/// <summary>
/// Compute the cycles of the extended smallest set of smallest rings (ESSSR)
/// for an existing minimum cycle basis. Choosing the set to be canonical
/// means the set depends on the order of the vertices and may <b>not</b> be
/// consistent in subgraphs. Given a different order of vertices the same
/// cycles may not be found.
/// </summary>
/// <param name="mcb">minimum cycle basis</param>
/// <param name="canonical">should the set be canonical (non-unique)</param>
public TripletShortCycles(MinimumCycleBasis mcb, bool canonical)
{
// don't reorder neighbors as the MCB was already done on this ordering
this.graph = Copy(mcb.graph);
this.canonical = canonical;
// all minimum cycle basis paths belong to the set
foreach (var path in mcb.GetPaths())
{
basis.Add(new Path(Arrays.CopyOf(path, path.Length - 1)));
}
// count the number of cycles each vertex belongs to and try to find a
// cycle though the triple of 'v' and two of it's neighbors
int ord = graph.Length;
int[] nCycles = NCycles(basis, ord);
for (int v = 0; v < ord; v++)
{
if (nCycles[v] > 1)
{
FindTriple(v);
}
}
}
public virtual void Size_norbornane()
{
int[][] norbornane = Norbornane;
MinimumCycleBasis mcb = new MinimumCycleBasis(norbornane);
int[][] paths = mcb.GetPaths();
Assert.AreEqual(2, paths.Length);
}
public virtual void Paths_cyclophane_even()
{
int[][] cyclophane_even = CyclophaneEven;
MinimumCycleBasis mcb = new MinimumCycleBasis(cyclophane_even);
int[][] paths = mcb.GetPaths();
Assert.AreEqual(2, paths.Length);
int[][] expected = new int[][] { new[] { 3, 2, 1, 0, 5, 4, 3 }, new[] { 3, 6, 7, 8, 9, 10, 11, 0, 1, 2, 3 } };
Assert.IsTrue(Compares.AreOrderLessDeepEqual(expected, paths));
}
public virtual void Paths_anthracene()
{
int[][] anthracene = Anthracene;
MinimumCycleBasis mcb = new MinimumCycleBasis(anthracene);
int[][] paths = mcb.GetPaths();
Assert.AreEqual(3, paths.Length);
int[][] expected = new int[][] { new[] { 5, 0, 1, 2, 3, 4, 5 }, new[] { 9, 6, 5, 4, 7, 8, 9 }, new[] { 9, 8, 10, 11, 12, 13, 9 } };
Assert.IsTrue(Compares.AreOrderLessDeepEqual(expected, paths));
}
public virtual void Paths_napthalene()
{
int[][] napthalene = Naphthalene;
MinimumCycleBasis mcb = new MinimumCycleBasis(napthalene);
int[][] paths = mcb.GetPaths();
Assert.AreEqual(2, paths.Length);
int[][] expected = new int[][] { new[] { 5, 0, 1, 2, 3, 4, 5 }, new[] { 5, 4, 7, 8, 9, 6, 5 } };
Assert.IsTrue(Compares.AreOrderLessDeepEqual(expected, paths));
}
public virtual void Paths_bicyclo()
{
int[][] bicyclo = Bicyclo;
MinimumCycleBasis mcb = new MinimumCycleBasis(bicyclo);
int[][] paths = mcb.GetPaths();
Assert.AreEqual(2, paths.Length);
int[][] expected = new int[][] { new[] { 5, 0, 1, 2, 3, 4, 5 }, new[] { 5, 0, 1, 2, 7, 6, 5 } };
Assert.IsTrue(Compares.AreOrderLessDeepEqual(expected, paths));
}
/// <inheritdoc/>
public override int[][] Apply(int[][] graph, int length)
{
InitialCycles ic = InitialCycles.OfBiconnectedComponent(graph, length);
MinimumCycleBasis mcb = new MinimumCycleBasis(ic, true);
// As per the old aromaticity detector if the MCB/SSSR is made
// of 2 or 3 rings we check all rings for aromaticity - otherwise
// we just check the MCB/SSSR
if (mcb.Count > 3)
{
return(mcb.GetPaths());
}
else
{
return(All.Apply(graph, length));
}
}