private IAtomContainer ParseSmiles(string smiles, bool isRxnPart)
{
try
{
// create the Beam object from the SMILES
Beam.Graph g = Beam.Graph.FromSmiles(smiles);
// convert the Beam object model to the CDK - note exception thrown
// if a kekule structure could not be assigned.
var mol = beamToCDK.ToAtomContainer(Kekulise ? g.Kekule() : g, Kekulise);
if (!isRxnPart)
{
try
{
// CXSMILES layer
ParseMolCXSMILES(g.Title, mol);
}
catch (Exception e)
{
// e.StackTrace
throw new InvalidSmilesException($"Error parsing CXSMILES: {e.Message}");
}
}
return(mol);
}
catch (IOException e)
{
throw new InvalidSmilesException($"could not parse '{smiles}', {e.Message}");
}
catch (Exception)
{
throw new InvalidSmilesException($"could not parse '{smiles}'");
}
}
void Main()
{
IAtomContainer m = TestMoleculeFactory.MakeBenzene();
// converter is thread-safe and can be used by multiple threads
CDKToBeam c2g = new CDKToBeam();
Beam.Graph g = c2g.ToBeamGraph(m);
// get the SMILES notation from the Beam graph
string smi = g.ToSmiles();
}