// minimum details
/// <summary> Partitions a RingSet into RingSets of connected rings. Rings which share
/// an Atom, a Bond or three or more atoms with at least on other ring in
/// the RingSet are considered connected.
///
/// </summary>
/// <param name="ringSet"> The RingSet to be partitioned
/// </param>
/// <returns> A Vector of connected RingSets
/// </returns>
public static System.Collections.ArrayList partitionRings(IRingSet ringSet)
{
System.Collections.ArrayList ringSets = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
if (ringSet.AtomContainerCount == 0)
{
return(ringSets);
}
IRingSet tempRingSet = null;
IRing ring = (IRing)ringSet.getAtomContainer(0);
if (ring == null)
{
return(ringSets);
}
IRingSet rs = ring.Builder.newRingSet();
for (int f = 0; f < ringSet.AtomContainerCount; f++)
{
rs.addAtomContainer(ringSet.getAtomContainer(f));
}
do
{
ring = (IRing)rs.getAtomContainer(0);
IRingSet newRs = ring.Builder.newRingSet();
newRs.addAtomContainer(ring);
tempRingSet = walkRingSystem(rs, ring, newRs);
if (debug)
{
System.Console.Out.WriteLine("found ringset with ringcount: " + tempRingSet.AtomContainerCount);
}
ringSets.Add(walkRingSystem(rs, ring, newRs));
}while (rs.AtomContainerCount > 0);
return(ringSets);
}
private static IRingSet toRingSet(IAtomContainer ac, System.Collections.ICollection cycles)
{
IRingSet ringSet = ac.Builder.newRingSet();
System.Collections.IEnumerator cycleIterator = cycles.GetEnumerator();
while (cycleIterator.MoveNext())
{
SimpleCycle cycle = (SimpleCycle)cycleIterator.Current;
IRing ring = ac.Builder.newRing();
System.Collections.IList vertices = cycle.vertexList();
IAtom[] atoms = new IAtom[vertices.Count];
atoms[0] = (IAtom)vertices[0];
for (int i = 1; i < vertices.Count; i++)
{
atoms[i] = (IAtom)vertices[i];
ring.addElectronContainer(ac.getBond(atoms[i - 1], atoms[i]));
}
ring.addElectronContainer(ac.getBond(atoms[vertices.Count - 1], atoms[0]));
ring.Atoms = atoms;
ringSet.addAtomContainer(ring);
}
return(ringSet);
}
/// <summary> Checks the pathes if a ring has been found
///
/// </summary>
/// <param name="pathes"> The pathes to check for rings
/// </param>
/// <param name="ringSet"> The ringset to add the detected rings to
/// </param>
/// <param name="ac"> The AtomContainer with the original structure
/// </param>
private void detectRings(System.Collections.ArrayList pathes, IRingSet ringSet, IAtomContainer ac)
{
Path path = null;
IRing ring = null;
IBond bond = null;
for (int f = 0; f < pathes.Count; f++)
{
path = (Path)pathes[f];
if (path.Count > 3 && path[path.Count - 1] == path[0])
{
if (debug)
{
System.Console.Out.WriteLine("Removing path " + path.toString(originalAc) + " which is a ring.");
}
path.RemoveAt(0);
ring = ac.Builder.newRing();
for (int g = 0; g < path.Count; g++)
{
ring.addAtom((IAtom)path[g]);
}
IBond[] bonds = ac.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
bond = bonds[g];
if (ring.contains(bond.getAtomAt(0)) && ring.contains(bond.getAtomAt(1)))
{
ring.addBond(bond);
}
}
ringSet.addAtomContainer(ring);
}
}
}
/// <summary> Sorts the rings in the set by size. The largest ring comes
/// first.
/// </summary>
public static void sort(IRingSet ringSet)
{
System.Collections.IList ringList = new System.Collections.ArrayList();
IAtomContainer[] rings = ringSet.AtomContainers;
for (int i = 0; i < rings.Length; i++)
{
ringList.Add(rings[i]);
}
SupportClass.CollectionsSupport.Sort(ringList, new RingSizeComparator(RingSizeComparator.LARGE_FIRST));
ringSet.removeAllAtomContainers();
System.Collections.IEnumerator iter = ringList.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (iter.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
ringSet.addAtomContainer((IRing)iter.Current);
}
}
/// <summary> Sorts the rings in the set by size. The largest ring comes
/// first.
