private SdfState ReadCtabFooter(StreamReader reader)
{
SdfState result = SdfState.Error;
while (!reader.EndOfStream)
{
string line = SdFileConverter.GetNextLine(reader);
if (!string.IsNullOrEmpty(line))
{
if (line.StartsWith(MDLConstants.M_CHG) ||
line.StartsWith(MDLConstants.M_ISO) ||
line.StartsWith(MDLConstants.M_RAD))
{
ReadAtomPropertyLine(line);
}
if (line.Equals(MDLConstants.M_END))
{
result = SdfState.EndOfCtab;
break;
}
}
}
return(result);
}
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);
}
public override SdfState ImportFromStream(StreamReader reader, Molecule molecule, out string message)
{
message = null;
_molecule = molecule;
SdfState result = SdfState.Null;
try
{
bool isFormula = false;
string internalName = "";
while (!reader.EndOfStream)
{
string line = SdFileConverter.GetNextLine(reader); //reader.ReadLine();;
if (!string.IsNullOrEmpty(line))
{
if (line.Equals(MDLConstants.SDF_END))
{
// End of SDF Section
result = SdfState.EndOfData;
break;
}
if (line.StartsWith(">"))
{
// Clear existing Property Name
internalName = string.Empty;
// See if we can find the property in our translation table
foreach (var property in _propertyTypes)
{
if (line.Equals(property.ExternalName))
{
isFormula = property.IsFormula;
internalName = property.InternalName;
break;
}
}
}
else
{
// Property Data
if (!string.IsNullOrEmpty(internalName))
{
if (isFormula)
{
var formula = new TextualProperty();
formula.FullType = internalName;
formula.Value = line;
_molecule.Formulas.Add(formula);
}
else
{
var name = new TextualProperty();
name.FullType = internalName;
name.Value = line;
_molecule.Names.Add(name);
}
}
}
}
else
{
internalName = string.Empty;
}
}
}
catch (System.Exception ex)
{
Debug.WriteLine(ex.Message);
result = SdfState.Error;
}
return(result);
}
public Model Import(object data)
{
Model model = null;
if (data != null)
{
string dataAsString = (string)data;
if (!dataAsString.Contains("v3000") && !dataAsString.Contains("V3000"))
{
model = new Model();
LineNumber = 0;
// Convert incoming string to a stream
MemoryStream stream = new MemoryStream();
StreamWriter writer = new StreamWriter(stream);
writer.Write(dataAsString);
writer.Flush();
stream.Position = 0;
StreamReader sr = new StreamReader(stream);
Molecule molecule = null;
SdfState state = SdfState.Null;
string message = null;
while (!sr.EndOfStream)
{
switch (state)
{
case SdfState.Null:
case SdfState.EndOfData:
molecule = new Molecule();
CtabProcessor pct = new CtabProcessor();
state = pct.ImportFromStream(sr, molecule, out message);
if (state == SdfState.Error)
{
model.GeneralErrors.Add(message);
}
//Ensure we add the molecule after it's populated
model.Molecules.Add(molecule);
if (model.Molecules.Count >= 16)
{
model.GeneralErrors.Add("This file has greater than 16 structures!");
sr.ReadToEnd();
}
break;
case SdfState.EndOfCtab:
DataProcessor dp = new DataProcessor(_propertyTypes);
state = dp.ImportFromStream(sr, molecule, out message);
break;
case SdfState.Error:
// Swallow rest of stream
sr.ReadToEnd();
break;
case SdfState.Unsupported:
// Swallow rest of stream
sr.ReadToEnd();
break;
}
}
// Can't use RebuildMolecules() as it trashes the formulae and labels
//model.RebuildMolecules();
model.RefreshMolecules();
}
}
return(model);
}
public Model Import(object data)
{
Model model = null;
if (data != null)
{
string dataAsString = (string)data;
if (!dataAsString.Contains("v3000") && !dataAsString.Contains("V3000"))
{
model = new Model();
LineNumber = 0;
// Convert incoming string to a stream
MemoryStream stream = new MemoryStream();
StreamWriter writer = new StreamWriter(stream);
writer.Write(dataAsString);
writer.Flush();
stream.Position = 0;
StreamReader sr = new StreamReader(stream);
Molecule molecule = null;
SdfState state = SdfState.Null;
string message = null;
while (!sr.EndOfStream)
{
switch (state)
{
case SdfState.Null:
case SdfState.EndOfData:
molecule = new Molecule();
CtabProcessor pct = new CtabProcessor();
state = pct.ImportFromStream(sr, molecule, out message);
if (state == SdfState.Error)
{
model.GeneralErrors.Add(message);
}
Molecule copy = molecule.Copy();
copy.SplitIntoChildren();
// If copy now contains (child) molecules, replace original
if (copy.Molecules.Count > 1)
{
molecule = copy;
}
//Ensure we add the molecule after it's populated
model.AddMolecule(molecule);
molecule.Parent = model;
if (model.Molecules.Count >= 16)
{
model.GeneralErrors.Add("This file has greater than 16 structures!");
sr.ReadToEnd();
}
break;
case SdfState.EndOfCtab:
DataProcessor dp = new DataProcessor(_propertyTypes);
state = dp.ImportFromStream(sr, molecule, out message);
break;
case SdfState.Error:
// Swallow rest of stream
sr.ReadToEnd();
break;
case SdfState.Unsupported:
// Swallow rest of stream
sr.ReadToEnd();
break;
}
}
model.Relabel(true);
model.Refresh();
}
}
return(model);
}
public Model Import(object data)
{
Model model = null;
if (data != null)
{
string dataAsString = (string)data;
if (!dataAsString.Contains("v3000") && !dataAsString.Contains("V3000"))
{
model = new Model();
// Convert incoming string to a stream
MemoryStream stream = new MemoryStream();
StreamWriter writer = new StreamWriter(stream);
writer.Write(dataAsString);
writer.Flush();
stream.Position = 0;
StreamReader sr = new StreamReader(stream);
Molecule molecule = null;
SdfState state = SdfState.Null;
string message = null;
while (!sr.EndOfStream)
{
switch (state)
{
case SdfState.Null:
case SdfState.EndOfData:
molecule = new Molecule();
//NOTE: do NOT add an empty molecule to the model. Add it AFTER it's been populated
//model.Molecules.Add(molecule);
CtabProcessor pct = new CtabProcessor();
state = pct.ImportFromStream(sr, molecule, out message);
//THIS is where you should add the molecule!
model.Molecules.Add(molecule);
break;
case SdfState.EndOfCtab:
DataProcessor dp = new DataProcessor(_propertyTypes);
state = dp.ImportFromStream(sr, molecule, out message);
break;
case SdfState.Error:
// Swallow rest of stream
string dumpOnError = sr.ReadToEnd();
break;
case SdfState.Unsupported:
// Swallow rest of stream
string dumponUnsupported = sr.ReadToEnd();
break;
}
}
// Can't use RebuildMolecules() as it trashes the formulae and labels
//model.RebuildMolecules();
model.RefreshMolecules();
}
}
return(model);
}
