/** {@inheritDoc} */
@Override
@TestMethod("testEmptyReaction")
public IRenderingElement generate(IReaction reaction, RendererModel model) {
if (!model.getParameter(ShowReactionBoxes.class).getValue()) return null;
double separation =
model.getParameter(BondLength.class).getValue()
/ model.getParameter(Scale.class).getValue();
Rectangle2D totalBounds = BoundsCalculator.calculateBounds(reaction);
if (totalBounds == null) return null;
ElementGroup diagram = new ElementGroup();
Color foregroundColor =
model.getParameter(BasicSceneGenerator.ForegroundColor.class).getValue();
diagram.add(
new RectangleElement(
totalBounds.getMinX() - separation,
totalBounds.getMinY() - separation,
totalBounds.getMaxX() + separation,
totalBounds.getMaxY() + separation,
foregroundColor));
if (reaction.getID() != null) {
diagram.add(
new TextElement(
(totalBounds.getMinX() + totalBounds.getMaxX()) / 2,
totalBounds.getMinY() - separation,
reaction.getID(),
foregroundColor));
}
return diagram;
}
// ~--- constructors -------------------------------------------------------
GameTheoryMin(
IReaction reaction,
boolean removeHydrogen,
Map<Integer, IAtomContainer> _educts,
Map<Integer, IAtomContainer> _products,
GameTheoryMatrix rpsh)
throws Exception {
if (DEBUG) {
out.println("I am MIN MIX");
}
this.canonLabeler = new SmilesMoleculeLabeller();
this.removeHydrogen = removeHydrogen;
this.reaction = reaction;
this.educts = _educts;
this.products = _products;
this.reactionName = reaction.getID();
this.eductList = synchronizedList(rpsh.getEductCounter());
this.productList = synchronizedList(rpsh.getProductCounter());
this.mh = rpsh.getMatrixHolder();
setReactionMolMapping(rpsh.getReactionMolMapping());
winner = new ChooseWinner(eductList, productList);
this._dirSuffix = super.getSuffix();
ReactionIsomorphismHandler RIH = new ReactionIsomorphismHandler(mh, eductList, productList);
if (RIH.getIsomorphismFlag()) {
// System.out.println("ISOMORPHISM");
mh = RIH.getMatrixHolder();
GenerateIsoMorphismMapping();
} else {
GenerateMapping(false);
}
}
private static void setReactionIDs(final IChemModel chemModel) {
// we give all reactions an ID, in case they have none
// IDs are needed for handling in JCP
final IReactionSet reactionSet = chemModel.getReactionSet();
if (reactionSet != null) {
int i = 0;
for (final IReaction reaction : reactionSet.reactions()) {
if (reaction.getID() == null) {
reaction.setID("Reaction " + ++i);
}
}
}
}
@Override
public void store(IReaction reaction) {
String id = reaction.getID();
File file = new File(reactionDir, id + ".rxn");
try {
FileWriter writer = new FileWriter(file);
rxnWriter = new MDLV2000RXNWriter(writer);
// rxnWriter.setWriter(writer);
rxnWriter.write(reaction);
// writer.flush();
// writer.close();
rxnWriter.close();
} catch (CDKException | IOException e) {
e.printStackTrace();
}
}
/**
* @param removeHydrogen
* @param reaction
* @param algorithm
*/
public CalculationProcess(
boolean removeHydrogen, IReaction reaction, IMappingAlgorithm algorithm) {
/*
* This case handles rings cases where 6 membered ring reduces to 5 membered rings Example KEGG reaction R01432
* of Isomerase class
*/
super(reaction);
// System.out.println("I am CalculationProcess");
this.removeHydrogen = removeHydrogen;
logger.debug("\n|++++++++++++++++++++++++++++|");
logger.debug("Performing Atom-Atom Mapping ....... " + reaction.getID() + " .......");
logger.debug("\n|++++++++++++++++++++++++++++|");
this.algorithm = algorithm;
run();
}