/// </summary>
public static void sort(IRingSet ringSet)
{
System.Collections.IList ringList = new System.Collections.ArrayList();
IAtomContainer[] rings = ringSet.AtomContainers;
for (int i = 0; i < rings.Length; i++)
{
ringList.Add(rings[i]);
}
SupportClass.CollectionsSupport.Sort(ringList, new RingSizeComparator(RingSizeComparator.LARGE_FIRST));
ringSet.removeAllAtomContainers();
System.Collections.IEnumerator iter = ringList.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (iter.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
ringSet.addAtomContainer((IRing)iter.Current);
}
}
/// <summary> Perform a walk in the given RingSet, starting at a given Ring and
/// recursivly searching for other Rings connected to this ring. By doing
/// this it finds all rings in the RingSet connected to the start ring,
/// putting them in newRs, and removing them from rs.
///
/// </summary>
/// <param name="rs"> The RingSet to be searched
/// </param>
/// <param name="ring"> The ring to start with
/// </param>
/// <param name="newRs"> The RingSet containing all Rings connected to ring
/// </param>
/// <returns> newRs The RingSet containing all Rings connected to ring
/// </returns>
private static IRingSet walkRingSystem(IRingSet rs, IRing ring, IRingSet newRs)
{
IRing tempRing;
System.Collections.IList tempRings = rs.getConnectedRings(ring);
if (debug)
{
System.Console.Out.WriteLine("walkRingSystem -> tempRings.size(): " + tempRings.Count);
}
rs.removeAtomContainer(ring);
System.Collections.IEnumerator iter = tempRings.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (iter.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
tempRing = (IRing)iter.Current;
if (!newRs.contains(tempRing))
{
newRs.addAtomContainer(tempRing);
newRs.add(walkRingSystem(rs, tempRing, newRs));
}
}
return(newRs);
}
/// <summary> Checks the pathes if a ring has been found
///
/// </summary>
/// <param name="pathes"> The pathes to check for rings
/// </param>
/// <param name="ringSet"> The ringset to add the detected rings to
/// </param>
/// <param name="ac"> The AtomContainer with the original structure
/// </param>
private void detectRings(System.Collections.ArrayList pathes, IRingSet ringSet, IAtomContainer ac)
{
Path path = null;
IRing ring = null;
IBond bond = null;
for (int f = 0; f < pathes.Count; f++)
{
path = (Path)pathes[f];
if (path.Count > 3 && path[path.Count - 1] == path[0])
{
if (debug)
{
System.Console.Out.WriteLine("Removing path " + path.toString(originalAc) + " which is a ring.");
}
path.RemoveAt(0);
ring = ac.Builder.newRing();
for (int g = 0; g < path.Count; g++)
{
ring.addAtom((IAtom)path[g]);
}
IBond[] bonds = ac.Bonds;
for (int g = 0; g < bonds.Length; g++)
{
bond = bonds[g];
if (ring.contains(bond.getAtomAt(0)) && ring.contains(bond.getAtomAt(1)))
{
ring.addBond(bond);
}
}
ringSet.addAtomContainer(ring);
}
}
}
/// <summary> Perform a walk in the given RingSet, starting at a given Ring and
/// recursivly searching for other Rings connected to this ring. By doing
/// this it finds all rings in the RingSet connected to the start ring,
/// putting them in newRs, and removing them from rs.
///
/// </summary>
/// <param name="rs"> The RingSet to be searched
/// </param>
/// <param name="ring"> The ring to start with
/// </param>
/// <param name="newRs"> The RingSet containing all Rings connected to ring
/// </param>
/// <returns> newRs The RingSet containing all Rings connected to ring
/// </returns>
private static IRingSet walkRingSystem(IRingSet rs, IRing ring, IRingSet newRs)
{
IRing tempRing;
System.Collections.IList tempRings = rs.getConnectedRings(ring);
if (debug)
{
System.Console.Out.WriteLine("walkRingSystem -> tempRings.size(): " + tempRings.Count);
}
rs.removeAtomContainer(ring);
System.Collections.IEnumerator iter = tempRings.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
while (iter.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
tempRing = (IRing)iter.Current;
if (!newRs.contains(tempRing))
{
newRs.addAtomContainer(tempRing);
newRs.add(walkRingSystem(rs, tempRing, newRs));
}
}
return newRs;
}
