public void TestRDFReactioniSet()
{
var filename = "NCDK.Data.MDL.qsar-reaction-test.rdf";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
MDLRXNReader reader = new MDLRXNReader(ins);
IReactionSet reactionSet = (IReactionSet)reader.Read(builder.NewReactionSet());
reader.Close();
Assert.IsNotNull(reactionSet);
Assert.AreEqual(2, reactionSet.Count);
Assert.AreEqual(2, reactionSet[0].Reactants.Count);
Assert.AreEqual(3, reactionSet[0].Reactants[0].Atoms.Count);
Assert.AreEqual(2, reactionSet[0].Reactants[1].Atoms.Count);
Assert.AreEqual(2, reactionSet[0].Products.Count);
Assert.AreEqual(2, reactionSet[0].Products[0].Atoms.Count);
Assert.AreEqual(2, reactionSet[0].Products[1].Atoms.Count);
Assert.AreEqual(1, reactionSet[1].Reactants.Count);
Assert.AreEqual(3, reactionSet[1].Reactants[0].Atoms.Count);
Assert.AreEqual(1, reactionSet[1].Products.Count);
Assert.AreEqual(2, reactionSet[1].Products[0].Atoms.Count);
}
public void TestGetAllMolecules_IReactionSet()
{
IReactionSet reactionSet = builder.NewReactionSet();
reactionSet.Add(builder.NewReaction()); // 1
reactionSet.Add(builder.NewReaction()); // 2
Assert.AreEqual(0, ReactionSetManipulator.GetAllMolecules(reactionSet).Count);
}
public void TestNewReactionSet()
{
IChemObjectBuilder builder = RootObject.Builder;
IReactionSet set = builder.NewReactionSet();
Assert.IsNotNull(set);
}
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 TestIsEmpty_ReactionSet()
{
var model = (IChemModel)NewChemObject();
IChemObjectBuilder builder = model.Builder;
IAtomContainer molecule = builder.NewAtomContainer();
IReaction reaction = builder.NewReaction();
reaction.Reactants.Add(molecule);
IReactionSet set = builder.NewReactionSet();
model.ReactionSet = set;
Assert.IsTrue(model.IsEmpty(), "model has an empty reaction set and should be empty");
set.Add(reaction);
Assert.IsFalse(model.IsEmpty(), "model has a reaction set and should not be empty");
model.ReactionSet = null;
Assert.IsTrue(model.IsEmpty(), "model has no reaction set");
}
public void TestReactionSet_2()
{
IReaction reaction11 = builder.NewReaction();
IAtomContainer hydroxide = builder.NewAtomContainer();
hydroxide.Atoms.Add(builder.NewAtom("O"));
reaction11.Reactants.Add(hydroxide);
IAtomContainer proton = builder.NewAtomContainer();
proton.Atoms.Add(builder.NewAtom("H"));
reaction11.Reactants.Add(proton);
IAtomContainer water = builder.NewAtomContainer();
water.Atoms.Add(builder.NewAtom("O"));
reaction11.Products.Add(water);
IReaction reaction12 = builder.NewReaction();
IAtomContainer h = builder.NewAtomContainer();
h.Atoms.Add(builder.NewAtom("H"));
IAtomContainer n = builder.NewAtomContainer();
n.Atoms.Add(builder.NewAtom("N"));
reaction12.Reactants.Add(h);
reaction12.Reactants.Add(n);
IAtomContainer ammonia = builder.NewAtomContainer();
ammonia.Atoms.Add(builder.NewAtom("N"));
ammonia.Atoms.Add(builder.NewAtom("H"));
ammonia.AddBond(ammonia.Atoms[0], ammonia.Atoms[1], BondOrder.Single);
reaction12.Products.Add(ammonia);
IReactionSet reactionSet = builder.NewReactionSet();
reactionSet.Add(reaction11);
reactionSet.Add(reaction12);
// now serialize to MDL RXN
StringWriter writer = new StringWriter();
string file = "";
MDLRXNWriter mdlWriter = new MDLRXNWriter(writer);
mdlWriter.Write(reactionSet);
mdlWriter.Close();
file = writer.ToString();
Assert.IsTrue(file.Length > 0);
// now deserialize the MDL RXN output
IReactionSet reactionSetF = builder.NewReactionSet();
MDLRXNReader reader = new MDLRXNReader(new StringReader(file));
reactionSetF = (IReactionSet)reader.Read(reactionSetF);
reader.Close();
Assert.AreEqual(2, reactionSetF.Count);
Assert.AreEqual(1, reactionSetF[0].Reactants[0].Atoms.Count);
Assert.AreEqual(1, reactionSetF[0].Reactants[1].Atoms.Count);
Assert.AreEqual(1, reactionSetF[0].Products.Count);
Assert.AreEqual(1, reactionSetF[0].Products[0].Atoms.Count);
}
public void TestCreateReactionScheme_IReactionSet()
{
IAtomContainer molA = builder.NewAtomContainer();
molA.Id = "A";
IAtomContainer molB = builder.NewAtomContainer();
molB.Id = "B";
IAtomContainer molC = builder.NewAtomContainer();
molC.Id = "C";
IAtomContainer molD = builder.NewAtomContainer();
molD.Id = "D";
IAtomContainer molE = builder.NewAtomContainer();
molE.Id = "E";
IReactionSet reactionSet = builder.NewReactionSet();
IReaction reaction1 = builder.NewReaction();
reaction1.Id = "r1";
reaction1.Reactants.Add(molA);
reaction1.Products.Add(molB);
reactionSet.Add(reaction1);
IReaction reaction2 = builder.NewReaction();
reaction2.Id = "r2";
reaction2.Reactants.Add(molB);
reaction2.Products.Add(molC);
reactionSet.Add(reaction2);
IReaction reaction3 = builder.NewReaction();
reaction3.Id = "r3";
reaction3.Reactants.Add(molB);
reaction3.Products.Add(molD);
reactionSet.Add(reaction3);
IReaction reaction4 = builder.NewReaction();
reaction4.Id = "r4";
reaction4.Reactants.Add(molC);
reaction4.Products.Add(molE);
reactionSet.Add(reaction4);
IReactionScheme scheme1 = ReactionSchemeManipulator.NewReactionScheme(reactionSet);
Assert.AreEqual(1, scheme1.Reactions.Count());
Assert.AreEqual("r1", scheme1.Reactions.ElementAt(0).Id);
Assert.AreEqual(1, scheme1.Schemes.Count);
IReactionScheme scheme2 = scheme1.Schemes.First();
Assert.AreEqual(2, scheme2.Reactions.Count());
Assert.AreEqual("r2", scheme2.Reactions.ElementAt(0).Id);
Assert.AreEqual("r3", scheme2.Reactions.ElementAt(1).Id);
Assert.AreEqual(1, scheme2.Schemes.Count);
IReactionScheme scheme3 = scheme2.Schemes.First();
Assert.AreEqual(1, scheme3.Reactions.Count());
Assert.AreEqual("r4", scheme3.Reactions.ElementAt(0).Id);
Assert.AreEqual(0, scheme3.Schemes.Count);
}