/// <summary> Construct the vertex short cycles for the given initial cycles.</summary>
public VertexShortCycles(InitialCycles initialCycles)
{
int[][] graph = initialCycles.Graph;
int[] sizeOf = new int[graph.Length];
this.paths = new List <int[]>(initialCycles.GetNumberOfCycles());
// cycles are returned ordered by length
foreach (var cycle in initialCycles.GetCycles())
{
int length = cycle.Length;
int[] path = cycle.Path;
bool found = false;
// check if any vertex is the shortest through a vertex in the path
foreach (var v in path)
{
if (sizeOf[v] < 1 || length <= sizeOf[v])
{
found = true;
sizeOf[v] = length;
}
}
if (found)
{
foreach (var p in cycle.GetFamily())
{
paths.Add(p);
}
}
}
}
/// <inheritdoc/>
public override int[][] Apply(int[][] graph, int length)
{
InitialCycles ic = InitialCycles.OfBiconnectedComponent(graph, length);
RelevantCycles rc = new RelevantCycles(ic);
return(new EssentialCycles(rc, ic).GetPaths());
}
public virtual void Cycles_cyclophane_odd_limit_5()
{
InitialCycles initial = new InitialCycles(CyclophaneOdd, 5);
var cycles = initial.GetCycles();
Assert.AreEqual(0, cycles.Count());
}
public EvenCycle(InitialCycles parent, ShortestPaths paths, int[] pathToP, int y, int[] pathToQ)
: base(parent, paths, Join(pathToP, y, pathToQ))
{
this.p = pathToP[pathToP.Length - 1];
this.q = pathToQ[pathToQ.Length - 1];
this.Y = y;
}
public Cycle(InitialCycles parent, ShortestPaths paths, int[] path)
{
this.parent = parent;
this.path = path;
this.paths = paths;
}
/// <summary> Construct the edge short cycles for the
/// given initial cycles. </summary>
public EdgeShortCycles(InitialCycles initialCycles)
{
int[][] graph = initialCycles.Graph;
int[] sizeOf = new int[initialCycles.GetNumberOfEdges()];
this.paths = new List <int[]>(initialCycles.GetNumberOfCycles());
// cycles are returned ordered by length
foreach (var cycle in initialCycles.GetCycles())
{
int length = cycle.Length;
int[] path = cycle.Path;
bool found = false;
// check if any vertex is the shortest through a vertex in the path
for (int i = 1; i < path.Length; i++)
{
int idx = initialCycles.IndexOfEdge(path[i - 1], path[i]);
if (sizeOf[idx] < 1 || length <= sizeOf[idx])
{
found = true;
sizeOf[idx] = length;
}
}
if (found)
{
foreach (var p in cycle.GetFamily())
{
paths.Add(p);
}
}
}
}
public virtual void JoinWith()
{
int[] a = new int[] { 0, 1, 2 };
int[] b = new int[] { 0, 3, 4 };
var expected = new int[] { 0, 1, 2, 5, 4, 3, 0 };
Assert.IsTrue(Compares.AreDeepEqual(expected, InitialCycles.Join(a, 5, b)));
}
public virtual void Cycles_K4()
{
InitialCycles initial = new InitialCycles(K4);
// todo replace with hasSize (hamcrest)
Assert.AreEqual(4, initial.GetCycles().Count());
Assert.AreEqual(4, initial.GetCyclesOfLength(3).Count());
}
public OddCycle(InitialCycles parent, ShortestPaths paths, int[] pathToY, int[] pathToZ)
: base(parent, paths, Join(pathToY, pathToZ))
{
this.parent = parent;
y = pathToY[pathToY.Length - 1];
z = pathToZ[pathToY.Length - 1];
}
public virtual void Lengths_cyclophane()
{
InitialCycles initial = new InitialCycles(CyclophaneOdd);
foreach (var i in new int[] { 6, 9 })
{
Assert.IsTrue(initial.Lengths.Contains(i));
}
Assert.AreEqual(2, initial.Lengths.Count());
}
public virtual void Cycles_cyclophane_odd_limit_7()
{
InitialCycles initial = new InitialCycles(CyclophaneOdd, 7);
var cycles = initial.GetCycles();
Assert.AreEqual(1, cycles.Count());
int[][] expecteds = new int[][] {
new int[] { 3, 2, 1, 0, 5, 4, 3 },
};
AssertInitialCycles(expecteds, cycles);
}
public virtual void Edge_K4()
{
InitialCycles initial = new InitialCycles(K4);
Assert.AreEqual(initial.GetEdge(0), new InitialCycles.Cycle.Edge(0, 1));
Assert.AreEqual(initial.GetEdge(1), new InitialCycles.Cycle.Edge(0, 2));
Assert.AreEqual(initial.GetEdge(2), new InitialCycles.Cycle.Edge(0, 3));
Assert.AreEqual(initial.GetEdge(3), new InitialCycles.Cycle.Edge(1, 2));
Assert.AreEqual(initial.GetEdge(4), new InitialCycles.Cycle.Edge(1, 3));
Assert.AreEqual(initial.GetEdge(5), new InitialCycles.Cycle.Edge(2, 3));
}
public virtual void Cycles_naphthalene()
{
InitialCycles initial = new InitialCycles(Naphthalene);
var cycles = initial.GetCycles();
Assert.AreEqual(2, cycles.Count());
int[][] expecteds = new int[][] {
new int[] { 5, 0, 1, 2, 3, 4, 5 },
new int[] { 5, 4, 7, 8, 9, 6, 5 },
};
AssertInitialCycles(expecteds, cycles);
}
/// <summary>
/// Generate the relevant cycle basis from a precomputed set of initial
/// cycles.
