Examples with ComputationException de.bioforscher.jstructure.model.feature.ComputationException used on opensource projects

Example 6 with ComputationException

use of de.bioforscher.jstructure.model.feature.ComputationException in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfiler method fetchLigandInteractions.

public InteractionContainer fetchLigandInteractions(Structure structure) {
    try {
        String pdbId = structure.getProteinIdentifier().getPdbId();
        String boundary = Long.toHexString(System.currentTimeMillis());
        URLConnection connection = (new URL("https://biosciences.hs-mittweida.de/plip/api/provided/ligand/" + pdbId)).openConnection();
        connection.setDoOutput(true);
        connection.setRequestProperty("Content-Type", "multipart/form-data; boundary=" + boundary);
        connection.setRequestProperty("Authorization", "Basic " + secret);
        BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream()));
        StringBuilder response = new StringBuilder();
        String outputContent;
        while ((outputContent = in.readLine()) != null) {
            response.append(outputContent);
        }
        in.close();
        Document document = Jsoup.parse(response.toString());
        return parseDocument(structure, document);
    } catch (Exception e) {
        // TODO this happens as no ligand interactions are precomputed at biosciences
        throw new ComputationException(e);
    }
}

Example 7 with ComputationException

use of de.bioforscher.jstructure.model.feature.ComputationException in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfiler method writePolymerInteractions.

public void writePolymerInteractions(Chain chain, Path outputPath) {
    try {
        Path outputDirectoryPath = createTemporaryOutputDirectory();
        Structure structure = chain.getParentStructure();
        String[] commandLineCall = composePolymerCommandLineCall(structure, outputDirectoryPath, chain.getChainIdentifier().getChainId());
        // execute command
        executeCommandLineCall(commandLineCall);
        Path output = outputDirectoryPath.resolve("report.xml");
        Files.copy(output, outputPath);
    } catch (Exception e) {
        throw new ComputationException(e);
    }
}

Example 8 with ComputationException

use of de.bioforscher.jstructure.model.feature.ComputationException in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfiler method writeLigandInteractions.

public void writeLigandInteractions(Structure structure, Path outputPath) {
    try {
        Path outputDirectoryPath = createTemporaryOutputDirectory();
        String[] commandLineCall = composeLigandCommandLineCall(structure, outputDirectoryPath);
        // execute command
        executeCommandLineCall(commandLineCall);
        Path output = outputDirectoryPath.resolve("report.xml");
        Files.copy(output, outputPath);
    } catch (Exception e) {
        throw new ComputationException(e);
    }
}

Example 9 with ComputationException

use of de.bioforscher.jstructure.model.feature.ComputationException in project jstructure by JonStargaryen.

the class ProteinLigandInteractionProfiler method annotateLigandInteractions.

public InteractionContainer annotateLigandInteractions(Structure structure) {
    try {
        Path outputDirectoryPath = createTemporaryOutputDirectory();
        String[] commandLineCall = composeLigandCommandLineCall(structure, outputDirectoryPath);
        // execute command
        executeCommandLineCall(commandLineCall);
        Path outputPath = outputDirectoryPath.resolve("report.xml");
        Document document = Jsoup.parse(outputPath.toFile(), "UTF-8");
        return parseDocument(structure, document);
    } catch (Exception e) {
        throw new ComputationException(e);
    }
}

Example 10 with ComputationException

use of de.bioforscher.jstructure.model.feature.ComputationException in project jstructure by JonStargaryen.

the class A02_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.parseStability(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"));
        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<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());
        ResidueGraph conventionalProteinGraph = ResidueGraph.createResidueGraph(chain, ContactDefinitionFactory.createAlphaCarbonContactDefinition(8));
        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 + "," + (stableResidues.contains(aminoAcid) ? "stable" : "unstable");
        }).collect(Collectors.joining(System.lineSeparator())));
    } catch (Exception e) {
        logger.info("calculation failed for {}", line, e);
        return Optional.empty();
    }
}