/// <summary>
/// Search if the setOfAtomContainer contains the atomContainer
/// </summary>
/// <param name="set">ISetOfAtomContainer object where to search</param>
/// <param name="atomContainer">IAtomContainer to search</param>
/// <returns>True, if the atomContainer is contained</returns>
private bool ExistAC(IChemObjectSet <IAtomContainer> set, IAtomContainer atomContainer)
{
IAtomContainer acClone = null;
acClone = (IAtomContainer)atomContainer.Clone();
if (!lookingSymmetry)
{ /* remove all aromatic flags */
foreach (var atom in acClone.Atoms)
{
atom.IsAromatic = false;
}
foreach (var bond in acClone.Bonds)
{
bond.IsAromatic = false;
}
}
for (int i = 0; i < acClone.Atoms.Count; i++)
{
acClone.Atoms[i].Id = "" + acClone.Atoms.IndexOf(acClone.Atoms[i]);
}
if (lookingSymmetry)
{
try
{
Aromaticity.CDKLegacy.Apply(acClone);
}
catch (CDKException e)
{
Console.Error.WriteLine(e.StackTrace);
}
}
else
{
if (!lookingSymmetry)
{ /* remove all aromatic flags */
foreach (var atom in acClone.Atoms)
{
atom.IsAromatic = false;
}
foreach (var bond in acClone.Bonds)
{
bond.IsAromatic = false;
}
}
}
for (int i = 0; i < set.Count; i++)
{
var ss = set[i];
for (int j = 0; j < ss.Atoms.Count; j++)
{
ss.Atoms[j].Id = "" + ss.Atoms.IndexOf(ss.Atoms[j]);
}
try
{
if (!lookingSymmetry)
{
var qAC = QueryAtomContainerCreator.CreateSymbolChargeIDQueryContainer(acClone);
if (new UniversalIsomorphismTester().IsIsomorph(ss, qAC))
{
var qAC2 = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(acClone);
if (new UniversalIsomorphismTester().IsIsomorph(ss, qAC2))
{
return(true);
}
}
}
else
{
var qAC = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(acClone);
Aromaticity.CDKLegacy.Apply(ss);
if (new UniversalIsomorphismTester().IsIsomorph(ss, qAC))
{
return(true);
}
}
}
catch (CDKException e1)
{
Console.Error.WriteLine(e1);
Trace.TraceError(e1.Message);
Debug.WriteLine(e1);
}
}
return(false);
}
