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;
}
private IMolecule checkForXMoleculeFile(IChemFile chemFile, int numberOfMolecules) {
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);
org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = model.getMoleculeSet();
Assert.assertNotNull(moleculeSet);
Assert.assertEquals(moleculeSet.getMoleculeCount(), numberOfMolecules);
IMolecule mol = null;
for (int i = 0; i < numberOfMolecules; i++) {
mol = moleculeSet.getMolecule(i);
Assert.assertNotNull(mol);
}
return mol;
}