/**
* Modules for cleaning a molecule
*
* @param molecule
* @return cleaned AtomContainer
*/
@TestMethod("testCheckAndCleanMolecule")
public static IAtomContainer checkAndCleanMolecule(IAtomContainer molecule) {
boolean isMarkush = false;
for (IAtom atom : molecule.atoms()) {
if (atom.getSymbol().equals("R")) {
isMarkush = true;
break;
}
}
if (isMarkush) {
System.err.println("Skipping Markush structure for sanity check");
}
// Check for salts and such
if (!ConnectivityChecker.isConnected(molecule)) {
// lets see if we have just two parts if so, we assume its a salt and just work
// on the larger part. Ideally we should have a check to ensure that the smaller
// part is a metal/halogen etc.
IMoleculeSet fragments = ConnectivityChecker.partitionIntoMolecules(molecule);
if (fragments.getMoleculeCount() > 2) {
System.err.println("More than 2 components. Skipped");
} else {
IMolecule frag1 = fragments.getMolecule(0);
IMolecule frag2 = fragments.getMolecule(1);
if (frag1.getAtomCount() > frag2.getAtomCount()) {
molecule = frag1;
} else {
molecule = frag2;
}
}
}
configure(molecule);
return molecule;
}
/**
* Get the resonance structures from an IMolecule.
*
* @param molecule The IMolecule to analyze
* @return The different resonance structures
*/
@TestMethod("testGetStructures_IMolecule")
public IMoleculeSet getStructures(IMolecule molecule) {
int countStructure = 0;
IMoleculeSet setOfMol = molecule.getBuilder().newMoleculeSet();
setOfMol.addMolecule(molecule);
for (int i = 0; i < setOfMol.getMoleculeCount(); i++) {
IMolecule mol = setOfMol.getMolecule(i);
for (IReactionProcess aReactionsList : reactionsList) {
IReactionProcess reaction = aReactionsList;
IMoleculeSet setOfReactants = molecule.getBuilder().newMoleculeSet();
setOfReactants.addMolecule(mol);
try {
IReactionSet setOfReactions = reaction.initiate(setOfReactants, null);
if (setOfReactions.getReactionCount() != 0)
for (int k = 0; k < setOfReactions.getReactionCount(); k++)
for (int j = 0;
j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount();
j++) {
IMolecule product = setOfReactions.getReaction(k).getProducts().getMolecule(j);
if (!existAC(setOfMol, product)) {
setOfMol.addMolecule(product);
countStructure++;
if (countStructure > maxStructures) return setOfMol;
}
}
} catch (CDKException e) {
e.printStackTrace();
}
}
}
return setOfMol;
}
/**
* 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;
}
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;
}
/**
* Initiate process.
*
* @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: RadicalChargeSiteInitiationReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("RadicalChargeSiteInitiationReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("RadicalChargeSiteInitiationReaction don't expects agents");
}
IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newReactionSet();
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<IAtom> atoms = reactants.getMolecule(0).atoms().iterator();
while (atoms.hasNext()) {
IAtom atomi = atoms.next();
if (atomi.getFlag(CDKConstants.REACTIVE_CENTER)
&& reactant.getConnectedSingleElectronsCount(atomi) == 1
&& atomi.getFormalCharge() == 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 (atomj.getFlag(CDKConstants.REACTIVE_CENTER) && atomj.getFormalCharge() == 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.SINGLE) {
IAtom atomk = bondj.getConnectedAtom(atomj);
if (atomk.getFlag(CDKConstants.REACTIVE_CENTER)
&& atomk.getSymbol().equals("C")
&& atomk.getFormalCharge() == 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);
IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet();
moleculeSet.addMolecule(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if (reaction == null) continue;
else setOfReactions.addReaction(reaction);
}
}
}
}
}
}
}
}
return setOfReactions;
}
/**
* Get the container which is found resonance from a IMolecule. It is based on looking if the
* order of the bond changes.
*
* @param molecule The IMolecule to analyze
* @return The different containers
*/
@TestMethod("testGetContainers_IMolecule")
public IAtomContainerSet getContainers(IMolecule molecule) {
IAtomContainerSet setOfCont = molecule.getBuilder().newAtomContainerSet();
IMoleculeSet setOfMol = getStructures(molecule);
if (setOfMol.getMoleculeCount() == 0) return setOfCont;
/*extraction of all bonds which has been produced a changes of order*/
List<IBond> bondList = new ArrayList<IBond>();
for (int i = 1; i < setOfMol.getMoleculeCount(); i++) {
IMolecule mol = setOfMol.getMolecule(i);
for (int j = 0; j < mol.getBondCount(); j++) {
IBond bond = molecule.getBond(j);
if (!mol.getBond(j).getOrder().equals(bond.getOrder())) {
if (!bondList.contains(bond)) bondList.add(bond);
}
}
}
if (bondList.size() == 0) return null;
int[] flagBelonging = new int[bondList.size()];
for (int i = 0; i < flagBelonging.length; i++) flagBelonging[i] = 0;
int[] position = new int[bondList.size()];
int maxGroup = 1;
/*Analysis if the bond are linked together*/
List<IBond> newBondList = new ArrayList<IBond>();
newBondList.add(bondList.get(0));
int pos = 0;
for (int i = 0; i < newBondList.size(); i++) {
if (i == 0) flagBelonging[i] = maxGroup;
else {
if (flagBelonging[position[i]] == 0) {
maxGroup++;
flagBelonging[position[i]] = maxGroup;
}
}
IBond bondA = newBondList.get(i);
for (int ato = 0; ato < 2; ato++) {
IAtom atomA1 = bondA.getAtom(ato);
List<IBond> bondA1s = molecule.getConnectedBondsList(atomA1);
for (int j = 0; j < bondA1s.size(); j++) {
IBond bondB = bondA1s.get(j);
if (!newBondList.contains(bondB))
for (int k = 0; k < bondList.size(); k++)
if (bondList.get(k).equals(bondB))
if (flagBelonging[k] == 0) {
flagBelonging[k] = maxGroup;
pos++;
newBondList.add(bondB);
position[pos] = k;
}
}
}
// if it is final size and not all are added
if (newBondList.size() - 1 == i)
for (int k = 0; k < bondList.size(); k++)
if (!newBondList.contains(bondList.get(k))) {
newBondList.add(bondList.get(k));
position[i + 1] = k;
break;
}
}
/*creating containers according groups*/
for (int i = 0; i < maxGroup; i++) {
IAtomContainer container = molecule.getBuilder().newAtomContainer();
for (int j = 0; j < bondList.size(); j++) {
if (flagBelonging[j] != i + 1) continue;
IBond bond = bondList.get(j);
IAtom atomA1 = bond.getAtom(0);
IAtom atomA2 = bond.getAtom(1);
if (!container.contains(atomA1)) container.addAtom(atomA1);
if (!container.contains(atomA2)) container.addAtom(atomA2);
container.addBond(bond);
}
setOfCont.addAtomContainer(container);
}
return setOfCont;
}