Examples with ReconstructionResult de.bioforscher.jstructure.si.model.ReconstructionResult used on opensource projects

Example 1 with ReconstructionResult

use of de.bioforscher.jstructure.si.model.ReconstructionResult 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 2 with ReconstructionResult

use of de.bioforscher.jstructure.si.model.ReconstructionResult 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 3 with ReconstructionResult

use of de.bioforscher.jstructure.si.model.ReconstructionResult 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);
    }
}

Example 4 with ReconstructionResult

use of de.bioforscher.jstructure.si.model.ReconstructionResult 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);
    }
}