/// <summary> Partitions the atoms in an AtomContainer into covalently connected components.
///
/// </summary>
/// <param name="atomContainer"> The AtomContainer to be partitioned into connected components, i.e. molecules
/// </param>
/// <returns> A SetOfMolecules.
///
/// </returns>
/// <cdk.dictref> blue-obelisk:graphPartitioning </cdk.dictref>
public static ISetOfMolecules partitionIntoMolecules(IAtomContainer atomContainer)
{
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
IAtom atom = null;
IElectronContainer eContainer = null;
IMolecule molecule = null;
ISetOfMolecules molecules = atomContainer.Builder.newSetOfMolecules();
System.Collections.ArrayList sphere = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atom = atomContainer.getAtomAt(f);
atom.setFlag(CDKConstants.VISITED, false);
ac.addAtom(atom);
}
IElectronContainer[] eContainers = atomContainer.ElectronContainers;
for (int f = 0; f < eContainers.Length; f++)
{
eContainer = eContainers[f];
eContainer.setFlag(CDKConstants.VISITED, false);
ac.addElectronContainer(eContainer);
}
while (ac.AtomCount > 0)
{
atom = ac.getAtomAt(0);
molecule = atomContainer.Builder.newMolecule();
sphere.Clear();
sphere.Add(atom);
atom.setFlag(CDKConstants.VISITED, true);
PathTools.breadthFirstSearch(ac, sphere, molecule);
molecules.addMolecule(molecule);
ac.remove(molecule);
}
return(molecules);
}
/// <summary> Uses precomputed set of ALL rings and performs an aromaticity detection
/// based on Hueckels 4n + 2 rule.
///
/// </summary>
/// <param name="ringSet"> set of ALL rings
/// </param>
/// <param name="removeAromaticityFlags"> Leaves ChemObjects that are already marked as
/// aromatic as they are
/// </param>
/// <param name="atomContainer"> AtomContainer to be searched for rings
/// </param>
/// <returns> True, if molecules contains an
/// aromatic feature
/// </returns>
public static bool detectAromaticity(IAtomContainer atomContainer, IRingSet ringSet, bool removeAromaticityFlags)
{
bool foundSomething = false;
if (removeAromaticityFlags)
{
for (int f = 0; f < atomContainer.AtomCount; f++)
{
atomContainer.getAtomAt(f).setFlag(CDKConstants.ISAROMATIC, false);
}
for (int f = 0; f < atomContainer.ElectronContainerCount; f++)
{
IElectronContainer electronContainer = atomContainer.getElectronContainerAt(f);
if (electronContainer is IBond)
{
electronContainer.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
((IRing)ringSet.getAtomContainer(f)).setFlag(CDKConstants.ISAROMATIC, false);
}
}
IRing ring = null;
RingSetManipulator.sort(ringSet);
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
ring = (IRing)ringSet.getAtomContainer(f);
//logger.debug("Testing for aromaticity in ring no ", f);
if (AromaticityCalculator.isAromatic(ring, atomContainer))
{
ring.setFlag(CDKConstants.ISAROMATIC, true);
for (int g = 0; g < ring.AtomCount; g++)
{
ring.getAtomAt(g).setFlag(CDKConstants.ISAROMATIC, true);
}
for (int g = 0; g < ring.ElectronContainerCount; g++)
{
IElectronContainer electronContainer = ring.getElectronContainerAt(g);
if (electronContainer is IBond)
{
electronContainer.setFlag(CDKConstants.ISAROMATIC, true);
}
}
foundSomething = true;
//logger.debug("This ring is aromatic: ", f);
}
else
{
//logger.debug("This ring is *not* aromatic: ", f);
}
}
return(foundSomething);
}