private static void replaceReferencesWithClones(final IChemModel chemModel)
throws CDKException {
// we make references in products/reactants clones, since same compounds
// in different reactions need separate layout (different positions etc)
if (chemModel.getReactionSet() != null) {
for (final IReaction reaction : chemModel.getReactionSet()
.reactions()) {
int i = 0;
final IAtomContainerSet products = reaction.getProducts();
for (final IAtomContainer product : products.atomContainers()) {
try {
products.replaceAtomContainer(i, product.clone());
} catch (final CloneNotSupportedException e) {
}
i++;
}
i = 0;
final IAtomContainerSet reactants = reaction.getReactants();
for (final IAtomContainer reactant : reactants.atomContainers()) {
try {
reactants.replaceAtomContainer(i, reactant.clone());
} catch (final CloneNotSupportedException e) {
}
i++;
}
}
}
}
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);
}
}
}
}
private static void removeDuplicateAtomContainers(final IChemModel chemModel) {
// we remove molecules which are in AtomContainerSet as well as in a
// reaction
final IReactionSet reactionSet = chemModel.getReactionSet();
final IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
if (reactionSet != null && moleculeSet != null) {
final List<IAtomContainer> aclist = ReactionSetManipulator
.getAllAtomContainers(reactionSet);
for (int i = moleculeSet.getAtomContainerCount() - 1; i >= 0; i--) {
for (int k = 0; k < aclist.size(); k++) {
final String label = moleculeSet.getAtomContainer(i)
.getID();
if (aclist.get(k).getID().equals(label)) {
chemModel.getMoleculeSet().removeAtomContainer(i);
break;
}
}
}
}
}
private IReaction checkForXReactionFile(IChemFile chemFile, int numberOfReactions) {
Assert.assertNotNull(chemFile);
Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
Assert.assertNotNull(seq);
Assert.assertEquals(seq.getChemModelCount(), 1);
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
Assert.assertNotNull(model);
IReactionSet reactionSet = model.getReactionSet();
Assert.assertNotNull(reactionSet);
Assert.assertEquals(reactionSet.getReactionCount(), numberOfReactions);
IReaction reaction = null;
for (int i = 0; i < numberOfReactions; i++) {
reaction = reactionSet.getReaction(i);
Assert.assertNotNull(reaction);
}
return reaction;
}