/// <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));
}
/// <summary>
/// Find and mark all cyclic atoms and bonds in the provided molecule.
/// </summary>
/// <param name="mol">molecule</param>
/// <returns>Number of rings found (circuit rank)</returns>
/// <seealso cref="IMolecularEntity.IsInRing"/>
/// <seealso href="https://en.wikipedia.org/wiki/Circuit_rank">Circuit Rank</seealso>
public static int MarkRingAtomsAndBonds(IAtomContainer mol)
{
var bonds = EdgeToBondMap.WithSpaceFor(mol);
return(MarkRingAtomsAndBonds(mol, GraphUtil.ToAdjList(mol, bonds), bonds));
}