Examples with AlignmentException de.bioforscher.jstructure.align.AlignmentException used on opensource projects

Example 1 with AlignmentException

use of de.bioforscher.jstructure.align.AlignmentException in project jstructure by JonStargaryen.

the class ContactTogglingReconstruction method computePerformance.

private void computePerformance(List<Chain> reconstructions) throws AlignmentException, IOException {
    List<TMAlignAlignmentResult> alignmentResults = new ArrayList<>();
    List<ReconstructionContactMap> reconstructionContactMaps = 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[] { baselineReconstruction.getTmalignPath(), baselineReconstruction.getReferenceChainPath().toFile().getAbsolutePath(), reconstructPath.toFile().getAbsolutePath() }));
        reconstructionContactMaps.add(ReconstructionContactMap.createReconstructionContactMap(reconstructedChain, baselineReconstruction.getFullMap().getContactDefinition()));
    }
    averageRmsd = alignmentResults.stream().map(TMAlignAlignmentResult::getRootMeanSquareDeviation).mapToDouble(RootMeanSquareDeviation::getScore).average().orElseThrow(() -> new ComputationException("could not generate toggled reconstructs"));
    averageTmScore = alignmentResults.stream().map(TMAlignAlignmentResult::getTemplateModelingScore1).mapToDouble(TemplateModelingScore::getScore).average().orElseThrow(() -> new ComputationException("could not generate toggled reconstructs"));
    averageQ = reconstructionContactMaps.stream().mapToDouble(reconstructContactMap -> BaselineReconstruction.computeQ(baselineReconstruction.getFullMap(), reconstructContactMap)).average().orElseThrow(() -> new ComputationException("could not generate toggled reconstructs"));
    logger.info("[{} / {}]: {} reconstruction of contact {}", counter, numberOfCombinations, contactWasRemoved ? "removal" : "addition", contactToToggle);
    logger.info("[{} / {}]: average RMSD: {}, average TM-score: {}, average Q: {}", counter, numberOfCombinations, StandardFormat.format(averageRmsd), StandardFormat.format(averageTmScore), StandardFormat.format(averageQ));
    if (contactWasRemoved) {
        decreaseRmsd = averageRmsd - baselineReconstruction.getAverageRmsd();
        increaseTMScore = baselineReconstruction.getAverageTmScore() - averageTmScore;
        increaseQ = baselineReconstruction.getAverageQ() - averageQ;
    } else {
        decreaseRmsd = baselineReconstruction.getAverageRmsd() - averageRmsd;
        increaseTMScore = averageTmScore - baselineReconstruction.getAverageTmScore();
        increaseQ = averageQ - baselineReconstruction.getAverageQ();
    }
    logger.info("[{} / {}]: decrease RMSD: {}, increase TM-score: {}, increase Q: {}", counter, numberOfCombinations, StandardFormat.format(decreaseRmsd), StandardFormat.format(increaseTMScore), StandardFormat.format(increaseQ));
    // cleanup
    for (Path tmpFile : tmpFiles) {
        Files.delete(tmpFile);
    }
}

Example 2 with AlignmentException

use of de.bioforscher.jstructure.align.AlignmentException in project jstructure by JonStargaryen.

the class TMAlignService method process.

public TMAlignAlignmentResult process(StructureAlignmentQuery structureAlignmentQuery) throws AlignmentException {
    try {
        Path referencePath = writeStructureToTemporaryFile(structureAlignmentQuery.getReference());
        Path queryPath = writeStructureToTemporaryFile(structureAlignmentQuery.getQuery());
        String[] arguments = new String[] { getServiceLocation(), referencePath.toFile().toString(), queryPath.toFile().toString() };
        TMAlignAlignmentResult result = process(arguments);
        Files.delete(referencePath);
        Files.delete(queryPath);
        return result;
    } catch (IOException e) {
        throw new AlignmentException("could not run tmalign", e);
    }
}

Example 3 with AlignmentException

use of de.bioforscher.jstructure.align.AlignmentException 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 AlignmentException

use of de.bioforscher.jstructure.align.AlignmentException 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 AlignmentException

use of de.bioforscher.jstructure.align.AlignmentException in project jstructure by JonStargaryen.

the class TMAlignService method process.

private synchronized TMAlignAlignmentResult process(String[] arguments, int run) throws AlignmentException {
    try {
        logger.debug("spawning tmalign process with arguments:{}{}", System.lineSeparator(), arguments);
        ProcessBuilder processBuilder = new ProcessBuilder(arguments);
        Process process = processBuilder.start();
        List<String> outputLines;
        try (BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()))) {
            outputLines = br.lines().collect(Collectors.toList());
        }
        List<String> errorLines;
        try (BufferedReader br = new BufferedReader(new InputStreamReader(process.getErrorStream()))) {
            errorLines = br.lines().collect(Collectors.toList());
        }
        process.waitFor();
        if (outputLines.stream().anyMatch(line -> line.startsWith("Can not open file:"))) {
            throw new ComputationException("error during tmalign execution:" + System.lineSeparator() + outputLines.stream().collect(Collectors.joining(System.lineSeparator())));
        }
        // errors are not reported in error stream
        if (!errorLines.isEmpty()) {
            throw new ComputationException("error during tmalign execution:" + System.lineSeparator() + errorLines.stream().collect(Collectors.joining(System.lineSeparator())));
        }
        int length1 = 0;
        int length2 = 0;
        int alignedLength = 0;
        RootMeanSquareDeviation rootMeanSquareDeviation = null;
        double seqId = 0;
        TemplateModelingScore templateModelingScore1 = null;
        TemplateModelingScore templateModelingScore2 = null;
        for (String outputLine : outputLines) {
            if (outputLine.startsWith("Length of Chain_1")) {
                length1 = Integer.valueOf(outputLine.split(":")[1].trim().split("\\s+")[0]);
            } else if (outputLine.startsWith("Length of Chain_2")) {
                length2 = Integer.valueOf(outputLine.split(":")[1].trim().split("\\s+")[0]);
            } else if (outputLine.startsWith("Aligned length")) {
                String[] split = outputLine.split("=");
                alignedLength = Integer.valueOf(split[1].split(",")[0].trim());
                rootMeanSquareDeviation = new RootMeanSquareDeviation(Double.valueOf(split[2].split(",")[0].trim()));
                seqId = Double.valueOf(split[4].trim());
            } else if (outputLine.startsWith("TM-score")) {
                double tmscore = Double.valueOf(outputLine.split("=")[1].split("\\(")[0].trim());
                TemplateModelingScore templateModelingScore = new TemplateModelingScore(tmscore);
                if (outputLine.contains("Chain_1")) {
                    templateModelingScore1 = templateModelingScore;
                } else {
                    templateModelingScore2 = templateModelingScore;
                }
            }
        }
        return new TMAlignAlignmentResult(length1, length2, alignedLength, rootMeanSquareDeviation, seqId, templateModelingScore1, templateModelingScore2);
    } catch (Exception e) {
        if (run > 3) {
            logger.warn("tmalign computation finally failed:{}{}", System.lineSeparator(), Arrays.toString(arguments), e);
            throw new AlignmentException("could not run tmalign", e);
        }
        return process(arguments, run + 1);
    }
}