/// <summary>
/// Serializes the IChemObject to CML and redirects it to the output Writer.
/// </summary>
/// <param name="obj">A Molecule of AtomContaineSet object</param>
public override void Write(IChemObject obj)
{
if (!(obj is IAtomContainer) && !(obj is IEnumerableChemObject <IAtomContainer>) &&
!(obj is IReaction) && !(obj is IReactionSet) &&
!(obj is IChemSequence) && !(obj is IChemModel) &&
!(obj is IChemFile) && !(obj is ICrystal) && !(obj is IAtom) &&
!(obj is IBond))
{
throw new CDKException("Cannot write this unsupported IChemObject: " + obj.GetType().Name);
}
Debug.WriteLine($"Writing obj in CML of type: {obj.GetType().Name}");
CustomizeJob();
Convertor convertor = new Convertor(cmlIds.IsSet,
(namespacePrefix.Setting.Length > 0) ? namespacePrefix.Setting : null);
// adding the customizer
if (customizers != null)
{
foreach (var customizer in customizers)
{
convertor.RegisterCustomizer(customizer);
}
}
// now convert the obj
XElement root = null;
if (obj is IPDBPolymer)
{
root = convertor.CDKPDBPolymerToCMLMolecule((IPDBPolymer)obj);
}
else if (obj is ICrystal)
{
root = convertor.CDKCrystalToCMLMolecule((ICrystal)obj);
}
else if (obj is IAtom)
{
root = convertor.CDKAtomToCMLAtom(null, (IAtom)obj);
}
else if (obj is IBond)
{
root = convertor.CDKJBondToCMLBond((IBond)obj);
}
else if (obj is IReaction)
{
root = convertor.CDKReactionToCMLReaction((IReaction)obj);
}
else if (obj is IReactionScheme)
{
root = convertor.CDKReactionSchemeToCMLReactionSchemeAndMoleculeList((IReactionScheme)obj);
}
else if (obj is IReactionSet)
{
root = convertor.CDKReactionSetToCMLReactionList((IReactionSet)obj);
}
else if (obj is IEnumerableChemObject <IAtomContainer> )
{
root = convertor.CDKAtomContainerSetToCMLList((IEnumerableChemObject <IAtomContainer>)obj);
}
else if (obj is IChemSequence)
{
root = convertor.CDKChemSequenceToCMLList((IChemSequence)obj);
}
else if (obj is IChemModel)
{
root = convertor.CDKChemModelToCMLList((IChemModel)obj);
}
else if (obj is IAtomContainer)
{
root = convertor.CDKAtomContainerToCMLMolecule((IAtomContainer)obj);
}
else if (obj is IChemFile)
{
root = convertor.CDKChemFileToCMLList((IChemFile)obj);
}
var encoding = "ISO-8859-1";
var se = new XmlWriterSettings
{
Encoding = Encoding.GetEncoding(encoding)
};
if (indent.IsSet)
{
Trace.TraceInformation("Indenting XML output");
se.Indent = true;
se.IndentChars = new string(' ', 2);
}
XNamespace xsi = "http://www.w3.org/2001/XMLSchema-instance";
if (schemaInstanceOutput.IsSet)
{
root.SetAttributeValue(XNamespace.Xmlns + "xsi", xsi.NamespaceName);
root.SetAttributeValue(xsi + "schemaLocation", "http://www.xml-cml.org/schema/cml2/core " + instanceLocation.Setting);
}
var de = new XDeclaration(null, encoding, null);
XDocument doc = new XDocument(de, root);
doc.Save(output);
}
/// <summary>
/// Writes a <see cref="IChemObject"/> to the MDL molfile formated output.
