Examples with PLIPInteractionContainer de.bioforscher.jstructure.feature.interactions.PLIPInteractionContainer used on opensource projects

Example 1 with PLIPInteractionContainer

use of de.bioforscher.jstructure.feature.interactions.PLIPInteractionContainer in project jstructure by JonStargaryen.

the class AbstractItemSetMinerDataSetComposer method handleLine.

private String handleLine(Protein protein, String line, boolean functional) {
    try {
        String[] sectionSplit = line.split("_");
        PLIPInteractionContainer container = protein.getFeatureContainer().getFeature(PLIPInteractionContainer.class);
        // extract peculiar residues
        List<Group> groups = Stream.of(sectionSplit).skip(1).map(residueSection -> extractResidue(protein, residueSection)).collect(Collectors.toList());
        return groups.stream().map(group -> mapToString(container, group)).collect(Collectors.joining(",", line + ",", "," + (functional ? "" : "non-") + "functional"));
    } catch (Exception e) {
        e.fillInStackTrace();
        // thrown upon missing backbone atoms during secondary structure assignment
        return "";
    }
}

Example 2 with PLIPInteractionContainer

use of de.bioforscher.jstructure.feature.interactions.PLIPInteractionContainer in project jstructure by JonStargaryen.

the class A03_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.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<Integer> functionalResidueNumbers = Start2FoldConstants.extractFunctioanlResidueNumbers(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());
        ProteinGraph conventionalProteinGraph = ProteinGraphFactory.createProteinGraph(chain, ProteinGraphFactory.InteractionScheme.CALPHA8);
        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;
        }).collect(Collectors.joining(System.lineSeparator())));
    } catch (Exception e) {
        logger.info("calculation failed for {}", line, e);
        return Optional.empty();
    }
}

Example 3 with PLIPInteractionContainer

use of de.bioforscher.jstructure.feature.interactions.PLIPInteractionContainer in project jstructure by JonStargaryen.

the class A05_WriteEarlyFoldingContactCsv method handleLineLocally.

private static Optional<String> handleLineLocally(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.parseSpecificExperiment(chain, Start2FoldConstants.XML_DIRECTORY.resolve(entryId + ".xml"), experimentIds);
        earlyFoldingResidues = chain.aminoAcids().filter(aminoAcid -> aminoAcid.getFeature(Start2FoldResidueAnnotation.class).isEarly()).collect(Collectors.toList());
        // filter for contacts of EFR
        PLIPInteractionContainer plipInteractionContainer = chain.getFeature(PLIPInteractionContainer.class);
        System.out.println(pdbId + "\t" + earlyFoldingResidues.size() + "\t" + StandardFormat.format(plipInteractionContainer.getInteractions().size() / (double) earlyFoldingResidues.size()) + "\t" + plipInteractionContainer.getInteractions().size());
        // ignore really small or non-interacting groups of EFR
        if (plipInteractionContainer.getInteractions().size() < 2) {
            return Optional.empty();
        }
        return Optional.of(plipInteractionContainer.getInteractions().stream().map(A05_WriteEarlyFoldingContactCsv::handleInteraction).collect(Collectors.joining(System.lineSeparator())));
    } catch (Exception e) {
        e.printStackTrace();
        logger.info("calculation failed for {}", line, e);
        return Optional.empty();
    }
}

Example 4 with PLIPInteractionContainer

use of de.bioforscher.jstructure.feature.interactions.PLIPInteractionContainer in project jstructure by JonStargaryen.

the class RawFeatureVector method assignRawFeatureVector.

public static void assignRawFeatureVector(AminoAcid aminoAcid) {
    GenericSecondaryStructure sse = aminoAcid.getFeature(GenericSecondaryStructure.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()));
    ResidueTopologicPropertiesContainer residueTopologicPropertiesContainer = aminoAcid.getFeature(ResidueTopologicPropertiesContainer.class);
    // assign features to smooth
    RawFeatureVector featureVector = new RawFeatureVector(sse.getSurroundingSecondaryStructureElement(aminoAcid).getSize(), localPlipInteractionContainer.getHydrogenBonds().size(), localPlipInteractionContainer.getHydrophobicInteractions().size(), localPlipInteractionContainer.getBackboneInteractions().size(), localPlipInteractionContainer.getInteractions().size(), nonLocalPlipInteractionContainer.getHydrogenBonds().size(), nonLocalPlipInteractionContainer.getHydrophobicInteractions().size(), nonLocalPlipInteractionContainer.getBackboneInteractions().size(), nonLocalPlipInteractionContainer.getInteractions().size(), aminoAcid.getFeature(EnergyProfile.class).getSolvationEnergy(), aminoAcid.getFeature(EgorAgreement.class).getEgorPrediction(), aminoAcid.getFeature(AccessibleSurfaceArea.class).getRelativeAccessibleSurfaceArea(), residueTopologicPropertiesContainer.getFullPlip().getBetweenness(), residueTopologicPropertiesContainer.getFullPlip().getCloseness(), residueTopologicPropertiesContainer.getFullPlip().getClusteringCoefficient(), residueTopologicPropertiesContainer.getHydrogenPlip().getBetweenness(), residueTopologicPropertiesContainer.getHydrogenPlip().getCloseness(), residueTopologicPropertiesContainer.getHydrogenPlip().getClusteringCoefficient(), residueTopologicPropertiesContainer.getHydrophobicPlip().getBetweenness(), residueTopologicPropertiesContainer.getHydrophobicPlip().getCloseness(), residueTopologicPropertiesContainer.getHydrophobicPlip().getClusteringCoefficient(), residueTopologicPropertiesContainer.getConventional().getBetweenness(), residueTopologicPropertiesContainer.getConventional().getCloseness(), residueTopologicPropertiesContainer.getConventional().getClusteringCoefficient(), residueTopologicPropertiesContainer.getFullPlip().getDistinctNeighborhoodCount(), residueTopologicPropertiesContainer.getConventional().getDistinctNeighborhoodCount());
    aminoAcid.getFeatureContainer().addFeature(featureVector);
}