalign did not yield any alignments");
                }
                for (TMAlignAlignmentResult alignmentResult : alignmentResults) {
                    double rmsd = alignmentResult.getRootMeanSquareDeviation().getScore();
                    String line = explorerChain.getStfId() + "," + name + "," + rmsd;
                    logger.info("[{}][{}] {}", explorerChain.getStfId(), name, line);
                    fileWriter.write(line + System.lineSeparator());
                    fileWriter.flush();
                }
                // cleanup
                for (Path tmpFile : tmpFiles) {
                    Files.delete(tmpFile);
                }
            } catch (IOException e) {
                throw new ComputationException(e);
            }
        }
    } catch (IOException | AlignmentException e) {
        throw new ComputationException(e);
    }
}

Example 4 with Pair

use of de.bioforscher.jstructure.mathematics.Pair in project jstructure by JonStargaryen.

the class A04_CreateRmsdVsCoveragePlot method handleChain.

private static void handleChain(ExplorerChain explorerChain) {
    logger.info("handling chain {}", explorerChain.getStfId());
    try {
        Chain nativeChain = explorerChain.getChain();
        Path nativeChainPath = Files.createTempFile("nativechain-", ".pdb");
        Files.write(nativeChainPath, nativeChain.getPdbRepresentation().getBytes());
        ReconstructionContactMap nativeContactMap = ReconstructionContactMap.createReconstructionContactMap(nativeChain, ContactDefinitionFactory.createAlphaCarbonContactDefinition(8.0));
        List<AminoAcid> aminoAcids = nativeChain.getAminoAcids();
        List<Pair<AminoAcid, AminoAcid>> contacts = nativeContactMap.getLongRangeContacts();
        int numberNativeLongRangeContacts = contacts.size();
        List<ReconstructionContactMap> reconstructionContactMaps = new ArrayList<>();
        for (int coverage = 5; coverage <= 100; coverage = coverage + 5) {
            int numberOfContactsToSelect = (int) Math.round(0.01 * coverage * numberNativeLongRangeContacts);
            for (int run = 0; run < REDUNDANCY; run++) {
                Collections.shuffle(contacts);
                List<Pair<AminoAcid, AminoAcid>> selectedContacts = contacts.subList(0, numberOfContactsToSelect);
                ReconstructionContactMap contactMap = new ReconstructionContactMap(aminoAcids, selectedContacts, nativeContactMap.getContactDefinition());
                contactMap.setName("p" + coverage + "-" + (run + 1));
                reconstructionContactMaps.add(contactMap);
            }
        }
        Map<String, List<Future<ReconstructionResult>>> reconstructionFutures = new HashMap<>();
        for (ReconstructionContactMap contactMap : reconstructionContactMaps) {
            String name = contactMap.getName().split("-")[0];
            logger.info("handling contact map with coverage {}", name);
            if (!reconstructionFutures.containsKey(name)) {
                reconstructionFutures.put(name, new ArrayList<>());
            }
            List<Future<ReconstructionResult>> bin = reconstructionFutures.get(name);
            bin.add(executorService.submit(new ConfoldServiceWorker("/home/sb/programs/confold_v1.0/confold.pl", contactMap.getSequence(), contactMap.getSecondaryStructureElements(), contactMap.getCaspRRRepresentation(), nativeContactMap.getConfoldRRType())));
        }
        for (Map.Entry<String, List<Future<ReconstructionResult>>> reconstructionFuture : reconstructionFutures.entrySet()) {
            try {
                String name = reconstructionFuture.getKey();
                List<Chain> reconstructions = reconstructionFuture.getValue().stream().map(future -> {
                    try {
                        return future.get();
                    } catch (Exception e) {
                        throw new ComputationException(e);
                    }
                }).map(ReconstructionResult::getChains).flatMap(Collection::stream).collect(Collectors.toList());
                List<TMAlignAlignmentResult> alignmentResults = new ArrayList<>();
                List<Path> tmpFiles = new ArrayList<>();
                for (Chain reconstructedChain : reconstructions) {
                    Path reconstructPath = Files.createTempFile("confoldservice-recon", ".pdb");
                    tmpFiles.add(reconstructPath);
                    Files.write(reconstructPath, reconstructedChain.getPdbRepresentation().getBytes());
                    alignmentResults.add(TM_ALIGN_SERVICE.process(new String[] { "/home/sb/programs/tmalign", nativeChainPath.toFile().getAbsolutePath(), reconstructPath.toFile().getAbsolutePath() }));
                }
                if (alignmentResults.isEmpty()) {
                    throw new ComputationException("tmalign did not yield any alignments");
                }
                for (TMAlignAlignmentResult alignmentResult : alignmentResults) {
                    double rmsd = alignmentResult.getRootMeanSquareDeviation().getScore();
                    String line = explorerChain.getStfId() + "," + name.replace("p", "") + "," + rmsd;
                    logger.info(line);
                    fileWriter.write(line + System.lineSeparator());
                    fileWriter.flush();
                }
                // cleanup
                for (Path tmpFile : tmpFiles) {
                    Files.delete(tmpFile);
                }
            } catch (IOException e) {
                throw new ComputationException(e);
            }
        }
    } catch (IOException | AlignmentException e) {
        throw new ComputationException(e);
    }
}

