/// <summary>
/// Creates a molecule graph for use with jgrapht.
/// Bond orders are not respected.
/// </summary>
/// <param name="molecule">the specified molecule</param>
/// <returns>a graph representing the molecule</returns>
static public SimpleGraph getMoleculeGraph(IAtomContainer molecule) {
SimpleGraph graph = new SimpleGraph();
for (int i=0; i<molecule.AtomCount; i++ ) {
IAtom atom = molecule.Atoms[i];
graph.addVertex(atom);
}
for (int i=0; i<molecule.getBondCount(); i++ ) {
IBond bond = molecule.Bonds[i];
/*
int order = (int) bond.getOrder();
for (int j=0; j<order; j++) {
graph.addEdge(bond.getAtoms()[0], bond.getAtoms()[1]);
}
*/
graph.addEdge(bond.getAtoms()[0], bond.getAtoms()[1]);
}
return graph;
}
public virtual System.Collections.IList equivalenceClasses()
{
int[] weight = weightVector();
System.Object[] cyclesArray = (System.Object[])SupportClass.ICollectionSupport.ToArray(cycles_Renamed_Field);
System.Array.Sort(cyclesArray, new AnonymousClassComparator(this));
System.Collections.ICollection essentialCycles = this.essentialCycles();
bool[][] u = new bool[cyclesArray.Length][];
for (int i = 0; i < cyclesArray.Length; i++)
{
u[i] = new bool[edgeList.Count];
}
bool[][] a = getCycleEdgeIncidenceMatrix(cyclesArray);
bool[][] ai = inverseBinaryMatrix(a, cyclesArray.Length);
for (int i = 0; i < cyclesArray.Length; i++)
{
for (int j = 0; j < cyclesArray.Length; j++)
{
u[i][j] = ai[j][i];
}
}
UndirectedGraph h = new SimpleGraph();
h.addAllVertices(cycles_Renamed_Field);
ConnectivityInspector connectivityInspector = new ConnectivityInspector(h);
int left = 0;
for (int right = 0; right < weight.Length; right++)
{
if ((right < weight.Length - 1) && (weight[right + 1] == weight[right]))
continue;
// cyclesArray[left] to cyclesArray[right] have same weight
// First test (compute pre-classes):
// Check if there is a cycle that can replace a[i] as well as a[j] in a basis
// This is done by finding a cycle C with <C,u[i]>=1 and <C,u[j]>=1
for (int i = left; i <= right; i++)
{
if (SupportClass.ICollectionSupport.Contains(essentialCycles, (SimpleCycle)cyclesArray[i]))
continue;
for (int j = i + 1; j <= right; j++)
{
if (SupportClass.ICollectionSupport.Contains(essentialCycles, (SimpleCycle)cyclesArray[j]))
continue;
// check if cyclesArray[i] and cyclesArray[j] are already in the same class
if (connectivityInspector.pathExists(cyclesArray[i], cyclesArray[j]))
continue;
bool sameClass = false;
AuxiliaryGraph2 auxGraph = new AuxiliaryGraph2(this, graph, edgeList, u[i], u[j]);
//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'"
for (System.Collections.IEnumerator it = graph.vertexSet().GetEnumerator(); it.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'"
System.Object vertex = it.Current;
// check if the vertex is incident to an edge with u[edge] == 1
bool shouldSearchCycle = false;
System.Collections.ICollection incidentEdges = graph.edgesOf(vertex);
System.Collections.IEnumerator edgeIterator = incidentEdges.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 (edgeIterator.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'"
Edge edge = (Edge)edgeIterator.Current;
int index = getEdgeIndex(edge);
if (u[i][index] || u[j][index])
{
shouldSearchCycle = true;
break;
}
}
if (shouldSearchCycle)
{
System.Object auxVertex00 = auxGraph.auxVertex00(vertex);
System.Object auxVertex11 = auxGraph.auxVertex11(vertex);
System.Collections.IList auxPath = BFSShortestPath.findPathBetween(auxGraph, auxVertex00, auxVertex11);
double pathWeight = auxPath.Count;
if (pathWeight == weight[left])
{
sameClass = true;
break;
}
}
}
if (sameClass)
{
h.addEdge(cyclesArray[i], cyclesArray[j]);
}
}
}
// Second test (compute equivalence classes):
// Check if there are two cycle Ci, Cj that can replace a[i], a[j]
// and have a common cycle a[k] in their basis representation
// This is done by finding a cycle a[k] with <u[k],u[i]>=1 and <u[k],u[j]>=1
for (int i = left; i <= right; i++)
{
if (SupportClass.ICollectionSupport.Contains(essentialCycles, (SimpleCycle)cyclesArray[i]))
continue;
for (int j = i + 1; j <= right; j++)
{
if (SupportClass.ICollectionSupport.Contains(essentialCycles, (SimpleCycle)cyclesArray[j]))
continue;
// check if cyclesArray[i] and cyclesArray[j] are already in the same class
if (connectivityInspector.pathExists(cyclesArray[i], cyclesArray[j]))
continue;
bool sameClass = false;
for (int k = 0; ((SimpleCycle)cyclesArray[k]).weight() < weight[left]; k++)
{
AuxiliaryGraph2 auxGraph = new AuxiliaryGraph2(this, graph, edgeList, u[i], u[k]);
