/// <summary>
/// Recognise the cyclic carbohydrate projections.
/// </summary>
/// <param name="projections">the types of projections to recognise</param>
/// <returns>recognised stereocenters</returns>
public IEnumerable <IStereoElement <IChemObject, IChemObject> > Recognise(ICollection <Projection> projections)
{
if (!projections.Contains(Projection.Haworth) && !projections.Contains(Projection.Chair))
{
yield break;
}
var ringSearch = new RingSearch(container, graph);
foreach (var isolated in ringSearch.Isolated())
{
if (isolated.Length < 5 || isolated.Length > 7)
{
continue;
}
var cycle = Arrays.CopyOf(GraphUtil.Cycle(graph, isolated),
isolated.Length);
var points = CoordinatesOfCycle(cycle, container);
var turns = GetTurns(points);
var projection = WoundProjection.OfTurns(turns);
if (!projections.Contains(projection.Projection))
{
continue;
}
// ring is not aligned correctly for Haworth
if (projection.Projection == Projection.Haworth && !CheckHaworthAlignment(points))
{
continue;
}
var horizontalXy = HorizontalOffset(points, turns, projection.Projection);
// near vertical, should also flag as potentially ambiguous
if (1 - Math.Abs(horizontalXy.Y) < QuartCardinalityThreshold)
{
continue;
}
var above = (int[])cycle.Clone();
var below = (int[])cycle.Clone();
if (!AssignSubstituents(cycle, above, below, projection, horizontalXy))
{
continue;
}
foreach (var center in NewTetrahedralCenters(cycle, above, below, projection))
{
yield return(center);
}
}
yield break;
}
/// <summary>
/// Compute all rings up to and including the <paramref name="maxRingSize"/>. The
/// container is first partitioned into ring systems which are then processed
/// separately. If the molecule has already be partitioned, consider using <see cref="FindAllRingsInIsolatedRingSystem(IAtomContainer, int)"/>.
/// </summary>
/// <param name="container">The AtomContainer to be searched for rings</param>
/// <param name="maxRingSize">Maximum ring size to consider. Provides a possible
/// breakout from recursion for complex compounds.</param>
/// <returns>A RingSet with all rings in the AtomContainer</returns>
/// <exception cref="CDKException">An exception thrown if the threshold was exceeded</exception>
public IRingSet FindAllRings(IAtomContainer container, int maxRingSize)
{
var edges = EdgeToBondMap.WithSpaceFor(container);
var graph = GraphUtil.ToAdjList(container, edges);
var rs = new RingSearch(container, graph);
var ringSet = container.Builder.NewRingSet();
// don't need to run on isolated rings, just need to put vertices in
// cyclic order
foreach (var isolated in rs.Isolated())
{
if (isolated.Length <= maxRingSize)
{
var ring = ToRing(container, edges, GraphUtil.Cycle(graph, isolated));
ringSet.Add(ring);
}
}
// for each set of fused cyclic vertices run the separate search
foreach (var fused in rs.Fused())
{
var ac = new AllCycles(GraphUtil.Subgraph(graph, fused), Math.Min(maxRingSize, fused.Length), threshold.Value);
if (!ac.Completed)
{
throw new CDKException("Threshold exceeded for AllRingsFinder");
}
foreach (var path in ac.GetPaths())
{
IRing ring = ToRing(container, edges, path, fused);
ringSet.Add(ring);
}
}
return(ringSet);
}