/// <summary>
/// Public method to get tautomers for an input molecule, based on the InChI which will be calculated by .NET prot of JNI-InChI.
/// </summary>
/// <param name="mol">molecule for which to generate tautomers</param>
/// <returns>a list of tautomers, if any</returns>
/// <exception cref="CDKException"></exception>
public ICollection <IAtomContainer> GetTautomers(IAtomContainer mol)
{
string opt = "";
if ((flags & Options.KetoEnol) != 0)
{
opt += " -KET";
}
if ((flags & Options.OneFiveShift) != 0)
{
opt += " -15T";
}
InChIGenerator gen = InChIGeneratorFactory.Instance.GetInChIGenerator(mol, opt);
string inchi = gen.InChI;
string aux = gen.AuxInfo;
long[] amap = new long[mol.Atoms.Count];
InChINumbersTools.ParseAuxInfo(aux, amap);
if (inchi == null)
{
throw new CDKException($"{typeof(InChIGenerator)} failed to create an InChI for the provided molecule, InChI -> null.");
}
return(GetTautomers(mol, inchi, amap));
}
/// <summary>
/// Obtain the InChI numbering for canonising SMILES. The cdk-smiles module
/// does not and should not depend on cdk-inchi and so the numbers are loaded
/// via reflection. If the class cannot be found on the path an
/// exception is thrown.
/// </summary>
/// <param name="container">a structure</param>
/// <returns>the inchi numbers</returns>
/// <exception cref="CDKException">the inchi numbers could not be obtained</exception>
private static long[] InChINumbers(IAtomContainer container)
{
var rgrps = GetRgrps(container, AtomicNumbers.Rutherfordium);
foreach (var rgrp in rgrps)
{
rgrp.AtomicNumber = AtomicNumbers.Rutherfordium;
rgrp.Symbol = ChemicalElement.Rf.Symbol;
}
var numbers = InChINumbersTools.GetUSmilesNumbers(container);
foreach (var rgrp in rgrps)
{
rgrp.AtomicNumber = AtomicNumbers.Unknown;
rgrp.Symbol = "*";
}
return(numbers);
}