Example 5 with Pair

use of de.bioforscher.jstructure.mathematics.Pair in project jstructure by JonStargaryen.

the class A04A_CreatePyMolRendering method handleChain.

private static void handleChain(ExplorerChain explorerChain) {
    logger.info("handling chain {}", explorerChain.getStfId());
    try {
        Chain nativeChain = explorerChain.getChain();
        Path nativeChainPath = Files.createTempFile("nativechain-", ".pdb");
        Files.write(nativeChainPath, nativeChain.getPdbRepresentation().getBytes());
        ReconstructionContactMap nativeContactMap = ReconstructionContactMap.createReconstructionContactMap(nativeChain, ContactDefinitionFactory.createAlphaCarbonContactDefinition(8.0));
        List<AminoAcid> aminoAcids = nativeChain.getAminoAcids();
        List<Pair<AminoAcid, AminoAcid>> contacts = nativeContactMap.getLongRangeContacts();
        int numberNativeLongRangeContacts = contacts.size();
        List<ReconstructionContactMap> reconstructionContactMaps = new ArrayList<>();
        IntStream.of(5, 30, 100).forEach(coverage -> {
            int numberOfContactsToSelect = (int) Math.round(0.01 * coverage * numberNativeLongRangeContacts);
            for (int run = 0; run < REDUNDANCY; run++) {
                Collections.shuffle(contacts);
                List<Pair<AminoAcid, AminoAcid>> selectedContacts = contacts.subList(0, numberOfContactsToSelect);
                ReconstructionContactMap contactMap = new ReconstructionContactMap(aminoAcids, selectedContacts, nativeContactMap.getContactDefinition());
                contactMap.setName("p" + coverage + "-" + (run + 1));
                reconstructionContactMaps.add(contactMap);
            }
        });
        Map<String, List<Future<ReconstructionResult>>> reconstructionFutures = new HashMap<>();
        for (ReconstructionContactMap contactMap : reconstructionContactMaps) {
            String name = contactMap.getName().split("-")[0];
            logger.info("handling contact map with coverage {}", name);
            if (!reconstructionFutures.containsKey(name)) {
                reconstructionFutures.put(name, new ArrayList<>());
            }
            List<Future<ReconstructionResult>> bin = reconstructionFutures.get(name);
            bin.add(executorService.submit(new ConfoldServiceWorker("/home/sb/programs/confold_v1.0/confold.pl", contactMap.getSequence(), contactMap.getSecondaryStructureElements(), contactMap.getCaspRRRepresentation(), nativeContactMap.getConfoldRRType())));
        }
        for (Map.Entry<String, List<Future<ReconstructionResult>>> reconstructionFuture : reconstructionFutures.entrySet()) {
            try {
                String name = reconstructionFuture.getKey();
                List<Chain> reconstructions = reconstructionFuture.getValue().stream().map(future -> {
                    try {
                        return future.get();
                    } catch (Exception e) {
                        throw new ComputationException(e);
                    }
                }).map(ReconstructionResult::getChains).flatMap(Collection::stream).collect(Collectors.toList());
                for (Chain reconstructedChain : reconstructions) {
                    Files.write(OUTPUT_PATH.resolve(name + ".pdb"), reconstructedChain.getPdbRepresentation().getBytes());
                }
            } catch (IOException e) {
                throw new ComputationException(e);
            }
        }
    } catch (IOException e) {
        throw new ComputationException(e);
    }
}