/// </summary>
/// <param name="initial">set of initial cycles.</param>
/// <exception cref="System.ArgumentNullException">null InitialCycles provided</exception>
internal RelevantCycles(InitialCycles initial)
{
CheckNotNull(initial, nameof(initial), "No InitialCycles provided");
this.basis = new GreedyBasis(initial.GetNumberOfCycles(), initial.GetNumberOfEdges());
// processing by size add cycles which are independent of smaller cycles
foreach (var length in initial.Lengths)
{
basis.AddAll(Independent(initial.GetCyclesOfLength(length)));
}
}
public virtual void Cycles_cyclophane()
{
InitialCycles initial = new InitialCycles(CyclophaneOdd);
var cycles = initial.GetCycles();
Assert.AreEqual(2, cycles.Count());
int[][] expecteds = new int[][] {
new int[] { 3, 2, 1, 0, 5, 4, 3 },
new int[] { 3, 2, 1, 0, 10, 9, 8, 7, 6, 3 },
};
AssertInitialCycles(expecteds, cycles);
}
public virtual void ToEdgeVector_K4()
{
InitialCycles initial = new InitialCycles(K4);
BitArray expected, actual;
expected = new BitArray(new bool[] { true, false, true, true, false, true });
actual = initial.ToEdgeVector(new int[] { 0, 1, 2, 3, 0 });
Assert.IsTrue(Compares.AreDeepEqual(expected, actual));
expected = new BitArray(new bool[] { true, true, false, true, false, false });
actual = initial.ToEdgeVector(new int[] { 0, 1, 2, 0 });
Assert.IsTrue(Compares.AreDeepEqual(expected, actual));
}
public virtual void Cycles_bicyclo()
{
InitialCycles initial = new InitialCycles(Bicyclo);
var cycles = initial.GetCycles();
Assert.AreEqual(3, cycles.Count());
int[][] expecteds = new int[][] {
new int[] { 5, 0, 1, 2, 3, 4, 5 },
new int[] { 5, 0, 1, 2, 7, 6, 5 },
new int[] { 5, 4, 3, 2, 7, 6, 5 },
};
AssertInitialCycles(expecteds, cycles);
}
public virtual void Cycles_anthracene()
{
InitialCycles initial = new InitialCycles(Anthracene);
var cycles = initial.GetCycles();
Assert.AreEqual(3, cycles.Count());
int[][] expecteds = new int[][]
{
new int[] { 5, 0, 1, 2, 3, 4, 5 },
new int[] { 9, 6, 5, 4, 7, 8, 9 },
new int[] { 9, 8, 10, 11, 12, 13, 9 },
};
AssertInitialCycles(expecteds, cycles);
}
public virtual void IndexOfEdge_K4()
{
InitialCycles initial = new InitialCycles(K4);
Assert.AreEqual(0, initial.IndexOfEdge(0, 1));
Assert.AreEqual(0, initial.IndexOfEdge(1, 0));
Assert.AreEqual(1, initial.IndexOfEdge(0, 2));
Assert.AreEqual(1, initial.IndexOfEdge(2, 0));;
Assert.AreEqual(2, initial.IndexOfEdge(0, 3));
Assert.AreEqual(2, initial.IndexOfEdge(3, 0));
Assert.AreEqual(3, initial.IndexOfEdge(1, 2));
Assert.AreEqual(3, initial.IndexOfEdge(1, 2));
Assert.AreEqual(4, initial.IndexOfEdge(1, 3));
Assert.AreEqual(4, initial.IndexOfEdge(1, 3));
Assert.AreEqual(5, initial.IndexOfEdge(2, 3));
Assert.AreEqual(5, initial.IndexOfEdge(2, 3));
}
/// <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));
}
}
/// <summary>
/// Determine the essential cycles from a precomputed set of initial cycles
/// and relevant cycles.