bool shortestPathFound = false;
//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'"
for (System.Collections.IEnumerator it = graph.vertexSet().GetEnumerator(); it.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'"
System.Object vertex = it.Current;
System.Object auxVertex00 = auxGraph.auxVertex00(vertex);
System.Object auxVertex11 = auxGraph.auxVertex11(vertex);
System.Collections.IList auxPath = BFSShortestPath.findPathBetween(auxGraph, auxVertex00, auxVertex11);
double pathWeight = auxPath.Count;
if (pathWeight == weight[left])
{
shortestPathFound = true;
break;
}
}
if (!shortestPathFound)
continue;
auxGraph = new AuxiliaryGraph2(this, graph, edgeList, u[j], u[k]);
//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'"
for (System.Collections.IEnumerator it = graph.vertexSet().GetEnumerator(); it.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'"
System.Object vertex = it.Current;
System.Object auxVertex00 = auxGraph.auxVertex00(vertex);
System.Object auxVertex11 = auxGraph.auxVertex11(vertex);
System.Collections.IList auxPath = BFSShortestPath.findPathBetween(auxGraph, auxVertex00, auxVertex11);
double pathWeight = auxPath.Count;
if (pathWeight == weight[left])
{
sameClass = true;
break;
}
}
if (sameClass)
break;
}
if (sameClass)
{
h.addEdge(cyclesArray[i], cyclesArray[j]);
}
}
}
left = right + 1;
}
return connectivityInspector.connectedSets();
}
private System.Collections.IList lazyFindBiconnectedSets()
{
if (biconnectedSets_Renamed_Field == null)
{
biconnectedSets_Renamed_Field = new System.Collections.ArrayList();
IList inspector = new ConnectivityInspector(graph).connectedSets();
System.Collections.IEnumerator connectedSets = inspector.GetEnumerator();
while (connectedSets.MoveNext())
{
object obj = ((DictionaryEntry)connectedSets.Current).Value;
if (!(obj is CSGraphT.SupportClass.HashSetSupport))
continue;
CSGraphT.SupportClass.SetSupport connectedSet = (CSGraphT.SupportClass.SetSupport)obj;
if (connectedSet.Count == 1)
{
continue;
}
org._3pq.jgrapht.Graph subgraph = new Subgraph(graph, connectedSet, null);
// do DFS
// Stack for the DFS
System.Collections.ArrayList vertexStack = new System.Collections.ArrayList();
CSGraphT.SupportClass.SetSupport visitedVertices = new CSGraphT.SupportClass.HashSetSupport();
IDictionary parent = new System.Collections.Hashtable();
IList dfsVertices = new System.Collections.ArrayList();
CSGraphT.SupportClass.SetSupport treeEdges = new CSGraphT.SupportClass.HashSetSupport();
System.Object currentVertex = subgraph.vertexSet()[0];//.ToArray()[0];
vertexStack.Add(currentVertex);
visitedVertices.Add(currentVertex);
while (!(vertexStack.Count == 0))
{
currentVertex = SupportClass.StackSupport.Pop(vertexStack);
System.Object parentVertex = parent[currentVertex];
if (parentVertex != null)
{
Edge edge = subgraph.getEdge(parentVertex, currentVertex);
// tree edge
treeEdges.Add(edge);
}
visitedVertices.Add(currentVertex);
dfsVertices.Add(currentVertex);
System.Collections.IEnumerator edges = subgraph.edgesOf(currentVertex).GetEnumerator();
while (edges.MoveNext())
{
// find a neighbour vertex of the current vertex
Edge edge = (Edge)edges.Current;
if (!treeEdges.Contains(edge))
{
System.Object nextVertex = edge.oppositeVertex(currentVertex);
if (!visitedVertices.Contains(nextVertex))
{
vertexStack.Add(nextVertex);
parent[nextVertex] = currentVertex;
}
else
{
// non-tree edge
}
}
}
}
// DFS is finished. Now create the auxiliary graph h
// Add all the tree edges as vertices in h
SimpleGraph h = new SimpleGraph();
h.addAllVertices(treeEdges);
visitedVertices.Clear();
CSGraphT.SupportClass.SetSupport connected = new CSGraphT.SupportClass.HashSetSupport();
for (System.Collections.IEnumerator it = dfsVertices.GetEnumerator(); it.MoveNext(); )
{
System.Object v = it.Current;
visitedVertices.Add(v);
// find all adjacent non-tree edges
for (System.Collections.IEnumerator adjacentEdges = subgraph.edgesOf(v).GetEnumerator(); adjacentEdges.MoveNext();)
{
Edge l = (Edge)adjacentEdges.Current;
if (!treeEdges.Contains(l))
{
h.addVertex(l);
System.Object u = l.oppositeVertex(v);
// we need to check if (u,v) is a back-edge
if (!visitedVertices.Contains(u))
{
while (u != v)
{
System.Object pu = parent[u];
Edge f = subgraph.getEdge(u, pu);
h.addEdge(f, l);
if (!connected.Contains(f))
{
connected.Add(f);
u = pu;
}
else
{
u = v;
}
}
}
}
}
}
ConnectivityInspector connectivityInspector = new ConnectivityInspector(h);
biconnectedSets_Renamed_Field.Add(connectivityInspector.connectedSets());
}
}
return biconnectedSets_Renamed_Field;
}