/**
* The keyword is generated from the reactants and products using {@link GenerateReactionKeywords}
*
* @param reaction The reaction parsed from the text
* @return the generated keyword
*/
private String getKeyword(ChemkinReaction reaction) {
ArrayList<String> reactantNames = createMoleculeArrayList(reaction.getReactants());
ArrayList<String> productNames = createMoleculeArrayList(reaction.getProducts());
String reactionEquation = keywordGenerator.getReactionName(reactantNames, productNames);
String keyword = keywordGenerator.getReactionFullName(reactionEquation);
return keyword;
}
@Override
protected void createObjects() throws IOException {
ChemkinMechanism mechanism = parse();
MechanismMoleculesToDatabaseTransaction moltransaction =
(MechanismMoleculesToDatabaseTransaction) getInputSource(moleculesS);
moleculeNamesTable = moltransaction.getMoleculeMap();
ChemkinReactionList reactionList = mechanism.getReactionList();
ArrayList<DatabaseObject> chemkinReactionList = new ArrayList<DatabaseObject>();
ArrayList<DatabaseObject> coefficients = new ArrayList<DatabaseObject>();
ArrayList<DatabaseObject> photoList = new ArrayList<DatabaseObject>();
for (ChemkinReaction reaction : reactionList) {
String rxnkeyword = getKeyword(reaction);
ChemkinReactionData rxndata = create(rxnkeyword, reaction, coefficients);
if (reaction.isHvLight()) {
PhotoChemicalReaction photo =
new PhotoChemicalReaction(keyword, rxnkeyword, reaction.isHvLightAsReactant());
photoList.add(photo);
}
chemkinReactionList.add(rxndata);
}
StorageAndRetrievalUtilities.storeDatabaseObjects(chemkinReactionList);
StorageAndRetrievalUtilities.storeDatabaseObjects(coefficients);
StorageAndRetrievalUtilities.storeDatabaseObjects(photoList);
rxntransaction.setReactionCount(chemkinReactionList.size());
}
/**
* From {@link ChemkinReaction} form the {@link ChemkinReactionData} This routine parses through
* all the coefficient types using createCoeffs: forward, reverse, low, high troe, sri, plog The
* third body is parsed using createThirdBody
*
* @param reaction that has been parsed from the text
* @return The reaction data
*/
private ChemkinReactionData create(
String rxnkeyword, ChemkinReaction reaction, ArrayList<DatabaseObject> coefficients) {
System.out.println("ChemkinReactionData create: " + rxnkeyword);
ArrayList<String> reactantNames = createMoleculeArrayList(reaction.getReactants());
ArrayList<String> productNames = createMoleculeArrayList(reaction.getProducts());
ArrayList<String> reactantReactionNames = new ArrayList<String>();
for (String name : reactantNames) {
String rxnmolname = moleculeNamesTable.get(name);
reactantReactionNames.add(rxnmolname);
}
ArrayList<String> productReactionNames = new ArrayList<String>();
for (String name : productNames) {
String rxnmolname = moleculeNamesTable.get(name);
productReactionNames.add(rxnmolname);
}
ChemkinCoefficientsData forwardCoefficients = null;
if (reaction.getForwardCoefficients() != null) {
forwardCoefficients = createCoeffs(keyword, rxnkeyword, reaction.getForwardCoefficients());
forward = true;
coefficients.add(forwardCoefficients);
}
ChemkinCoefficientsData reverseCoefficients = null;
if (reaction.getReverseCoefficients() != null) {
reverseCoefficients = createCoeffs(keyword, rxnkeyword, reaction.getReverseCoefficients());
reverse = true;
coefficients.add(reverseCoefficients);
}
ChemkinCoefficientsData lowCoefficients = null;
if (reaction.getLowCoefficients() != null) {
lowCoefficients = createCoeffs(keyword, rxnkeyword, reaction.getLowCoefficients());
lowCoefficients.setLow(true);
low = true;
coefficients.add(lowCoefficients);
}
ChemkinCoefficientsData highCoefficients = null;
if (reaction.getHighCoefficients() != null) {
highCoefficients = createCoeffs(keyword, rxnkeyword, reaction.getHighCoefficients());
highCoefficients.setHigh(true);
high = true;
coefficients.add(highCoefficients);
}
ChemkinCoefficientsData troeCoefficients = null;
if (reaction.getTroeCoefficients() != null) {
troeCoefficients = createCoeffs(keyword, rxnkeyword, reaction.getTroeCoefficients());
troeCoefficients.setTroe(true);
troe = true;
coefficients.add(troeCoefficients);
}
ChemkinCoefficientsData sriCoefficients = null;
if (reaction.getSriCoefficients() != null) {
sriCoefficients = createCoeffs(keyword, rxnkeyword, reaction.getSriCoefficients());
sriCoefficients.setSri(true);
sri = true;
coefficients.add(sriCoefficients);
}
// ArrayList<ChemkinCoefficientsData> plogCoefficients = null;
if (reaction.getPlogCoefficients() != null) {
plog = true;
// plogCoefficients = new ArrayList<ChemkinCoefficientsData>();
for (ChemkinCoefficients plog : reaction.getPlogCoefficients()) {
ChemkinCoefficientsData plogC = createCoeffs(keyword, rxnkeyword, plog);
coefficients.add(plogC);
// plogCoefficients.add(plogC);
// plogC.setPlog(true);
}
}
ChemkinReactionData data =
new ChemkinReactionData(
keyword,
rxnkeyword,
reactantReactionNames,
productReactionNames,
forward,
reverse,
low,
high,
troe,
sri,
plog);
if (reaction.getThirdBodyMolecules() != null) {
addThirdBody(reaction.getThirdBodyMolecules(), data);
}
return data;
}