public void EnsureConsistentRepresentation()
{
IAtomContainer a = CreateFromSmiles("C1=CC2=CC3=CC4=C(C=CC=C4)C=C3C=C2C=C1");
IAtomContainer b = CreateFromSmiles("c1cc2cc3cc4c(cccc4)cc3cc2cc1");
Aromaticity arom = new Aromaticity(ElectronDonation.DaylightModel, Cycles.AllSimpleFinder);
arom.Apply(a);
arom.Apply(b);
Assert.IsTrue(AtomContainerDiff.Diff(a, b).Count() == 0);
}
public void ClearFlags_cyclobutadiene()
{
IAtomContainer cyclobutadiene = CreateFromSmiles("c1ccc1");
daylight.Apply(cyclobutadiene);
foreach (var bond in cyclobutadiene.Bonds)
{
Assert.IsFalse(bond.IsAromatic);
}
foreach (var atom in cyclobutadiene.Atoms)
{
Assert.IsFalse(atom.IsAromatic);
}
}
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
}
}