public override SdfState ImportFromStream(StreamReader reader, Molecule molecule, out string message)
{
_molecule = molecule;
atomByNumber = new Dictionary <int, Atom>();
bondByNumber = new Dictionary <int, Bond>();
numberByAtom = new Dictionary <Atom, int>();
message = null;
SdfState result = SdfState.Null;
try
{
while (!reader.EndOfStream)
{
MDLCounts counts = ReadCtabHeader(reader);
if (!string.IsNullOrEmpty(counts.Message))
{
if (counts.Message.Contains("Unsupported"))
{
result = SdfState.Unsupported;
}
else
{
result = SdfState.Error;
}
message = counts.Message;
break;
}
else
{
ReadAtoms(reader, counts.Atoms);
ReadBonds(reader, counts.Bonds);
result = ReadCtabFooter(reader);
break;
}
}
}
catch (System.Exception ex)
{
Debug.WriteLine(ex.Message);
message = ex.Message;
result = SdfState.Error;
}
return(result);
}
private MDLCounts ReadCtabHeader(StreamReader reader)
{
MDLCounts result = new MDLCounts();
// Read Line #1 - Title
string title = SdFileConverter.GetNextLine(reader);
if (!string.IsNullOrEmpty(title))
{
if (title.ToUpper().StartsWith("$MDL"))
{
_molecule.Errors.Add("RGFiles are currently not supported");
throw new InvalidDataException("RGFiles are currently not supported");
}
if (title.ToUpper().StartsWith("$RXN"))
{
_molecule.Errors.Add("RXNFiles are currently not supported");
throw new InvalidDataException("RXNFiles are currently not supported");
}
if (title.ToUpper().StartsWith("$RDFILE"))
{
_molecule.Errors.Add("RDFiles are currently not supported");
throw new InvalidDataException("RDFiles are currently not supported");
}
if (title.ToUpper().StartsWith("<XDFILE>"))
{
_molecule.Errors.Add("XDFiles are currently not supported");
throw new InvalidDataException("XDFiles are currently not supported");
}
}
// Read and discard Line #2 - Header
SdFileConverter.GetNextLine(reader);
// Read and discard Line #3 - Comment
SdFileConverter.GetNextLine(reader);
// Read Line #4 - Counts
string counts = SdFileConverter.GetNextLine(reader);
if (counts.ToLower().Contains("v2000"))
{
try
{
result.Atoms = ParseInteger(counts, 0, 3);
result.Bonds = ParseInteger(counts, 3, 3);
result.Version = GetSubString(counts, 34, 5).ToUpper();
}
catch (Exception ex)
{
_molecule.Errors.Add($"Exception {ex.Message}");
result.Message = $"Exception {ex.Message}";
Debug.WriteLine(ex.Message);
}
}
else
{
result.Message = "Line containing atom and bond counts not found!";
}
return(result);
}