/// <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;
}
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;
}