public void TestRDFModel()
{
var filename = "NCDK.Data.MDL.qsar-reaction-test.rdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
MDLRXNReader reader = new MDLRXNReader(ins);
IChemModel chemModel = (IChemModel)reader.Read(builder.NewChemModel());
reader.Close();
Assert.IsNotNull(chemModel);
Assert.AreEqual(2, chemModel.ReactionSet.Count);
Assert.AreEqual(2, chemModel.ReactionSet[0].Reactants.Count);
Assert.AreEqual(3, chemModel.ReactionSet[0].Reactants[0]
.Atoms.Count);
Assert.AreEqual(2, chemModel.ReactionSet[0].Reactants[1]
.Atoms.Count);
Assert.AreEqual(2, chemModel.ReactionSet[0].Products.Count);
Assert.AreEqual(2, chemModel.ReactionSet[0].Products[0]
.Atoms.Count);
Assert.AreEqual(2, chemModel.ReactionSet[0].Products[1]
.Atoms.Count);
Assert.AreEqual(1, chemModel.ReactionSet[1].Reactants.Count);
Assert.AreEqual(3, chemModel.ReactionSet[1].Reactants[0]
.Atoms.Count);
Assert.AreEqual(1, chemModel.ReactionSet[1].Products.Count);
Assert.AreEqual(2, chemModel.ReactionSet[1].Products[0]
.Atoms.Count);
}
public override void StartDocument()
{
ChemFile = builder.NewChemFile();
chemSequence = builder.NewChemSequence();
chemModel = builder.NewChemModel();
setOfMolecules = builder.NewChemObjectSet <IAtomContainer>();
}
public void TestNewChemModel()
{
IChemObjectBuilder builder = RootObject.Builder;
var model = builder.NewChemModel();
Assert.IsNotNull(model);
}
public void SetUp()
{
molecule1 = builder.NewAtomContainer();
atomInMol1 = builder.NewAtom("Cl");
molecule1.Atoms.Add(atomInMol1);
molecule1.Atoms.Add(builder.NewAtom("Cl"));
bondInMol1 = builder.NewBond(atomInMol1, molecule1.Atoms[1]);
molecule1.Bonds.Add(bondInMol1);
molecule2 = builder.NewAtomContainer();
atomInMol2 = builder.NewAtom("O");
atomInMol2.ImplicitHydrogenCount = 2;
molecule2.Atoms.Add(atomInMol2);
moleculeSet = builder.NewChemObjectSet <IAtomContainer>();
moleculeSet.Add(molecule1);
moleculeSet.Add(molecule2);
reaction = builder.NewReaction();
reaction.Reactants.Add(molecule1);
reaction.Products.Add(molecule2);
reactionSet = builder.NewReactionSet();
reactionSet.Add(reaction);
chemModel = builder.NewChemModel();
chemModel.MoleculeSet = moleculeSet;
chemModel.ReactionSet = reactionSet;
chemSequence1 = builder.NewChemSequence();
chemSequence1.Add(chemModel);
chemSequence2 = builder.NewChemSequence();
chemFile = builder.NewChemFile();
chemFile.Add(chemSequence1);
chemFile.Add(chemSequence2);
}
public void TestExample()
{
var testfile = "!Header mm1gp 100\n" + "!Info 1\n" + "!Atoms 6\n" + "0 6 \n" + "1 6 \n" + "2 1 \n"
+ "3 1 \n" + "4 1 \n" + "5 1 \n" + "!Bonds 5\n" + "1 0 D \n" + "2 0 S \n" + "3 0 S \n" + "4 1 S \n"
+ "5 1 S \n" + "!Coord\n" + "0 0.06677 -0.00197151 4.968e-07 \n"
+ "1 -0.0667699 0.00197154 -5.19252e-07 \n" + "2 0.118917 -0.097636 2.03406e-06 \n"
+ "3 0.124471 0.0904495 -4.84021e-07 \n" + "4 -0.118917 0.0976359 -2.04017e-06 \n"
+ "5 -0.124471 -0.0904493 5.12591e-07 \n" + "!Charges\n" + "0 -0.2\n" + "1 -0.2\n" + "2 0.1\n"
+ "3 0.1\n" + "4 0.1\n" + "5 0.1\n" + "!End";
var stringReader = new StringReader(testfile);
var reader = new GhemicalMMReader(stringReader);
var model = reader.Read(builder.NewChemModel());
reader.Close();
Assert.IsNotNull(model);
Assert.IsNotNull(model.MoleculeSet);
var som = model.MoleculeSet;
Assert.IsNotNull(som);
Assert.AreEqual(1, som.Count);
var m = som[0];
Assert.IsNotNull(m);
Assert.AreEqual(6, m.Atoms.Count);
Assert.AreEqual(5, m.Bonds.Count);
// test reading of formal charges
var a = m.Atoms[0];
Assert.IsNotNull(a);
Assert.AreEqual(6, a.AtomicNumber);
Assert.AreEqual(-0.2, a.Charge.Value, 0.01);
Assert.AreEqual(0.06677, a.Point3D.Value.X, 0.01);
}
public void TestChemModeID()
{
var writer = new StringWriter();
var chemModel = builder.NewChemModel();
chemModel.Id = "cm0";
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(chemModel);
cmlWriter.Close();
string cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<list convention=\"cdk:model\" id=\"cm0") != -1);
}
public IChemModel ParseSubstance(XElement parser)
{
IChemModel model = builder.NewChemModel();
// assume the current element is PC-Compound
if (!parser.Name.Equals(Name_EL_PCSUBSTANCE))
{
return(null);
}
foreach (var elm in parser.Descendants(Name_EL_PCCOMPOUNDS))
{
var set = ParseCompoundsBlock(elm);
model.MoleculeSet = set;
}
foreach (var elm in parser.Descendants(Name_EL_PCSUBSTANCE_SID))
{
string sid = GetSID(elm);
model.SetProperty(CDKPropertyName.Title, sid);
}
return(model);
}
protected static IChemObject[] AcceptableChemObjects()
{
return(new IChemObject[] { builder.NewChemFile(), builder.NewChemModel(), builder.NewAtomContainer(), builder.NewReaction(), new RGroupQuery() });
}