/// <summary>
/// Generate Smiles
/// </summary>
/// <param name="mol"></param>
/// <param name="flags"></param>
/// <returns></returns>
public static String AtomContainerToSmiles(
IAtomContainer mol,
SmilesGeneratorType flags)
{
ApplyAromaticity(mol);
SmilesGenerator sg = null;
if ((flags & SmilesGeneratorType.Generic) != 0)
{
sg = SmilesGenerator.generic();
}
else if ((flags & SmilesGeneratorType.Isomeric) != 0)
{
sg = SmilesGenerator.isomeric();
}
else if ((flags & SmilesGeneratorType.Unique) != 0)
{
sg = SmilesGenerator.unique();
}
else if ((flags & SmilesGeneratorType.Absolute) != 0)
{
sg = SmilesGenerator.unique();
}
else
{
throw new Exception("Canonical/Stereo/Isotop types not defined");
}
if ((flags & SmilesGeneratorType.NotAromatic) != 0)
{
} // not aromatic
else
{
sg = sg.aromatic(); // aromatic by default even if not specified
}
if ((flags & SmilesGeneratorType.WithAtomClasses) != 0)
{
sg = sg.withAtomClasses();
}
string smiles = sg.create(mol);
return(smiles);
}
public static string CanonicalizeSmiles(
string smiles,
SmilesGeneratorType smiGenFlags)
{
IAtomContainer mol = SmilesToAtomContainer(smiles);
if (mol.getAtomCount() == 0)
{
return("");
}
else
{
string smiles2 = AtomContainerToSmiles(mol, smiGenFlags);
return(smiles2);
}
}
/// <summary>
/// CanonicalizeSmiles
/// </summary>
/// <param name="smiles"></param>
/// <returns></returns>
public static string CanonicalizeSmiles(string smiles)
{
SmilesGeneratorType smiGenFlags = SmilesGeneratorType.Unique | SmilesGeneratorType.Aromatic;
return(CanonicalizeSmiles(smiles, smiGenFlags));
}
