/**
* Test generation of a reaction SMILES. I know, it's a stupid alchemic reaction, but it serves
* its purpose.
*/
@Test
public void testReactionSMILES() {
Reaction reaction = new Reaction();
IAtomContainer methane = new AtomContainer();
methane.addAtom(new Atom("C"));
reaction.addReactant(methane);
IAtomContainer magic = new AtomContainer();
magic.addAtom(new PseudoAtom("magic"));
reaction.addAgent(magic);
IAtomContainer gold = new AtomContainer();
gold.addAtom(new Atom("Au"));
reaction.addProduct(gold);
SmilesGenerator sg = new SmilesGenerator();
try {
String smiles = sg.createSMILES(reaction);
// logger.debug("Generated SMILES: " + smiles);
Assert.assertEquals("C>[*]>[Au]", smiles);
} catch (Exception exc) {
System.out.println(exc);
}
}
public void removeListener(IChemObjectListener col) {
logger.debug("Removing listener: ", col);
super.removeListener(col);
}
public void addListener(IChemObjectListener col) {
logger.debug("Adding listener: ", col);
super.addListener(col);
}
public void setDirection(IReaction.Direction direction) {
logger.debug("Setting direction: ", direction);
super.setDirection(direction);
}
public void addProduct(IMolecule product, Double coefficient) {
logger.debug("Adding product with coefficient: ", product, "" + coefficient);
super.addProduct(product, coefficient);
}
public void addProduct(IMolecule product) {
logger.debug("Adding product: ", product);
super.addProduct(product);
}
public void setID(String identifier) {
logger.debug("Setting ID: ", identifier);
super.setID(identifier);
}
public void setProperty(Object description, Object property) {
logger.debug("Setting property: ", description + "=" + property);
super.setProperty(description, property);
}
public void addReactant(IMolecule reactant) {
logger.debug("Adding reactant: ", reactant);
super.addReactant(reactant);
}
public void setProducts(IMoleculeSet products) {
logger.debug("Setting products: ", products);
super.setProducts(products);
}
public void setReactants(IMoleculeSet reactants) {
logger.debug("Setting reactants: ", reactants);
super.setReactants(reactants);
}
public void setFlags(boolean[] flagsNew) {
logger.debug("Setting flags:", flagsNew.length);
super.setFlags(flagsNew);
}
public void setProperties(Map<Object, Object> properties) {
logger.debug("Setting properties: ", properties);
super.setProperties(properties);
}
public void setFlag(int flag_type, boolean flag_value) {
logger.debug("Setting flag: ", flag_type + "=" + flag_value);
super.setFlag(flag_type, flag_value);
}
public void notifyChanged() {
logger.debug("Notifying changed");
super.notifyChanged();
}
public void notifyChanged(IChemObjectChangeEvent evt) {
logger.debug("Notifying changed event: ", evt);
super.notifyChanged(evt);
}
public void addAgent(IMolecule agent) {
logger.debug("Adding agent: ", agent);
super.addAgent(agent);
}
public void removeProperty(Object description) {
logger.debug("Removing property: ", description);
super.removeProperty(description);
}
public void addReactant(IMolecule reactant, Double coefficient) {
logger.debug("Adding reactant with coefficient: ", reactant, "" + coefficient);
super.addReactant(reactant, coefficient);
}