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);
}
static void Prepare(IAtomContainer target)
{
// apply the daylight aromaticity model
try
{
Cycles.MarkRingAtomsAndBonds(target);
arom.Apply(target);
}
catch (CDKException e)
{
Trace.TraceError(e.Message);
}
}
/// <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,
ICycleFinder 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);
}
}
public override IReadOnlyDictionary <string, int> GetRawFingerprint(IAtomContainer atomContainer)
{
aromaticity.Apply(atomContainer);
var smiles = ReplaceDigits(gen.Create(atomContainer));
var map = new Dictionary <string, int>();
for (int i = 0, l = smiles.Length - n + 1; i < l; i++)
{
string subsmi = smiles.Substring(i, n);
if (!map.TryGetValue(subsmi, out int count))
{
map[subsmi] = 1;
}
else
{
map[subsmi] = count + 1;
}
}
return(map);
}
/// <summary>
/// Prepare the target molecule for analysis.
/// <para>
/// We perform ring perception and aromaticity detection and set up
/// the appropriate properties. Right now, this function is called each time we need to do a query and this is
/// inefficient.</para>
/// </summary>
/// <exception cref="CDKException">if there is a problem in ring perception or aromaticity detection, which is usually related to a timeout in the ring finding code.</exception>
private void InitializeMolecule()
{
// initialise required invariants - the query has ISINRING set if
// the query contains ring queries [R?] [r?] [x?] etc.
SmartsMatchers.Prepare(atomContainer, true);
// providing skip aromaticity has not be set apply the desired
// aromaticity model
try
{
if (!skipAromaticity)
{
aromaticity.Apply(atomContainer);
}
}
catch (CDKException e)
{
Debug.WriteLine(e.ToString());
throw new CDKException(e.ToString(), e);
}
}