/// <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);
}
private IRing combineRings(IRingSet ringset, int i, int j)
{
int c = 0;
for (int b = 0; b < cb[i].Length; b++)
{
c = cb[i][b] + cb[j][b];
if (c > 1)
{
break; //at least one common bond
}
}
if (c < 2)
{
return(null);
}
IRing ring = molecule.Builder.newRing();
IRing ring1 = (IRing)ringset.getAtomContainer(i);
IRing ring2 = (IRing)ringset.getAtomContainer(j);
for (int b = 0; b < cb[i].Length; b++)
{
c = cb[i][b] + cb[j][b];
if ((c == 1) && (cb[i][b] == 1))
{
ring.addBond(molecule.getBondAt(b));
}
else if ((c == 1) && (cb[j][b] == 1))
{
ring.addBond(molecule.getBondAt(b));
}
}
for (int a = 0; a < ring1.AtomCount; a++)
{
ring.addAtom(ring1.getAtomAt(a));
}
for (int a = 0; a < ring2.AtomCount; a++)
{
ring.addAtom(ring2.getAtomAt(a));
}
return(ring);
}
/// <summary> Returns all the rings in the RingSet that share
/// one or more atoms with a given ring.
///
/// </summary>
/// <param name="ring"> A ring with which all return rings must share one or more atoms
/// </param>
/// <returns> All the rings that share one or more atoms with a given ring.
/// </returns>
public virtual System.Collections.IList getConnectedRings(IRing ring)
{
System.Collections.IList connectedRings = new System.Collections.ArrayList();
IRing tempRing;
IAtom atom;
for (int i = 0; i < ring.AtomCount; i++)
{
atom = ring.getAtomAt(i);
for (int j = 0; j < AtomContainerCount; j++)
{
tempRing = (IRing)getAtomContainer(j);
if (tempRing != ring && tempRing.contains(atom))
{
connectedRings.Add(tempRing);
}
}
}
return(connectedRings);
}