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;
}
public MetabolicParticipantImplementation parseParticipant(
final String participant, final Compartment defaultCompartment, final PreparsedReaction rxn)
throws UnparsableReactionError {
String entityAbbr = participant.trim();
String entityAbbrComp = entityAbbr;
Compartment compartment = defaultCompartment;
Double coef = 1d;
// stoichiometric coefficients
Matcher coefMatcher = COEFFICIENT_PATTERN.matcher(entityAbbr);
if (coefMatcher.find()) {
coef =
Double.parseDouble(
coefMatcher.group(1) == null ? coefMatcher.group(2) : coefMatcher.group(1));
entityAbbr = coefMatcher.replaceAll("");
entityAbbrComp = entityAbbr;
}
// compartment
Matcher compartmentMatcher = COMPARTMENT_PATTERN.matcher(entityAbbr);
if (compartmentMatcher.find()) {
compartment = resolver.getCompartment(compartmentMatcher.group(1));
entityAbbr = compartmentMatcher.replaceAll("");
}
// trim the abbreviation
entityAbbr = entityAbbr.trim();
// try fetching with compartment attached and without
// PreparsedMetabolite entity = entites.getEntity(entityAbbrComp.trim());
Metabolite entity = entites.getReconciledMetabolite(entityAbbr);
if (entity != null) {
// System.out.println( coef + " " + entity.getName() + " " + compartment );
return new MetabolicParticipantImplementation(entity, coef, (Compartment) compartment);
} else {
messages.add(
new WarningMessage(
"The metabolite "
+ entityAbbr
+ " was not found in the metabolite sheet for reaction "
+ rxn));
entity = entites.getNonReconciledMetabolite(entityAbbr);
return new MetabolicParticipantImplementation(entity, coef, (Compartment) compartment);
}
// TODO:
// ?ion match
// ?remove _ext part
// pmf associated?
// match name with + and without + and then with number and without numbers
// e.g.
// YGH+FHD, 1) YGH+FHD 2) YGH, FHD
// 35FGD+1400DH 1) 35FGD+1400DH 2) 35FGD 1400DH 3) FGD, DH
}
/** 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;
}