/// <inheritdoc/>
public override int[][] Apply(int[][] graph, int length)
{
int threshold = 684; // see. AllRingsFinder.Threshold.Pubchem_99
AllCycles ac = new AllCycles(graph, Math.Min(length, graph.Length), threshold);
return(ac.Completed ? ac.GetPaths() : VertexShort.Apply(graph, length));
}
public virtual void Impractical()
{
// k12 - ouch
AllCycles ac = new AllCycles(RegularPathGraphTest.CompleteGraphOfSize(12), 12, 100);
Assert.IsFalse(ac.Completed);
}
public virtual void CompletedTest()
{
AllCycles ac = new AllCycles(RegularPathGraphTest.CompleteGraphOfSize(4), 4, 100);
Assert.IsTrue(ac.Completed);
Assert.AreEqual(7, ac.Count);
}
/// <summary>
/// Find rings in a biconnected component.
/// </summary>
/// <param name="g">adjacency list</param>
/// <param name="length"></param>
/// <returns></returns>
/// <exception cref="IntractableException">computation was not feasible</exception>
private int[][] FindInFused(int[][] g, int length)
{
AllCycles allCycles = new AllCycles(g, Math.Min(g.Length, length), threshold);
if (!allCycles.Completed)
{
throw new IntractableException("A large number of cycles were being generated and the"
+ " computation was aborted. Please us AllCycles/AllRingsFinder with"
+ " and specify a larger threshold or an alternative cycle set.");
}
return(allCycles.GetPaths());
}
/// <inheritdoc/>
public override int[][] Apply(int[][] graph, int length)
{
int threshold = 684; // see. AllRingsFinder.Threshold.Pubchem_99
AllCycles ac = new AllCycles(graph, Math.Min(length, graph.Length), threshold);
if (!ac.Completed)
{
throw new IntractableException("A large number of cycles were being generated and the"
+ " computation was aborted. Please use AllCycles/AllRingsFinder with"
+ " and specify a larger threshold or use a " + nameof(ICycleFinder) + " with a fall-back"
+ " to a set unique cycles: e.g. " + nameof(Cycles) + "." + nameof(Cycles.AllOrVertexShortFinder) + ".");
}
return(ac.GetPaths());
}
public virtual void Rank()
{
// given vertices based on degree
int[][] g = new int[][] { new int [] { 0, 0, 0, 0 }, // 5th
new int [] { 0, 0, 0, 0 }, // 6th
new int [] { 0, 0, 0 }, // 4th
new int [] { 0 }, // 2nd
new int [] { 0, 0 }, // 3rd
new int [] {} // 1st
};
var actual = AllCycles.GetRank(g);
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 4, 5, 3, 1, 2, 0 }, actual));
}
public virtual void K5Paths()
{
AllCycles ac = new AllCycles(RegularPathGraphTest.CompleteGraphOfSize(5), 5, 1000);
Assert.IsTrue(Compares.AreDeepEqual(
new int[][] {
new[] { 2, 1, 0, 2 }, new[] { 3, 1, 0, 3 }, new[] { 4, 1, 0, 4 }, new[] { 3, 2, 0, 3 }, new[] { 3, 2, 1, 3 },
new[] { 3, 2, 1, 0, 3 }, new[] { 3, 2, 0, 1, 3 }, new[] { 4, 2, 0, 4 }, new[] { 4, 2, 1, 4 }, new[] { 4, 2, 1, 0, 4 }, new[] { 4, 2, 0, 1, 4 },
new[] { 3, 0, 2, 1, 3 }, new[] { 4, 0, 2, 1, 4 }, new[] { 4, 3, 0, 4 }, new[] { 4, 3, 1, 4 }, new[] { 4, 3, 1, 0, 4 }, new[] { 4, 3, 0, 1, 4 },
new[] { 4, 3, 2, 4 }, new[] { 4, 3, 2, 0, 4 }, new[] { 4, 3, 2, 1, 4 }, new[] { 4, 3, 2, 1, 0, 4 }, new[] { 4, 3, 2, 0, 1, 4 },
new[] { 4, 3, 0, 2, 4 }, new[] { 4, 3, 1, 2, 4 }, new[] { 4, 3, 0, 1, 2, 4 }, new[] { 4, 3, 1, 0, 2, 4 }, new[] { 4, 3, 0, 2, 1, 4 },
new[] { 4, 3, 1, 2, 0, 4 }, new[] { 4, 0, 3, 1, 4 }, new[] { 4, 0, 3, 2, 4 }, new[] { 4, 0, 3, 2, 1, 4 }, new[] { 4, 0, 3, 1, 2, 4 },
new[] { 4, 1, 3, 2, 4 }, new[] { 4, 1, 3, 2, 0, 4 }, new[] { 4, 1, 3, 0, 2, 4 }, new[] { 4, 0, 1, 3, 2, 4 }, new[] { 4, 1, 0, 3, 2, 4 }
},
ac.GetPaths()));
}
public static void Main(string[] args)
{
// convert the molecule to adjacency list - may be redundant in future
IAtomContainer m = TestMoleculeFactory.MakeAlphaPinene();
int[][] g = GraphUtil.ToAdjList(m);
// efficient computation/partitioning of the ring systems
RingSearch rs = new RingSearch(m, g);
// isolated cycles don't need to be run
rs.Isolated();
// process fused systems separately
foreach (var fused in rs.Fused())
{
const int maxDegree = 100;
// given the fused subgraph, max cycle size is
// the number of vertices
AllCycles ac = new AllCycles(GraphUtil.Subgraph(g, fused), fused.Length, maxDegree);
// cyclic walks
int[][] paths = ac.GetPaths();
}
}
public virtual void K5Size()
{
AllCycles ac = new AllCycles(RegularPathGraphTest.CompleteGraphOfSize(5), 5, 1000);
Assert.AreEqual(37, ac.Count);
}
public virtual void VerticesInOrder()
{
var vertices = AllCycles.GetVerticesInOrder(new int[] { 4, 3, 1, 2, 0 });
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 4, 2, 3, 1, 0 }, vertices));
}
public virtual void K7Size()
{
AllCycles ac = new AllCycles(RegularPathGraphTest.CompleteGraphOfSize(7), 7, 1000);
Assert.AreEqual(1172, ac.Count);
}