public void TestIsolated()
{
var search = new RingSearch(hexaphenylene);
var isolated = search.Isolated();
Assert.AreEqual(0, isolated.Length);
}
public void TestIsolated()
{
var search = new RingSearch(spiro);
var isolated = search.Isolated();
Assert.AreEqual(2, isolated.Length);
Assert.IsTrue(Compares.AreOrderLessDeepEqual(new[] { 4, 7 }, new int[] { isolated[0].Length, isolated[1].Length }));
}
public void TestIsolated()
{
var search = new RingSearch(benzene);
var isolated = search.Isolated();
Assert.AreEqual(1, isolated.Length);
Assert.AreEqual(6, isolated[0].Length);
}
public void TestIsolated()
{
var search = new RingSearch(biphenyl);
var isolated = search.Isolated();
Assert.AreEqual(2, isolated.Length);
Assert.AreEqual(6, isolated[0].Length);
Assert.AreEqual(6, isolated[1].Length);
}
public void TestIsolated()
{
var mock_cyclicSearch = new Mock <ICyclicVertexSearch>();
ICyclicVertexSearch cyclicSearch = mock_cyclicSearch.Object;
IAtomContainer container = new Mock <IAtomContainer>().Object;
IAtom atom = new Mock <IAtom>().Object;
RingSearch ringSearch = new RingSearch(container, cyclicSearch);
ringSearch.Isolated();
mock_cyclicSearch.Verify(n => n.Isolated(), Times.Once());
}
/// <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);
}
public void TestIsolated()
{
var ringSearch = new RingSearch(fusedRings);
Assert.AreEqual(0, ringSearch.Isolated().Length);
}
static void Main(string[] args)
{
{
#region
// construct the search for a given molecule, if an adjacency list
// representation (int[][]) is available this can be passed to the
// constructor for improved performance
IAtomContainer container = TestMoleculeFactory.MakeAlphaPinene();
RingSearch ringSearch = new RingSearch(container);
// indices of cyclic vertices
int[] cyclic = ringSearch.Cyclic();
// iterate over fused systems (atom indices)
foreach (int[] fused in ringSearch.Fused())
{
// ...
}
// iterate over isolated rings (atom indices)
foreach (int[] isolated in ringSearch.Isolated())
{
// ...
}
// convenience methods for getting the fragments
IAtomContainer fragments = ringSearch.RingFragments();
foreach (IAtomContainer fragment in ringSearch.FusedRingFragments())
{
// ...
}
foreach (IAtomContainer fragment in ringSearch.IsolatedRingFragments())
{
// ...
}
#endregion
}
{
#region Cyclic
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
RingSearch ringSearch = new RingSearch(mol);
foreach (var atom in mol.Atoms)
{
if (ringSearch.Cyclic(atom))
{
// ...
}
}
#endregion
}
{
#region Cyclic_int
IAtomContainer mol = TestMoleculeFactory.MakeAlphaPinene();
RingSearch tester = new RingSearch(mol);
int n = mol.Atoms.Count;
for (int i = 0; i < n; i++)
{
if (tester.Cyclic(i))
{
// ...
}
}
#endregion
}
{
#region Isolated
IAtomContainer biphenyl = TestMoleculeFactory.MakeBiphenyl();
RingSearch ringSearch = new RingSearch(biphenyl);
int[][] isolated = ringSearch.Isolated();
Console.WriteLine(isolated.Length); // 2 isolated rings in biphenyl
Console.WriteLine(isolated[0].Length); // 6 vertices in one benzene
Console.WriteLine(isolated[1].Length); // 6 vertices in the other benzene
#endregion
}
if (true)
{
#region Fused
IAtomContainer mol = new Smiles.SmilesParser().ParseSmiles("c1cc(cc2cc(ccc12)C3C4CC34)C6CC5CCC6(C5)");
RingSearch ringSearch = new RingSearch(mol);
int[][] fused = ringSearch.Fused();
Console.WriteLine(fused.Length); // e.g. 3 separate fused ring systems
Console.WriteLine(fused[0].Length); // e.g. 10 vertices in the first system
Console.WriteLine(fused[1].Length); // e.g. 4 vertices in the second system
Console.WriteLine(fused[2].Length); // e.g. 7 vertices in the third system
#endregion
}
}
