/// <summary>
/// Create an aromaticity model using the specified electron donation
/// <paramref name="model"/> which is tested on the <paramref name="cycles"/>. The <paramref name="model"/> defines
/// how many π-electrons each atom may contribute to an aromatic system. The
/// <paramref name="cycles"/> defines the <see cref="ICycleFinder"/> which is used to find
/// cycles in a molecule. The total electron donation from each atom in each
/// cycle is counted and checked. If the electron contribution is equal to
/// "4n + 2" for a "n >= 0" then the cycle is considered
/// aromatic.
/// </summary>
/// <remarks>
/// Changing the electron contribution model or which cycles
/// are tested affects which atoms/bonds are found to be aromatic. There are
/// several <see cref="ElectronDonation"/> models and <see cref="Cycles"/>
/// available. A good choice for the cycles
/// is to use <see cref="Cycles.AllSimpleFinder()"/> falling back to
/// <see cref="Cycles.RelevantFinder"/> on failure. Finding all cycles is very
/// fast but may produce an exponential number of cycles. It is therefore not
/// feasible for complex fused systems and an exception is thrown.
/// In such cases the aromaticity can either be skipped or a simpler
/// polynomial cycle set <see cref="Cycles.RelevantFinder"/> used.
/// </remarks>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Aromaticities.Aromaticity_Example.cs+ctor"]/*' />
/// </example>
/// <param name="model"></param>
/// <param name="cycles"></param>
/// <seealso cref="ElectronDonation"/>
/// <seealso cref="Cycles"/>
public Aromaticity(ElectronDonation model, ICycleFinder cycles)
{
this.model = model ?? throw new ArgumentNullException(nameof(model));
this.cycles = cycles ?? throw new ArgumentNullException(nameof(cycles));
}
public static void Main(string[] args)
{
{
var molecules = new Silent.AtomContainerSet();
#region
ElectronDonation model = ElectronDonation.DaylightModel;
ICycleFinder cycles = Cycles.Or(Cycles.AllSimpleFinder, Cycles.GetAllFinder(6));
Aromaticity aromaticity = new Aromaticity(model, cycles);
// apply our configured model to each molecule
foreach (IAtomContainer molecule in molecules)
{
aromaticity.Apply(molecule);
}
#endregion
}
{
#region ctor
// mimics the CDKHuckelAromaticityDetector
Aromaticity aromaticity_cdk = new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder);
// mimics the DoubleBondAcceptingAromaticityDetector
Aromaticity aromaticity_exo = new Aromaticity(ElectronDonation.CDKAllowingExocyclicModel, Cycles.CDKAromaticSetFinder);
// a good model for writing SMILES
Aromaticity aromaticity_smi = new Aromaticity(ElectronDonation.DaylightModel, Cycles.AllSimpleFinder);
// a good model for writing MDL/Mol2
Aromaticity aromaticity_mdl = new Aromaticity(ElectronDonation.PiBondsModel, Cycles.AllSimpleFinder);
#endregion
}
{
#region FindBonds
Aromaticity aromaticity = new Aromaticity(ElectronDonation.CDKModel, Cycles.AllSimpleFinder);
IAtomContainer container = TestMoleculeFactory.MakeAnthracene();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(container);
try
{
var bonds = aromaticity.FindBonds(container);
int nAromaticBonds = bonds.Count();
}
catch (CDKException)
{
// cycle computation was intractable
}
#endregion
}
{
#region Apply
Aromaticity aromaticity = new Aromaticity(ElectronDonation.CDKModel, Cycles.AllSimpleFinder);
IAtomContainer container = TestMoleculeFactory.MakeAnthracene();
try
{
if (aromaticity.Apply(container))
{
//
}
}
catch (CDKException)
{
// cycle computation was intractable
}
#endregion
}
{
#region CDKLegacy_CDKAromaticSetFinder
new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder);
#endregion
}
{
#region CDKLegacy_AllFinder_RelevantFinder
new Aromaticity(ElectronDonation.CDKModel, Cycles.Or(Cycles.AllSimpleFinder, Cycles.RelevantFinder));
#endregion
}
}
