/// <inheritdoc/>
public Cycles Find(IAtomContainer molecule, int[][] graph, int length)
{
RingSearch ringSearch = new RingSearch(molecule, graph);
if (this.predefinedLength < length)
{
length = this.predefinedLength;
}
IList <int[]> walks = new List <int[]>(6);
// all isolated cycles are relevant - all we need to do is walk around
// the vertices in the subset 'isolated'
foreach (var isolated in ringSearch.Isolated())
{
if (isolated.Length <= length)
{
walks.Add(GraphUtil.Cycle(graph, isolated));
}
}
// each biconnected component which isn't an isolated cycle is processed
// separately as a subgraph.
foreach (var fused in ringSearch.Fused())
{
// make a subgraph and 'apply' the cycle computation - the walk
// (path) is then lifted to the original graph
foreach (var cycle in FindInFused(GraphUtil.Subgraph(graph, fused), length))
{
walks.Add(Lift(cycle, fused));
}
}
return(new Cycles(walks.ToArray(), molecule, null));
}
/// <inheritdoc/>
public Cycles Find(IAtomContainer molecule, int length)
{
var bondMap = EdgeToBondMap.WithSpaceFor(molecule);
var graph = GraphUtil.ToAdjList(molecule, bondMap);
var ringSearch = new RingSearch(molecule, graph);
var walks = new List <int[]>(6);
// all isolated cycles are relevant - all we need to do is walk around
// the vertices in the subset 'isolated'
foreach (var isolated in ringSearch.Isolated())
{
if (isolated.Length <= length)
{
walks.Add(GraphUtil.Cycle(graph, isolated));
}
}
// each biconnected component which isn't an isolated cycle is processed
// separately as a subgraph.
foreach (var fused in ringSearch.Fused())
{
// make a subgraph and 'apply' the cycle computation - the walk
// (path) is then lifted to the original graph
foreach (var cycle in Apply(GraphUtil.Subgraph(graph, fused), length))
{
walks.Add(Lift(cycle, fused));
}
}
return(new Cycles(walks.ToArray(), molecule, bondMap));
}
public virtual void TestCycle()
{
// 0-1-2-3-4-5-
int[][] g = new int[][] { new int[] { 1, 5 }, new int[] { 0, 2 }, new int[] { 1, 3 }, new int[] { 2, 4 }, new int[] { 3, 5 }, new int[] { 4, 0 } };
int[] path = GraphUtil.Cycle(g, new int[] { 0, 3, 4, 1, 5, 2 });
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 0, 1, 2, 3, 4, 5, 0 }, path));
}
public virtual void TestAcyclic2()
{
// 0-1-2 3-4-5- (2 and 3) not connected
int[][] g = new int[][] { new int[] { 1 }, new int[] { 0, 2 }, new int[] { 1 }, new int[] { 4 }, new int[] { 3, 5 }, new int[] { 4 } };
GraphUtil.Cycle(g, new int[] { 0, 3, 4, 1, 5, 2 });
}
public virtual void TestAcyclic()
{
// 0-1-2-3-4-5 (5 and 0 not connected)
int[][] g = new int[][] { new int[] { 1 }, new int[] { 0, 2 }, new int[] { 1, 3 }, new int[] { 2, 4 }, new int[] { 3, 5 }, new int[] { 4 } };
GraphUtil.Cycle(g, new int[] { 0, 3, 4, 1, 5, 2 });
}