// private functions
/// <summary>
/// Reads a ChemFile object from input.
/// </summary>
/// <returns>ChemFile with the content read from the input</returns>
private IChemFile ReadChemFile(IChemFile cf)
{
// have to do stuff here
try
{
string line = null;
while ((line = input.ReadLine()) != null)
{
if (line.StartsWith("INChI=", StringComparison.Ordinal) || line.StartsWith("InChI=", StringComparison.Ordinal))
{
// ok, the fun starts
cf = cf.Builder.NewChemFile();
// ok, we need to parse things like:
// INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H
string INChI = line.Substring(6);
var tok = Strings.Tokenize(INChI, '/');
// ok, we expect 4 tokens
// tok[0]; // 1.12Beta not stored since never used
string formula = tok[1]; // C6H6
string connections = null;
if (tok.Count > 2)
{
connections = tok[2].Substring(1); // 1-2-4-6-5-3-1
}
//final string hydrogens = tokenizer.NextToken().Substring(1); // 1-6H
IAtomContainer parsedContent = InChIContentProcessorTool.ProcessFormula(
cf.Builder.NewAtomContainer(), formula);
if (connections != null)
{
InChIContentProcessorTool.ProcessConnections(connections, parsedContent, -1);
}
var moleculeSet = cf.Builder.NewAtomContainerSet();
moleculeSet.Add(cf.Builder.NewAtomContainer(parsedContent));
var model = cf.Builder.NewChemModel();
model.MoleculeSet = moleculeSet;
var sequence = cf.Builder.NewChemSequence();
sequence.Add(model);
cf.Add(sequence);
}
}
}
catch (Exception exception)
{
if (exception is IOException || exception is ArgumentException)
{
Console.Error.WriteLine(exception.StackTrace);
throw new CDKException($"Error while reading INChI file: {exception.Message}", exception);
}
else
{
throw;
}
}
return(cf);
}
public override void EndElement(XElement element)
{
Debug.WriteLine($"end element: {element.ToString()}");
if (string.Equals("identifier", element.Name.LocalName, StringComparison.Ordinal))
{
if (tautomer != null)
{
// ok, add tautomer
setOfMolecules.Add(tautomer);
chemModel.MoleculeSet = setOfMolecules;
chemSequence.Add(chemModel);
}
}
else if (string.Equals("formula", element.Name.LocalName, StringComparison.Ordinal))
{
if (tautomer != null)
{
Trace.TraceInformation("Parsing <formula> chars: ", element.Value);
tautomer = builder.NewAtomContainer(
InChIContentProcessorTool.ProcessFormula(setOfMolecules.Builder.NewAtomContainer(), element.Value));
}
else
{
Trace.TraceWarning("Cannot set atom info for empty tautomer");
}
}
else if (string.Equals("connections", element.Name.LocalName, StringComparison.Ordinal))
{
if (tautomer != null)
{
Trace.TraceInformation("Parsing <connections> chars: ", element.Value);
InChIContentProcessorTool.ProcessConnections(element.Value, tautomer, -1);
}
else
{
Trace.TraceWarning("Cannot set dbond info for empty tautomer");
}
}
else
{
// skip all other elements
}
}