/// <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));
}
/// <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));
}
public virtual void SequentialSubgraph()
{
int[][] graph = new int[][] { new int[] { 1, 2 }, new int[] { 0, 2 }, new int[] { 0, 1 } };
int[][] subgraph = GraphUtil.Subgraph(graph, new int[] { 0, 1 });
int[][] expected = new int[][] { new int[] { 1 }, new int[] { 0 } };
Assert.IsTrue(Compares.AreDeepEqual(expected, subgraph));
}
public virtual void IntermittentSubgraph()
{
int[][]
graph = new int[][] { new int[] { 1, 2 }, new int[] { 0, 2, 3 }, new int[] { 0, 1 }, new int[] { 1 } };
int[][] subgraph = GraphUtil.Subgraph(graph, new int[] { 0, 2, 3 });
int[][] expected = new int[][] { new int[] { 1 }, new int[] { 0 }, new int[] { } };
Assert.IsTrue(Compares.AreDeepEqual(expected, subgraph));
}
public void Main()
{
var naphthalene = TestMoleculeFactory.MakeNaphthalene();
#region Subgraph
int[][] g = GraphUtil.ToAdjList(naphthalene);
int[] vs = new int[] { 0, 1, 2, 3, 4, 5 };
int[][] h = GraphUtil.Subgraph(g, vs);
// for the vertices in h, the provided 'vs' gives the original index
for (int v = 0; v < h.Length; v++)
{
// vs[v] is 'v' in 'g'
}
#endregion
}
public virtual void ResizeSubgraph()
{
int[][] graph = new int[][] {
new int[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 },
new int[] { 0 }, new int[] { 0 }, new int[] { 0 }, new int[] { 0 },
new int[] { 0 }, new int[] { 0 }, new int[] { 0 }, new int[] { 0 },
new int[] { 0 }, new int[] { 0 }, new int[] { 0 }, new int[] { 0 },
new int[] { 0 }, new int[] { 0 }
};
int[][] subgraph = GraphUtil.Subgraph(graph, new int[] { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 });
int[][] expected = new int[][] {
new int[] { 1, 2, 3, 4, 5, 6, 7, 8, 9 },
new int[] { 0 }, new int[] { 0 }, new int[] { 0 }, new int[] { 0 },
new int[] { 0 }, new int[] { 0 }, new int[] { 0 }, new int[] { 0 },
new int[] { 0 },
};
Assert.IsTrue(Compares.AreDeepEqual(expected, subgraph));
}
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();
}
}