/// </summary>
/// <param name="obj">Best choice is a set of molecules</param>
/// <see cref="IChemObjectWriter.Write(IChemObject)"/>
public override void Write(IChemObject obj)
{
try
{
XProcessingInstruction pi = new XProcessingInstruction("xml-stylesheet", "href=\"http://www.w3.org/2000/08/w3c-synd/style.css\" type=\"text/css\"");
var doc = new XDocument();
doc.Add(pi);
var rdfElement = new XElement(NS_RSS10 + "RDF");
rdfElement.SetAttributeValue(XNamespace.Xmlns + "rdf", NS_RSS10);
rdfElement.SetAttributeValue(XNamespace.Xmlns + "mn", "http://usefulinc.com/rss/manifest/");
rdfElement.SetAttributeValue(XNamespace.Xmlns + "dc", NS_DCELEMENTS);
rdfElement.SetAttributeValue(XNamespace.Xmlns + "cml", Convertor.NamespaceCML);
doc.Add(rdfElement);
var channelElement = new XElement(NS_RSS10 + "channel");
var titleElement = new XElement(NS_RSS10 + "title")
{
Value = this.Title
};
channelElement.Add(titleElement);
var linkElement = new XElement(NS_RSS10 + "link")
{
Value = Link
};
channelElement.Add(linkElement);
var descriptionElement = new XElement(NS_RSS10 + "description")
{
Value = Description
};
channelElement.Add(descriptionElement);
var publisherElement = new XElement(NS_DCELEMENTS + "publisher")
{
Value = Publisher
};
channelElement.Add(publisherElement);
var creatorElement = new XElement(NS_DCELEMENTS + "creator")
{
Value = Creator
};
channelElement.Add(creatorElement);
var imageElement = new XElement(NS_RSS10 + "image");
imageElement.SetAttributeValue(NS_RDF + "resource", ImageLink);
channelElement.Add(imageElement);
var itemsElement = new XElement(NS_RSS10 + "items");
var seqElement = new XElement(NS_RDF + "seq");
itemsElement.Add(seqElement);
channelElement.Add(itemsElement);
channelElement.SetAttributeValue(NS_RDF + "about", About);
rdfElement.Add(channelElement);
var list = new List <IChemObject>();
if (obj is IChemObjectSet <IAtomContainer> )
{
for (int i = 0; i < ((IChemObjectSet <IAtomContainer>)obj).Count; i++)
{
list.Add(((IChemObjectSet <IAtomContainer>)obj)[i]);
}
}
else
{
list.Add(obj);
}
for (int i = 0; i < list.Count; i++)
{
IChemObject chemObject = (IChemObject)list[i];
var itemElement = new XElement(NS_RSS10 + "item");
string easylink = LinkMap[chemObject];
if (easylink != null)
{
itemElement.SetAttributeValue(NS_RDF + "about", easylink);
}
var link2Element = new XElement(NS_RSS10 + "link")
{
Value = easylink
};
itemElement.Add(link2Element);
string title = chemObject.GetProperty <string>(CDKPropertyName.Title);
if (TitleMap[chemObject] != null)
{
var title2Element = new XElement(NS_RSS10 + "title")
{
Value = TitleMap[chemObject]
};
itemElement.Add(title2Element);
}
if (title != null)
{
var description2Element = new XElement(NS_RSS10 + "description")
{
Value = title
};
itemElement.Add(description2Element);
var subjectElement = new XElement(NS_DCELEMENTS + "subject")
{
Value = title
};
itemElement.Add(subjectElement);
}
if (DateMap[chemObject] != null)
{
var dateElement = new XElement(NS_DCELEMENTS + "date")
{
Value = DateMap[chemObject].ToString("yyyy-MM-dd'T'HH:mm:ss", DateTimeFormatInfo.InvariantInfo) + TimeZone
};
itemElement.Add(dateElement);
}
var creator2Element = new XElement(NS_DCELEMENTS + "creator")
{
Value = CreatorMap[chemObject]
};
itemElement.Add(creator2Element);
// add the InChI to the CMLRSS feed
if (InChIMap[chemObject] != null)
{
var inchiElement = new XElement(NS_CML + "identifier")
{
Value = InChIMap[chemObject]
};
itemElement.Add(inchiElement);
}
CMLElement root = null;
var convertor = new Convertor(true, null);
obj = list[i];
if (obj is ICrystal)
{
root = convertor.CDKCrystalToCMLMolecule((ICrystal)obj);
}
else if (obj is IAtomContainer)
{
root = convertor.CDKAtomContainerToCMLMolecule((IAtomContainer)obj);
}
else if (obj is IAtom)
{
root = convertor.CDKAtomToCMLAtom(null, (IAtom)obj);
}
else if (obj is IBond)
{
root = convertor.CDKJBondToCMLBond((IBond)obj);
}
else if (obj is IReaction)
{
root = convertor.CDKReactionToCMLReaction((IReaction)obj);
}
else if (obj is IReactionSet)
{
root = convertor.CDKReactionSetToCMLReactionList((IReactionSet)obj);
}
else if (obj is IChemObjectSet <IAtomContainer> )
{
root = convertor.CDKAtomContainerSetToCMLList((IChemObjectSet <IAtomContainer>)obj);
}
else if (obj is IChemSequence)
{
root = convertor.CDKChemSequenceToCMLList((IChemSequence)obj);
}
else if (obj is IChemModel)
{
root = convertor.CDKChemModelToCMLList((IChemModel)obj);
}
else if (obj is IChemFile)
{
root = convertor.CDKChemFileToCMLList((IChemFile)obj);
}
else
{
throw new CDKException($"Unsupported chemObject: {obj.GetType().Name}");
}
itemElement.Add(root);
if (MultiMap[chemObject] != null)
{
var coll = MultiMap[chemObject];
foreach (var e in coll)
{
itemElement.Add(e);
}
}
rdfElement.Add(itemElement);
var imageElement2 = new XElement(NS_RDF + "li");
imageElement2.SetAttributeValue(NS_RDF + "resource", LinkMap[chemObject]);
seqElement.Add(imageElement2);
}
writer.Write(doc.ToString());
writer.Flush();
}
catch (IOException ex)
{
throw new CDKException(ex.Message, ex);
}
}