private static Kinetics[] getReactionKinetics(Reaction r) {
Kinetics[] allKinetics;
if (r.isForward()) {
allKinetics = r.getKinetics();
} else if (r.isBackward()) {
allKinetics = r.getFittedReverseKinetics();
} else {
allKinetics = r.getKinetics();
}
return allKinetics;
}
public static String writeOutputString(Reaction r, TemplateReactionGenerator rtLibrary) {
String listOfReactions = "";
Temperature stdtemp = new Temperature(298, "K");
double Hrxn = r.calculateHrxn(stdtemp);
// If r Reaction is from Reaction Library add it to list of reaction append its kinetics and
// return
String source = r.getKineticsSource(0);
if (source == null) {
// If source is null I am assuming that its not a Reaction from Reaction Library or Seed
// Mechanism
source = "TemplateReaction:";
}
StringTokenizer st = new StringTokenizer(source, ":");
String reaction_type = st.nextToken();
// Reactions from Reaction Libraries:
if (reaction_type.equals("ReactionLibrary")) {
// We will get the forward reaction
if (r.isBackward()) {
r = r.getReverseReaction();
Hrxn = -Hrxn; // Reversing the heat of reaction
}
Kinetics[] allKinetics = getReactionKinetics(r);
for (int numKinetics = 0; numKinetics < allKinetics.length; ++numKinetics) {
listOfReactions +=
r.toString() + "\t" + getFormattedKinetics(allKinetics[numKinetics], Hrxn);
if (allKinetics.length != 1) listOfReactions += "\tDUP\n";
}
return listOfReactions;
}
// Reactions NOT from Reaction Libraries are from Templates:
if (r.isForward()) {
Kinetics[] allKinetics = r.getKinetics();
for (int numKinetics = 0; numKinetics < allKinetics.length; ++numKinetics) {
listOfReactions +=
r.toString() + "\t" + getFormattedKinetics(allKinetics[numKinetics], Hrxn);
if (allKinetics.length != 1) listOfReactions += "\tDUP\n";
}
} else if (r.isBackward()) {
LinkedHashSet reverseReactions = new LinkedHashSet();
Iterator iter2 = r.getStructure().getProducts();
Species species1 = (Species) iter2.next();
Species species2 = species1;
while (iter2.hasNext()) species2 = (Species) iter2.next();
String rxnFamilyName = "";
if (r instanceof TemplateReaction) {
rxnFamilyName = ((TemplateReaction) r.getReverseReaction()).getReactionTemplate().getName();
}
LinkedHashSet speciesHashSet = new LinkedHashSet();
speciesHashSet.add(species1);
reverseReactions = rtLibrary.react(speciesHashSet, species2, rxnFamilyName);
for (Iterator iter3 = reverseReactions.iterator(); iter3.hasNext(); ) {
Reaction currentRxn = (Reaction) iter3.next();
if (currentRxn.getStructure() == r.getReverseReaction().getStructure()) {
Kinetics[] allKinetics = currentRxn.getKinetics();
for (int numKinetics = 0; numKinetics < allKinetics.length; ++numKinetics) {
listOfReactions +=
currentRxn.toString()
+ "\t"
+ getFormattedKinetics(allKinetics[numKinetics], -Hrxn);
if (allKinetics.length != 1) listOfReactions += "\tDUP\n";
}
}
}
} else {
Kinetics[] allKinetics = r.getKinetics();
for (int numKinetics = 0; numKinetics < allKinetics.length; ++numKinetics) {
listOfReactions +=
r.toString() + "\t" + getFormattedKinetics(allKinetics[numKinetics], Hrxn);
if (allKinetics.length != 1) listOfReactions += "\tDUP\n";
}
}
return listOfReactions;
}
