/**
* Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file,
* database, internet etc). If the specific implementation does not support a specific IChemObject
* it will throw an Exception.
*
* @param object The object that subclasses IChemObject
* @return The IChemObject read
* @exception CDKException
*/
public IChemObject read(IChemObject object) throws CDKException {
if (object instanceof IReaction) {
return (IChemObject) readReaction(object.getBuilder());
} else if (object instanceof IReactionSet) {
IReactionSet reactionSet = object.getBuilder().newReactionSet();
reactionSet.addReaction(readReaction(object.getBuilder()));
return reactionSet;
} else if (object instanceof IChemModel) {
IChemModel model = object.getBuilder().newChemModel();
IReactionSet reactionSet = object.getBuilder().newReactionSet();
reactionSet.addReaction(readReaction(object.getBuilder()));
model.setReactionSet(reactionSet);
return model;
} else if (object instanceof IChemFile) {
IChemFile chemFile = object.getBuilder().newChemFile();
IChemSequence sequence = object.getBuilder().newChemSequence();
sequence.addChemModel((IChemModel) read(object.getBuilder().newChemModel()));
chemFile.addChemSequence(sequence);
return chemFile;
} else {
throw new CDKException(
"Only supported are Reaction and ChemModel, and not "
+ object.getClass().getName()
+ ".");
}
}
/**
* Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class
* tools.HydrogenAdder.
*
* @param reactants reactants of the reaction
* @param agents agents of the reaction (Must be in this case null)
* @exception CDKException Description of the Exception
*/
@TestMethod("testInitiate_IMoleculeSet_IMoleculeSet")
public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException {
logger.debug("initiate reaction: HeterolyticCleavagePBReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("HeterolyticCleavagePBReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("HeterolyticCleavagePBReaction don't expects agents");
}
IReactionSet setOfReactions =
DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class);
IMolecule reactant = reactants.getMolecule(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<IBond> bondis = reactant.bonds().iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
IAtom atom1 = bondi.getAtom(0);
IAtom atom2 = bondi.getAtom(1);
if (bondi.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondi.getOrder() != IBond.Order.SINGLE
&& atom1.getFlag(CDKConstants.REACTIVE_CENTER)
&& atom2.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
&& (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atom1) == 0
&& reactant.getConnectedSingleElectronsCount(atom2) == 0) {
/**/
for (int j = 0; j < 2; j++) {
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
if (j == 0) {
atomList.add(atom1);
atomList.add(atom2);
} else {
atomList.add(atom2);
atomList.add(atom1);
}
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
IMoleculeSet moleculeSet = reactant.getBuilder().newInstance(IMoleculeSet.class);
moleculeSet.addMolecule(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if (reaction == null) continue;
else setOfReactions.addReaction(reaction);
}
}
}
return setOfReactions;
}
@TestMethod("testReadReactions1")
public <T extends IChemObject> T read(T object) throws CDKException {
if (object instanceof IReaction) {
return (T) readReaction(object.getBuilder());
} else if (object instanceof IChemModel) {
IChemModel model = object.getBuilder().newInstance(IChemModel.class);
IReactionSet reactionSet = object.getBuilder().newInstance(IReactionSet.class);
reactionSet.addReaction(readReaction(object.getBuilder()));
model.setReactionSet(reactionSet);
return (T) model;
} else {
throw new CDKException(
"Only supported are Reaction and ChemModel, and not "
+ object.getClass().getName()
+ ".");
}
}
/**
* 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;
}