/// </summary>
/// <param name="relevant"></param>
/// <param name="initial">a molecule graph</param>
internal EssentialCycles(RelevantCycles relevant, InitialCycles initial)
{
CheckNotNull(relevant, nameof(relevant), "No RelevantCycles provided");
this.initial = CheckNotNull(initial, nameof(initial), "No InitialCycles provided");
this.basis = new GreedyBasis(initial.GetNumberOfCycles(), initial.GetNumberOfEdges());
this.essential = new List <Cycle>();
// for each cycle added to the basis, if it can be
// replaced with one of equal size it is non-essential
foreach (var cycles in GroupByLength(relevant))
{
foreach (var c in GetMembersOfBasis(cycles))
{
if (IsEssential(c, cycles))
{
essential.Add(c);
}
}
}
}
public virtual void Cycles_family_even()
{
InitialCycles initial = new InitialCycles(CyclophaneEven);
var cycles = initial.GetCycles();
int[] expected = new int[] { 3, 6, 7, 8, 9, 10, 11, 0, 1, 2, 3 };
var cycle = cycles.FirstOrDefault(n => Compares.AreDeepEqual(expected, n.Path));
Assert.IsNotNull(cycle);
int[][] family = cycle.GetFamily();
Assert.AreEqual(2, family.Length);
int[][] expecteds = new int[][] {
expected,
new int[] { 3, 6, 7, 8, 9, 10, 11, 0, 5, 4, 3 },
};
foreach (var f in family)
{
Assert.IsTrue(expecteds.Any(n => Compares.AreDeepEqual(n, f)));
}
}
/// <summary>
/// Generate the minimum cycle basis from a precomputed set of initial
/// cycles. This constructor allows on to specify that the graph is
/// connected which allows an optimisation to be used.
/// </summary>
/// <param name="initial">set of initial cycles.</param>
/// <param name="connected">the graph is known to be connected</param>
/// <exception cref="System.ArgumentNullException">null InitialCycles provided</exception>
internal MinimumCycleBasis(InitialCycles initial, bool connected)
{
CheckNotNull(initial, nameof(initial), "No InitialCycles provided");
this.graph = initial.Graph;
this.basis = new GreedyBasis(initial.GetNumberOfCycles(), initial.GetNumberOfEdges());
// a undirected unweighted connected graph there are |E| - (|V| + 1)
// cycles in the minimum basis
int lim = connected ? initial.GetNumberOfEdges() - graph.Length + 1 : int.MaxValue;
// processing by size add cycles which are independent of smaller cycles
foreach (var cycle in initial.GetCycles())
{
if (basis.Count < lim && basis.IsIndependent(cycle))
{
basis.Add(cycle);
}
}
}
public virtual void EndOverlap()
{
int[] a = new int[] { 0, 1, 3, 5, 7, 9, 10 };
int[] b = new int[] { 0, 2, 4, 6, 8, 9, 10 };
Assert.IsFalse(InitialCycles.GetSingletonIntersect(a, b));
}
/// <inheritdoc/>
public override int[][] Apply(int[][] graph, int length)
{
InitialCycles ic = InitialCycles.OfBiconnectedComponent(graph, length);
return(new EdgeShortCycles(ic).GetPaths());
}
/// <inheritdoc/>
public override int[][] Apply(int[][] graph, int length)
{
InitialCycles ic = InitialCycles.OfBiconnectedComponent(graph, length);
return(new TripletShortCycles(new MinimumCycleBasis(ic, true), false).GetPaths());
}
public virtual void StartOverlap()
{
int[] a = new int[] { 0, 1, 2, 3, 4, 6 };
int[] b = new int[] { 0, 1, 2, 3, 5, 7 };
Assert.IsFalse(InitialCycles.GetSingletonIntersect(a, b));
}
/// <summary>
/// Determine the essential cycles from a precomputed set of initial cycles.
/// </summary>
/// <param name="initial">a molecule graph</param>
internal EssentialCycles(InitialCycles initial)
: this(new RelevantCycles(initial), initial)
{
}
public virtual void Cycles_K1()
{
InitialCycles initial = new InitialCycles(K1);
Assert.AreEqual(0, initial.GetCycles().Count());
}
/// <summary>
/// Generate the minimum cycle basis from a precomputed set of initial cycles.
/// </summary>
/// <param name="initial">set of initial cycles.</param>
/// <exception cref="System.ArgumentNullException">null InitialCycles provided</exception>
internal MinimumCycleBasis(InitialCycles initial)
: this(initial, false)
{
}