public void InliningReactionsWithRadicals()
{
IChemObjectBuilder bldr = ChemObjectBuilder.Instance;
SmilesParser smipar = new SmilesParser(bldr);
IReaction reaction = smipar.ParseReactionSmiles("[CH2]CO.CC(=O)O>[H+]>CCOC(=O)C.O |^1:0| ethyl esterification");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxSmiles);
// convert to molecule
IAtomContainer mol = ReactionManipulator.ToMolecule(reaction);
Assert.AreEqual("[CH2]CO.CC(=O)O.[H+].CCOC(=O)C.O |^1:0|", smigen.Create(mol));
Assert.AreEqual("[CH2]CO.CC(=O)O>[H+]>CCOC(=O)C.O |^1:0|", smigen.CreateReactionSMILES(ReactionManipulator.ToReaction(mol)));
}
public void Generate(string text, string filename)
{
Depiction depict = null;
if (IsReactionSmilees(text))
{
var rxn = parser.ParseReactionSmiles(text);
ReactionManipulator.PerceiveDativeBonds(rxn);
ReactionManipulator.PerceiveRadicals(rxn);
depict = PictureGenerator.Depict(rxn);
}
else
{
var mol = NCDKExcel.Utility.Parse(text);
AtomContainerManipulator.PerceiveDativeBonds(mol);
AtomContainerManipulator.PerceiveRadicals(mol);
depict = PictureGenerator.Depict(mol);
}
depict.WriteTo(filename);
if (!filename.EndsWith(".svg"))
{
return;
}
string svg;
using (var r = new StreamReader(filename))
{
svg = r.ReadToEnd();
}
using (var r = new StreamWriter(filename))
{
r.Write(_rect_transparent.Replace(svg, ""));
}
}
public static IReaction ReactionFromSmiles(string smiles, bool sanitize = true)
{
var parser = new SmilesParser(CDK.Builder, kekulise: sanitize);
return(parser.ParseReactionSmiles(smiles));
}