public void TestAromaticBenzene()
{
var sp = CDK.SmilesParser;
var mol = sp.ParseSmiles("C1=CC=CC=C1"); // benzene
Aromaticity aromaticity = new Aromaticity(ElectronDonation.DaylightModel, Cycles.AllSimpleFinder);
aromaticity.Apply(mol);
AssertAtomTypesPerceived(mol);
AddExplicitHydrogens(mol);
Assert.AreEqual(2.02, CreateDescriptor(false).Calculate(mol, correctSalicylFactor: true).Value, 0.01);
}
/// <summary>
/// ApplyAromaticity
///
/// Mimics the CDKHuckelAromaticityDetector
/// Aromaticity aromaticity = new Aromaticity(ElectronDonation.cdk(), Cycles.cdkAromaticSet());
///
/// Mimics the DoubleBondAcceptingAromaticityDetector
/// Aromaticity aromaticity = new Aromaticity(ElectronDonation.cdkAllowingExocyclic(), Cycles.cdkAromaticSet());
///
/// A good model for writing SMILES
/// Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), Cycles.all());
///
/// A good model for writing MDL/Mol2
/// Aromaticity aromaticity = new Aromaticity(ElectronDonation.piBonds(), Cycles.all());
///
/// </summary>
/// <param name="mol"></param>
/// <param name="electronDonation"></param>
/// <param name="cycleFinder"></param>
/// <returns></returns>
public static bool ApplyAromaticity(
IAtomContainer mol,
ElectronDonation electronDonation,
CycleFinder cycleFinder)
{
Aromaticity aromaticity = new Aromaticity(electronDonation, cycleFinder);
try
{
bool isAromatic = aromaticity.apply(mol);
return(isAromatic);
}
catch (Exception e)
{
string msg = e.Message; // cycle computation was intractable
return(false);
}
}
/// <summary>
/// Set the aromaticity perception to use. Different aromaticity models
/// may required certain attributes to be set (e.g. atom typing). These
/// will not be automatically configured and should be preset before matching.
/// </summary>
/// <example>
/// <include file='IncludeExamples.xml' path='Comments/Codes[@id="NCDK.Smiles.SMARTS.SMARTSQueryTool_Example.cs+SetAromaticity"]/*' />
/// </example>
/// <param name="aromaticity">the new aromaticity perception</param>
/// <seealso cref="ElectronDonation"/>
/// <seealso cref="Cycles"/>
public void SetAromaticity(Aromaticity aromaticity)
{
this.aromaticity = CheckNotNull(aromaticity, "aromaticity was not provided");
}
