/// <summary>
/// Find the bonds of a <paramref name="molecule"/> which this model determined were aromatic.
/// </summary>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Aromaticities.Aromaticity_Example.cs+FindBonds"]/*' />
/// </example>
/// <param name="molecule">the molecule to apply the model to</param>
/// <returns>the set of bonds which are aromatic</returns>
/// <exception cref="CDKException">a problem occurred with the cycle perception - one can retry with a simpler cycle set</exception>
public IEnumerable <IBond> FindBonds(IAtomContainer molecule)
{
// build graph data-structures for fast cycle perception
var bondMap = EdgeToBondMap.WithSpaceFor(molecule);
var graph = GraphUtil.ToAdjList(molecule, bondMap);
// initial ring/cycle search and get the contribution from each atom
RingSearch ringSearch = new RingSearch(molecule, graph);
var electrons = model.Contribution(molecule, ringSearch);
// obtain the subset of electron contributions which are >= 0 (i.e.
// allowed to be aromatic) - we then find the cycles in this subgraph
// and 'lift' the indices back to the original graph using the subset
// as a lookup
var subset = Subset(electrons);
var subgraph = GraphUtil.Subgraph(graph, subset);
// for each cycle if the electron sum is valid add the bonds of the
// cycle to the set or aromatic bonds
foreach (var cycle in cycles.Find(molecule, subgraph, subgraph.Length).GetPaths())
{
if (CheckElectronSum(cycle, electrons, subset))
{
for (int i = 1; i < cycle.Length; i++)
{
yield return(bondMap[subset[cycle[i]], subset[cycle[i - 1]]]);
}
}
}
yield break;
}
/// <summary>Check the electron contribution is the same as expected.</summary>
static void Test(IAtomContainer m, params int[] expected)
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
Assert.IsTrue(Compares.AreDeepEqual(expected, model.Contribution(m, new RingSearch(m))));
}
