public void FragmentGroupingProducts()
{
IReaction reaction = smipar.ParseReactionSmiles("CC1=NC2=C(O)C=CC=C2C=C1.CC(Cl)=O>[O-][N+](=O)C1=CC=CC=C1>CC(=O)C1=C2C=CC(C)=NC2=C(O)C=C1.[Al+3].[Cl-].[Cl-].[Cl-] |f:3.4.5.6|");
Assert.AreEqual(2, reaction.Reactants.Count);
Assert.AreEqual(1, reaction.Agents.Count);
Assert.AreEqual(2, reaction.Products.Count);
Assert.AreEqual("", reaction.GetProperty <string>(CDKPropertyName.Title));
}
private Bounds GenerateReactionConditions(IReaction chemObj, Color fg, double scale)
{
var title = chemObj.GetProperty <string>(CDKPropertyName.ReactionConditions);
if (string.IsNullOrEmpty(title))
{
return(new Bounds());
}
return(new Bounds(MarkedElement.Markup(StandardGenerator.EmbedText(font, emSize, title, fg, 1 / scale), "conditions")));
}
public void TestReactionProperties()
{
var filename = "NCDK.Data.CML.reaction.2.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = builder.NewChemFile();
chemFile = (IChemFile)reader.Read(chemFile);
reader.Close();
IReaction reaction = chemFile[0][0].ReactionSet[0];
Assert.AreEqual("3", reaction.GetProperty <string>("Ka"));
}
public static Tuple <string, string, string> GetInchiKeyPair(IReaction edge)
{
var rctInchi = GenerateInchi(edge.Reactants[0]);
var prdInchi = GenerateInchi(edge.Products[0]);
if (rctInchi == null || prdInchi == null)
{
return(null);
}
else
{
return(Tuple.Create(rctInchi, prdInchi, edge.GetProperty <string>(CDKPropertyName.SMILES)));
}
}
public void EmptyCXSMILES()
{
IReaction reaction = smipar.ParseReactionSmiles("CC1=NC2=C(O)C=CC=C2C=C1.CC(Cl)=O>[Al+3].[Cl-].[Cl-].[Cl-].[O-][N+](=O)C1=CC=CC=C1>CC(=O)C1=C2C=CC(C)=NC2=C(O)C=C1 ||");
Assert.AreEqual("", reaction.GetProperty <string>(CDKPropertyName.Title));
}
/// <summary>
/// Writes a Reaction to an Stream in MDL sdf format.
/// </summary>
/// <param name="reaction">A Reaction that is written to an Stream</param>
private void WriteReaction(IReaction reaction)
{
int reactantCount = reaction.Reactants.Count;
int productCount = reaction.Products.Count;
if (reactantCount <= 0 || productCount <= 0)
{
throw new CDKException("Either no reactants or no products present.");
}
try
{
// taking care of the $$$$ signs:
// we do not write such a sign at the end of the first reaction, thus we have to write on BEFORE the second reaction
if (reactionNumber == 2)
{
writer.Write("$$$$");
writer.Write('\n');
}
writer.Write("$RXN");
writer.Write('\n');
// reaction name
string line = reaction.GetProperty <string>(CDKPropertyName.Title);
if (line == null)
{
line = "";
}
if (line.Length > 80)
{
line = line.Substring(0, 80);
}
writer.Write(line);
writer.Write('\n');
// user/program/date&time/reaction registry no. line
writer.Write('\n');
// comment line
line = reaction.GetProperty <string>(CDKPropertyName.Remark);
if (line == null)
{
line = "";
}
if (line.Length > 80)
{
line = line.Substring(0, 80);
}
writer.Write(line);
writer.Write('\n');
line = "";
line += FormatMDLInt(reactantCount, 3);
line += FormatMDLInt(productCount, 3);
writer.Write(line);
writer.Write('\n');
int i = 0;
foreach (var mapping in reaction.Mappings)
{
var it = mapping.GetRelatedChemObjects().ToReadOnlyList();
it[0].SetProperty(CDKPropertyName.AtomAtomMapping, i + 1);
it[1].SetProperty(CDKPropertyName.AtomAtomMapping, i + 1);
i++;
}
WriteAtomContainerSet(reaction.Reactants);
WriteAtomContainerSet(reaction.Products);
//write sdfields, if any
if (rdFields != null)
{
var set = rdFields.Keys;
foreach (var element in set)
{
writer.Write("> <" + (string)element + ">");
writer.Write('\n');
writer.Write(rdFields[element].ToString());
writer.Write('\n');
writer.Write('\n');
}
}
// taking care of the $$$$ signs:
// we write such a sign at the end of all except the first molecule
if (reactionNumber != 1)
{
writer.Write("$$$$");
writer.Write('\n');
}
reactionNumber++;
}
catch (IOException ex)
{
Trace.TraceError(ex.Message);
Debug.WriteLine(ex);
throw new CDKException("Exception while writing MDL file: " + ex.Message, ex);
}
}