/// <summary> Fings the set of all rings in a molecule
///
/// </summary>
/// <param name="atomContainer"> the molecule to be searched for rings
/// </param>
/// <param name="useSSSR"> use the SSSRFinder & RingPartitioner as pre-filter
/// </param>
/// <returns> a RingSet containing the rings in molecule
/// </returns>
/// <exception cref="CDKException"> An exception thrown if something goes wrong or if the timeout limit is reached
/// </exception>
public virtual IRingSet findAllRings(IAtomContainer atomContainer, bool useSSSR)
{
if (startTime == 0)
{
startTime = (System.DateTime.Now.Ticks - 621355968000000000) / 10000;
}
System.Collections.ArrayList pathes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
IRingSet ringSet = atomContainer.Builder.newRingSet();
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
originalAc = atomContainer;
ac.add(atomContainer);
if (debug)
{
System.Console.Out.WriteLine("AtomCount before removal of aliphatic atoms: " + ac.AtomCount);
}
removeAliphatic(ac);
if (debug)
{
System.Console.Out.WriteLine("AtomCount after removal of aliphatic atoms: " + ac.AtomCount);
}
if (useSSSR)
{
SSSRFinder sssrf = new SSSRFinder(atomContainer);
IRingSet sssr = sssrf.findSSSR();
System.Collections.ArrayList ringSets = RingPartitioner.partitionRings(sssr);
for (int r = 0; r < ringSets.Count; r++)
{
IAtomContainer tempAC = RingPartitioner.convertToAtomContainer((IRingSet)ringSets[r]);
doSearch(tempAC, pathes, ringSet);
}
}
else
{
doSearch(ac, pathes, ringSet);
}
atomContainer.setProperty(CDKConstants.ALL_RINGS, ringSet);
return(ringSet);
}
/// <summary> Fings the set of all rings in a molecule
///
/// </summary>
/// <param name="atomContainer"> the molecule to be searched for rings
/// </param>
/// <param name="useSSSR"> use the SSSRFinder & RingPartitioner as pre-filter
/// </param>
/// <returns> a RingSet containing the rings in molecule
/// </returns>
/// <exception cref="CDKException"> An exception thrown if something goes wrong or if the timeout limit is reached
/// </exception>
public virtual IRingSet findAllRings(IAtomContainer atomContainer, bool useSSSR)
{
if (startTime == 0)
{
startTime = (System.DateTime.Now.Ticks - 621355968000000000) / 10000;
}
System.Collections.ArrayList pathes = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
IRingSet ringSet = atomContainer.Builder.newRingSet();
IAtomContainer ac = atomContainer.Builder.newAtomContainer();
originalAc = atomContainer;
ac.add(atomContainer);
if (debug)
{
System.Console.Out.WriteLine("AtomCount before removal of aliphatic atoms: " + ac.AtomCount);
}
removeAliphatic(ac);
if (debug)
{
System.Console.Out.WriteLine("AtomCount after removal of aliphatic atoms: " + ac.AtomCount);
}
if (useSSSR)
{
SSSRFinder sssrf = new SSSRFinder(atomContainer);
IRingSet sssr = sssrf.findSSSR();
System.Collections.ArrayList ringSets = RingPartitioner.partitionRings(sssr);
for (int r = 0; r < ringSets.Count; r++)
{
IAtomContainer tempAC = RingPartitioner.convertToAtomContainer((IRingSet)ringSets[r]);
doSearch(tempAC, pathes, ringSet);
}
}
else
{
doSearch(ac, pathes, ringSet);
}
atomContainer.setProperty(CDKConstants.ALL_RINGS, ringSet);
return ringSet;
}
public virtual void saturateRingSystems(IAtomContainer atomContainer)
{
IRingSet rs = new SSSRFinder(atomContainer.Builder.newMolecule(atomContainer)).findSSSR();
System.Collections.ArrayList ringSets = RingPartitioner.partitionRings(rs);
IAtomContainer ac = null;
IAtom atom = null;
int[] temp;
for (int f = 0; f < ringSets.Count; f++)
{
rs = (IRingSet) ringSets[f];
ac = RingSetManipulator.getAllInOneContainer(rs);
temp = new int[ac.AtomCount];
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
temp[g] = atom.getHydrogenCount();
atom.setHydrogenCount(atomContainer.getBondCount(atom) - ac.getBondCount(atom) - temp[g]);
}
saturate(ac);
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
atom.setHydrogenCount(temp[g]);
}
}
}