Beispiel #1
0
  public MetabolicReaction parseReaction(PreparsedReaction reaction)
      throws UnparsableReactionError {

    String equation = reaction.getEquation();
    String[] rxnSides = getReactionSides(equation);

    // determine whether the reaction contains two sides or one.
    if (rxnSides.length == 2) {

      // standard reaction
      return parseTwoSidedReaction(reaction, rxnSides);

    } else if (rxnSides.length == 1) {

      // exchange reaction
      return parseExchangeReaction(reaction, rxnSides[0]);

    } else {

      throw new UnparsableReactionError("No equation found for rxn: " + reaction.getIdentifier());
    }
  }
Beispiel #2
0
  public MetabolicReaction getReaction(PreparsedReaction preparsed) {

    MetabolicReaction rxn =
        factory.ofClass(
            MetabolicReaction.class,
            BasicReactionIdentifier.nextIdentifier(),
            preparsed.hasValue(DESCRIPTION) ? preparsed.getValue(DESCRIPTION) : "",
            preparsed.hasValue(ABBREVIATION) ? preparsed.getValue(ABBREVIATION) : "");

    if (preparsed.hasValue(DIRECTION)) {
      rxn.setDirection(getReactionArrow(preparsed.getValue(DIRECTION)));
    } else {
      rxn.setDirection(getReactionArrow(preparsed.getEquation()));
    }

    // add subsytem annotation
    if (preparsed.hasValue(SUBSYSTEM)) {
      rxn.addAnnotation(new Subsystem(preparsed.getSubsystem()));
    }

    // add classification
    for (String classification : preparsed.getClassifications()) {
      // load EC code
      if (classification.matches("(?:\\d+\\.){3}\\d+") || classification.contains("EC")) {
        rxn.addAnnotation(new EnzymeClassification(new ECNumber(classification)));
      } else if (classification.contains("TC")) {
        rxn.addAnnotation(new Classification(new TransportClassificationNumber(classification)));
      }
    }

    // add loci
    for (String locus : preparsed.getLoci()) {
      rxn.addAnnotation(new Locus(locus));
    }

    // add delta g and delta g error
    if (preparsed.hasValue(FREE_ENERGY)) {
      try {
        if (preparsed.hasValue(FREE_ENERGY_ERROR)) {
          rxn.addAnnotation(
              new GibbsEnergy(
                  Double.parseDouble(preparsed.getValue(FREE_ENERGY)),
                  Double.parseDouble(preparsed.getValue(FREE_ENERGY_ERROR))));
        } else {
          rxn.addAnnotation(
              new GibbsEnergy(Double.parseDouble(preparsed.getValue(FREE_ENERGY)), 0d));
        }
      } catch (NumberFormatException ex) {
        LOGGER.error("Gibbs energy column(s) contained invalid value (not a double)");
      }
    }

    if (preparsed.hasValue(MIN_FLUX)) {
      try {
        rxn.addAnnotation(new FluxLowerBound(Double.parseDouble(preparsed.getValue(MIN_FLUX))));
      } catch (NumberFormatException ex) {
        LOGGER.error(
            "Min flux column contained invalid value (not a double): "
                + preparsed.getValue(MIN_FLUX));
      }
    }

    if (preparsed.hasValue(MAX_FLUX)) {
      try {
        rxn.addAnnotation(new FluxLowerBound(Double.parseDouble(preparsed.getValue(MAX_FLUX))));
      } catch (NumberFormatException ex) {
        LOGGER.error(
            "Max flux column contained invalid value (not a double): "
                + preparsed.getValue(MAX_FLUX));
      }
    }

    return rxn;
  }