public void WriteCustomTitle()
{
var builder = CDK.Builder;
var mol = builder.NewAtomContainer();
var atom = builder.NewAtom();
atom.Symbol = "C";
atom.ImplicitHydrogenCount = 4;
atom.Point3D = new Vector3(0.5, 0.5, 0.1);
mol.Atoms.Add(atom);
using (var sw = new StringWriter())
{
using (var mdlw = new MDLV3000Writer(sw))
{
var sdfWriterProps = new NameValueCollection
{
[MDLV2000Writer.OptProgramName] = "FakeNews"
};
mdlw.Listeners.Add(new PropertiesListener(sdfWriterProps));
mdlw.CustomizeJob();
mdlw.Write(mol);
}
Assert.IsTrue(sw.ToString().Contains("FakeNews", StringComparison.Ordinal));
}
}
private string WriteToStr(IAtomContainer mol)
{
var sw = new StringWriter();
using (var mdlw = new MDLV3000Writer(sw))
{
mdlw.Write(mol);
}
return(sw.ToString());
}
public void WriteDimensionField3D()
{
var builder = CDK.Builder;
var mol = builder.NewAtomContainer();
var atom = builder.NewAtom();
atom.Symbol = "C";
atom.ImplicitHydrogenCount = 4;
atom.Point3D = new Vector3(0.5, 0.5, 0.1);
mol.Atoms.Add(atom);
var sw = new StringWriter();
using (var mdlw = new MDLV3000Writer(sw))
{
mdlw.Write(mol);
}
Assert.IsTrue(sw.ToString().Contains("3D"));
}
private void WriteMolecule(IAtomContainer container)
{
try
{
// write the MDL molfile bits
StringWriter stringWriter = new StringWriter();
IChemObjectWriter mdlWriter;
if (WriteV3000(container))
{
mdlWriter = new MDLV3000Writer(stringWriter);
}
else
{
mdlWriter = new MDLV2000Writer(stringWriter);
}
mdlWriter.AddSettings(IOSettings.Settings);
mdlWriter.Write(container);
mdlWriter.Close();
writer.Write(stringWriter.ToString());
// write non-structural data (mol properties in our case)
if (paramWriteData.IsSet)
{
var sdFields = container.GetProperties();
bool writeAllProperties = propertiesToWrite == null;
if (sdFields != null)
{
foreach (var propKey in sdFields.Keys)
{
string headerKey = propKey.ToString();
if (!IsCDKInternalProperty(headerKey))
{
if (writeAllProperties || propertiesToWrite.Contains(headerKey))
{
string cleanHeaderKey = ReplaceInvalidHeaderChars(headerKey);
if (!cleanHeaderKey.Equals(headerKey, StringComparison.Ordinal))
{
Trace.TraceInformation("Replaced characters in SDfile data header: ", headerKey, " written as: ", cleanHeaderKey);
}
Object val = sdFields[propKey];
if (IsPrimitiveDataValue(val))
{
writer.Write("> <" + cleanHeaderKey + ">");
writer.Write('\n');
if (val != null)
{
writer.Write(val.ToString());
}
writer.Write('\n');
writer.Write('\n');
}
else
{
Trace.TraceInformation("Skipped property " + propKey + " because only primitive and string properties can be written by SDFWriter");
}
}
}
}
}
}
writer.Write("$$$$\n");
}
catch (IOException exception)
{
throw new CDKException("Error while writing a SD file entry: " + exception.Message, exception);
}
}