/**
* set the active center for this molecule. The active center will be those which correspond with
* [A*]-B=C .
*
* <pre>
* A: Atom with single electron
* -: Single bond
* B: Atom
* =: Double bond
* C: Atom
* </pre>
*
* @param reactant The molecule to set the activity
* @throws CDKException
*/
private void setActiveCenters(IAtomContainer reactant) throws CDKException {
if (AtomContainerManipulator.getTotalNegativeFormalCharge(reactant)
!= 0 /*|| AtomContainerManipulator.getTotalPositiveFormalCharge(reactant) != 0*/) return;
Iterator<IAtom> atoms = reactant.atoms().iterator();
while (atoms.hasNext()) {
IAtom atomi = atoms.next();
if (reactant.getConnectedSingleElectronsCount(atomi) == 1) {
Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
if (bondi.getOrder() == IBond.Order.SINGLE) {
IAtom atomj = bondi.getConnectedAtom(atomi);
if ((atomj.getFormalCharge() == CDKConstants.UNSET ? 0 : atomj.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atomj) == 0) {
Iterator<IBond> bondjs = reactant.getConnectedBondsList(atomj).iterator();
while (bondjs.hasNext()) {
IBond bondj = bondjs.next();
if (bondj.equals(bondi)) continue;
if (bondj.getOrder() == IBond.Order.DOUBLE) {
IAtom atomk = bondj.getConnectedAtom(atomj);
if ((atomk.getFormalCharge() == CDKConstants.UNSET ? 0 : atomk.getFormalCharge())
== 0
&& reactant.getConnectedSingleElectronsCount(atomk) == 0) {
atomi.setFlag(CDKConstants.REACTIVE_CENTER, true);
atomj.setFlag(CDKConstants.REACTIVE_CENTER, true);
atomk.setFlag(CDKConstants.REACTIVE_CENTER, true);
bondi.setFlag(CDKConstants.REACTIVE_CENTER, true);
bondj.setFlag(CDKConstants.REACTIVE_CENTER, true);
}
}
}
}
}
}
}
}
}
/**
* Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class
* tools.HydrogenAdder.
*
* @exception CDKException Description of the Exception
* @param reactants reactants of the reaction.
* @param agents agents of the reaction (Must be in this case null).
*/
@TestMethod("testInitiate_IAtomContainerSet_IAtomContainerSet")
public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
throws CDKException {
logger.debug("initiate reaction: RearrangementRadicalReaction");
if (reactants.getAtomContainerCount() != 1) {
throw new CDKException("RearrangementRadicalReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("RearrangementRadicalReaction don't expects agents");
}
IReactionSet setOfReactions =
DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class);
IAtomContainer reactant = reactants.getAtomContainer(0);
/* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
IParameterReact ipr = super.getParameterClass(SetReactionCenter.class);
if (ipr != null && !ipr.isSetParameter()) setActiveCenters(reactant);
Iterator<IAtom> atoms = reactants.getAtomContainer(0).atoms().iterator();
while (atoms.hasNext()) {
IAtom atomi = atoms.next();
if (atomi.getFlag(CDKConstants.REACTIVE_CENTER)
&& reactant.getConnectedSingleElectronsCount(atomi) == 1) {
Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
if (bondi.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondi.getOrder() == IBond.Order.SINGLE) {
IAtom atomj = bondi.getConnectedAtom(atomi);
if (atomi.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atomj.getFormalCharge() == CDKConstants.UNSET ? 0 : atomj.getFormalCharge())
== 0
&& reactant.getConnectedSingleElectronsCount(atomj) == 0) {
Iterator<IBond> bondjs = reactant.getConnectedBondsList(atomj).iterator();
while (bondjs.hasNext()) {
IBond bondj = bondjs.next();
if (bondj.equals(bondi)) continue;
if (bondj.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondj.getOrder() == IBond.Order.DOUBLE) {
IAtom atomk = bondj.getConnectedAtom(atomj);
if (atomk.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atomk.getFormalCharge() == CDKConstants.UNSET
? 0
: atomk.getFormalCharge())
== 0
&& reactant.getConnectedSingleElectronsCount(atomk) == 0) {
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
atomList.add(atomi);
atomList.add(atomj);
atomList.add(atomk);
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
bondList.add(bondj);
IAtomContainerSet moleculeSet =
reactant.getBuilder().newInstance(IAtomContainerSet.class);
moleculeSet.addAtomContainer(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if (reaction == null) continue;
else setOfReactions.addReaction(reaction);
}
}
}
}
}
}
}
}
return setOfReactions;
}