public MetabolicReaction parseTwoSidedReaction(
PreparsedReaction preparsed, String[] equationSides) throws UnparsableReactionError {
Matcher reactionCompartment = REACTION_COMPARTMENT.matcher(equationSides[0]);
MetabolicReaction rxn = getReaction(preparsed);
Compartment defaultCompartment = Organelle.CYTOPLASM;
if (reactionCompartment.find()) {
defaultCompartment = resolver.getCompartment(reactionCompartment.group(1));
equationSides[0] = reactionCompartment.replaceAll("");
}
for (MetabolicParticipantImplementation p :
parseParticipants(equationSides[0], defaultCompartment, preparsed)) {
rxn.addReactant(p);
}
for (MetabolicParticipantImplementation p :
parseParticipants(equationSides[1], defaultCompartment, preparsed)) {
rxn.addProduct(p);
}
return rxn;
}
/** Only have left side (or some weird reaction operator) */
public MetabolicReaction parseExchangeReaction(PreparsedReaction reaction, String equationSide)
throws UnparsableReactionError {
Matcher reactionCompartment = REACTION_COMPARTMENT.matcher(equationSide);
MetabolicReaction rxn = getReaction(reaction);
Compartment defaultCompartment = Organelle.CYTOPLASM;
if (reactionCompartment.find()) {
defaultCompartment = resolver.getCompartment(reactionCompartment.group(1));
equationSide = reactionCompartment.replaceAll("");
}
for (MetabolicParticipantImplementation p :
parseParticipants(equationSide, defaultCompartment, reaction)) {
rxn.addReactant(p);
}
return rxn;
}