static void Test(string delocalised, string localised)
{
Graph g = Graph.FromSmiles(delocalised);
Graph h = Localise.GenerateLocalise(g);
Assert.AreEqual(localised, h.ToSmiles()); //fixed Beam
}
public static Graph LocaliseInPlace(Graph delocalised)
{
// nothing to do, return fast
if (delocalised.GetFlags(Graph.HAS_AROM) == 0)
{
return(delocalised);
}
BitArray aromatic = new BitArray(delocalised.Order);
BitArray subset = BuildSet(delocalised, aromatic);
if (HasOddCardinality(subset))
{
throw new InvalidSmilesException("a valid kekulé structure could not be assigned");
}
return(Localise.GenerateKekuleForm(delocalised, subset, aromatic, true));
}
[TestMethod()] public void SmallRingTest_linked()
{
Graph g = Graph.FromSmiles("C1CCC(CC1)=C1CCCCC1");
Assert.IsFalse(Localise.InSmallRing(g, g.CreateEdge(3, 6)));
}
[TestMethod()] public void SmallRingTest_7()
{
Graph g = Graph.FromSmiles("C1CCCCCC1");
Assert.IsTrue(Localise.InSmallRing(g, g.CreateEdge(0, 1)));
}
/// <summary>
/// Localise delocalized (aromatic) bonds in this molecule producing the Kekulé form.
/// </summary>
/// <remarks>
/// The original graph is not modified.
/// <code>
/// Graph furan = Graph.FromSmiles("o1cccc1");
/// </code>
/// If the graph could not be converted to a kekulé representation then a
/// checked exception is thrown. Graphs cannot be converted if their
/// structures are erroneous and there is no valid way to assign the
/// delocalised electrons.
/// <para>
/// Some reasons are shown below.
/// <list type="bullet">
/// <item>
/// <term>n1cncc1</term>
/// <description>pyrole (incorrect) could be either C1C=NC=N1 or N1C=CN=C1</description>
/// </item>
/// <item>
/// <term>[Hg+2][c-]1ccccc1</term>
/// <description>Mercury(2+) ion benzenide (incorrect)</description>
/// </item>
/// <item>
/// <term>[Hg+2].[c-]1ccccc1</term>
/// <description>Mercury(2+) ion benzenide (correct)</description>
/// </item>
/// </list>
/// </para>
/// </remarks>
/// <returns>kekulé representation</returns>
/// <exception cref="InvalidSmilesException">molecule exploded on contact with reality</exception>"
public Graph Kekule()
{
return(Localise.LocaliseInPlace(this));
}
/// <summary>
/// Resonate bond assignments in conjugate rings such that two SMILES with
/// the same Ordering have the same kekulé assignment.
/// </summary>
/// <returns>(self) - the graph is mutated</returns>
public Graph Resonate()
{
return(Localise.Resonate(this));
}
/// <summary>
/// Utility method to verify electrons can be assigned.
/// </summary>
/// <param name="g">graph to check</param>
/// <returns>electrons could be assigned to delocalised structure</returns>
public static bool Verify(Graph g)
{
return(g.GetFlags(Graph.HAS_AROM) == 0 || !ContainsOddCardinalitySubgraph(g, Localise.BuildSet(g, new BitArray(g.Order))));
}