public void TestAsadExamples()
{
var filename = "NCDK.Data.MDL.output.rxn";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
MDLRXNReader reader = new MDLRXNReader(ins);
IReactionSet reactionSet = (IReactionSet)reader.Read(builder.NewReactionSet());
reader.Close();
filename = "NCDK.Data.MDL.output_Cleaned.rxn";
Trace.TraceInformation("Testing: " + filename);
ins = ResourceLoader.GetAsStream(filename);
reader = new MDLRXNReader(ins);
IReactionSet reactionSet2 = (IReactionSet)reader.Read(builder.NewReactionSet());
reader.Close();
Assert.AreEqual(reactionSet[0].Mappings.Count, reactionSet2[0].Mappings.Count);
for (int i = 0; i < reactionSet[0].Mappings.Count; i++)
{
Assert.AreEqual(
_GetAtomNumber(reactionSet, reactionSet[0].Mappings[i][0]),
_GetAtomNumber(reactionSet2, reactionSet2[0].Mappings[i][0]));
Assert.AreEqual(
_GetAtomNumber(reactionSet, reactionSet[0].Mappings[i][1]),
_GetAtomNumber(reactionSet2, reactionSet2[0].Mappings[i][1]));
}
}
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 TestAccepts()
{
MDLRXNReader reader = new MDLRXNReader(new StringReader(""));
Assert.IsTrue(reader.Accepts(typeof(IChemFile)));
Assert.IsTrue(reader.Accepts(typeof(IChemModel)));
Assert.IsTrue(reader.Accepts(typeof(IReaction)));
Assert.IsTrue(reader.Accepts(typeof(IReactionSet)));
Assert.IsFalse(reader.Accepts(typeof(IChemObjectSet <IAtomContainer>)));
Assert.IsFalse(reader.Accepts(typeof(IAtomContainer)));
}
public void TestReadReactions2()
{
string filename2 = "NCDK.Data.MDL.reaction-2.rxn";
Trace.TraceInformation("Testing: " + filename2);
var ins2 = ResourceLoader.GetAsStream(filename2);
MDLRXNReader reader2 = new MDLRXNReader(ins2);
IReaction reaction2 = builder.NewReaction();
reaction2 = (IReaction)reader2.Read(reaction2);
reader2.Close();
Assert.IsNotNull(reaction2);
Assert.AreEqual(2, reaction2.Reactants.Count);
Assert.AreEqual(2, reaction2.Products.Count);
}
public void TestReadMapping()
{
string filename2 = "NCDK.Data.MDL.mappingTest.rxn";
Trace.TraceInformation("Testing: " + filename2);
var ins2 = ResourceLoader.GetAsStream(filename2);
MDLRXNReader reader2 = new MDLRXNReader(ins2);
IReaction reaction2 = builder.NewReaction();
reaction2 = (IReaction)reader2.Read(reaction2);
reader2.Close();
Assert.IsNotNull(reaction2);
IEnumerator <IMapping> maps = reaction2.Mappings.GetEnumerator();
Assert.IsTrue(maps.MoveNext());
}
public void TestReactionSet_1()
{
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);
IReactionSet reactionSet = new ReactionSet();
reactionSet.Add(reaction11);
// 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
IReaction reaction2 = builder.NewReaction();
MDLRXNReader reader = new MDLRXNReader(new StringReader(file));
reaction2 = (IReaction)reader.Read(reaction2);
reader.Close();
Assert.AreEqual(2, reaction2.Reactants.Count);
Assert.AreEqual(1, reaction2.Reactants[0].Atoms.Count);
Assert.AreEqual(1, reaction2.Reactants[1].Atoms.Count);
Assert.AreEqual(1, reaction2.Products.Count);
Assert.AreEqual(1, reaction2.Products[0].Atoms.Count);
}
public void TestReadReactions1()
{
string filename1 = "NCDK.Data.MDL.reaction-1.rxn";
Trace.TraceInformation("Testing: " + filename1);
var ins1 = ResourceLoader.GetAsStream(filename1);
MDLRXNReader reader1 = new MDLRXNReader(ins1);
IReaction reaction1 = builder.NewReaction();
reaction1 = (IReaction)reader1.Read(reaction1);
reader1.Close();
Assert.IsNotNull(reaction1);
Assert.AreEqual(2, reaction1.Reactants.Count);
Assert.AreEqual(1, reaction1.Products.Count);
var educts = reaction1.Reactants;
// Check Atom symbols of first educt
string[] atomSymbolsOfEduct1 = { "C", "C", "O", "Cl" };
for (int i = 0; i < educts[0].Atoms.Count; i++)
{
Assert.AreEqual(atomSymbolsOfEduct1[i], educts[0].Atoms[i].Symbol);
}
// Check Atom symbols of second educt
for (int i = 0; i < educts[1].Atoms.Count; i++)
{
Assert.AreEqual("C", educts[1].Atoms[i].Symbol);
}
// Check Atom symbols of first product
var products = reaction1.Products;
string[] atomSymbolsOfProduct1 = { "C", "C", "C", "C", "C", "C", "C", "O", "C" };
for (int i = 0; i < products[0].Atoms.Count; i++)
{
Assert.AreEqual(atomSymbolsOfProduct1[i], products[0].Atoms[i].Symbol);
}
}