public static IReaction RoundTripReaction(Convertor convertor, IReaction reaction)
{
string cmlString = "<!-- failed -->";
var cmlDOM = convertor.CDKReactionToCMLReaction(reaction);
cmlString = cmlDOM.ToString();
IReaction roundTrippedReaction = null;
Debug.WriteLine("CML string: ", cmlString);
CMLReader reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlString)));
IChemFile file = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
Assert.IsNotNull(file);
Assert.AreEqual(1, file.Count);
IChemSequence sequence = file[0];
Assert.IsNotNull(sequence);
Assert.AreEqual(1, sequence.Count);
IChemModel chemModel = sequence[0];
Assert.IsNotNull(chemModel);
IReactionSet reactionSet = chemModel.ReactionSet;
Assert.IsNotNull(reactionSet);
Assert.AreEqual(1, reactionSet.Count);
roundTrippedReaction = reactionSet[0];
Assert.IsNotNull(roundTrippedReaction);
return(roundTrippedReaction);
}
public void TestCMLWithFormula()
{
var filename = "NCDK.Data.CML.cmlWithFormula.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, 1);
var model = seq[0];
Assert.IsNotNull(model);
var mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
Assert.AreEqual("a", mol.Id);
Assert.AreEqual("a1", mol.Atoms[0].Id);
Assert.AreEqual(27, mol.Atoms.Count);
Assert.AreEqual(32, mol.Bonds.Count);
}
public void TestCephNS()
{
var filename = "NCDK.Data.CML.ceph-ns.xml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, 1);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(model.MoleculeSet.Count, 1);
// test the molecule
IAtomContainer mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
Assert.AreEqual(mol.Atoms.Count, 15);
Assert.AreEqual(mol.Bonds.Count, 16);
Assert.IsFalse(GeometryUtil.Has3DCoordinates(mol));
Assert.IsTrue(GeometryUtil.Has2DCoordinates(mol));
}
public void TestCMLConciseFormula2()
{
var filename = "NCDK.Data.CML.cmlConciseFormula2.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, 1);
var model = seq[0];
Assert.IsNotNull(model);
var mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
// FIXME: REACT: It should return two different formulas
Assert.AreEqual("[C 18 H 21 Cl 2 Mn 1 N 5 O 1, C 4 H 10]",
Strings.ToJavaString(mol.GetProperty <IList <string> >(CDKPropertyName.Formula)));
}
public void TestCMLReactionList()
{
var filename = "NCDK.Data.CML.reactionList.1.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(2, model.ReactionSet.Count);
Assert.AreEqual("1.3.2", model.ReactionSet[0].Id);
// test the reaction
IReaction reaction = model.ReactionSet[0];
Assert.IsNotNull(reaction);
Assert.AreEqual("actey", reaction.Reactants[0].Id);
Assert.AreEqual("a14293164", reaction.Reactants[0].Atoms[0].Id);
Assert.AreEqual(6, reaction.Products[0].Atoms.Count);
Assert.AreEqual(6, reaction.Reactants[0].Atoms.Count);
}
public void TestMethanolOne()
{
var filename = "NCDK.Data.CML.methanol1.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
//Debug.WriteLine($"NO sequences: {chemFile.Count}");
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
//Debug.WriteLine($"NO models: {seq.Count}");
var model = seq[0];
Assert.IsNotNull(model);
var som = model.MoleculeSet;
Assert.AreEqual(1, som.Count);
// test the molecule
IAtomContainer mol = som[0];
Assert.IsNotNull(mol);
Assert.AreEqual(mol.Atoms.Count, 6);
Assert.IsTrue(GeometryUtil.Has3DCoordinates(mol));
}
public void TestNucleustest()
{
var filename = "NCDK.Data.CML.nucleustest.xml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, 1);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(model.MoleculeSet.Count, 1);
// test the molecule
IAtomContainer mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
Assert.AreEqual(11, mol.Atoms.Count, "Incorrect number of atoms");
Assert.AreEqual(12, mol.Bonds.Count, "Incorrect number of bonds");
Assert.IsFalse(GeometryUtil.Has3DCoordinates(mol), "File does not have 3D coordinates");
Assert.IsFalse(GeometryUtil.Has2DCoordinates(mol), "File does not have 2D coordinates");
}
[TestMethod(), Ignore()] // It is broken, but not used, AFAIK
public void TestAnimation()
{
var filename = "NCDK.Data.CML.SN1_reaction.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(34, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
var som = model.MoleculeSet;
Assert.IsNotNull(som);
Assert.AreEqual(1, som.Count);
// test the molecule
IAtomContainer mol = som[0];
Assert.IsNotNull(mol);
Assert.AreEqual(mol.Atoms.Count, 25);
Assert.IsTrue(GeometryUtil.Has3DCoordinates(mol));
}
public void TestSFBug1085912_1()
{
string filename_pdb = "NCDK.Data.PDB.1CKV.pdb";
var ins1 = ResourceLoader.GetAsStream(this.GetType(), filename_pdb);
ISimpleChemObjectReader reader = new PDBReader(ins1);
IChemFile chemFile1 = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
IChemSequence seq1 = chemFile1[0];
IChemModel model1 = seq1[0];
IAtomContainer container = model1.MoleculeSet[0];
IBioPolymer polymer1 = (IBioPolymer)container;
int countchemFile1 = chemFile1.Count;
int countmodel1 = model1.MoleculeSet.Count;
int countpolymer1 = polymer1.Atoms.Count;
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(polymer1);
cmlWriter.Close();
string cmlContent1 = writer.ToString();
CMLReader reader2 = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlContent1)));
var chemFil2 = reader2.Read(builder.NewChemFile());
reader2.Close();
IChemSequence seq2 = chemFil2[0];
IChemModel model2 = seq2[0];
var polymer2 = (IPDBPolymer)model2.MoleculeSet[0];
int countchemFile2 = chemFil2.Count;
int countmodel2 = model2.MoleculeSet.Count;
int countpolymer2 = polymer2.Atoms.Count;
Assert.AreEqual(countchemFile1, countchemFile2);
Assert.AreEqual(countmodel1, countmodel2);
Assert.AreEqual(countpolymer1, countpolymer2);
writer = new StringWriter();
cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(polymer2);
cmlWriter.Close();
string cmlContent2 = writer.ToString();
string conte1 = cmlContent1.Substring(0, 1000);
string conte2 = cmlContent2.Substring(0, 1000);
Assert.AreEqual(conte1, conte2);
}
public void TestBug2697568()
{
var filename = "NCDK.Data.CML.AlanineTreeReverse.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = builder.NewChemFile();
chemFile = (IChemFile)reader.Read(chemFile);
reader.Close();
Assert.AreSame(chemFile[0][0].MoleculeSet[0], chemFile
[0][0].ReactionSet[0].Reactants[0]);
}
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 void TestAtomProperties()
{
var filename = "NCDK.Data.CML.custompropertiestest.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
ChemFile chemFile = (ChemFile)reader.Read((ChemFile) new ChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
IAtomContainer container = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
for (int i = 0; i < container.Atoms.Count; i++)
{
Assert.AreEqual(2, container.Atoms[i].GetProperties().Count);
}
}
public void TestCMLTestCase()
{
var filename = "NCDK.Data.CML.olaCmlAtomType.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = builder.NewChemFile();
chemFile = (IChemFile)reader.Read(chemFile);
reader.Close();
var container = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
foreach (var atom in container.Atoms)
{
Assert.AreEqual(null, atom.ImplicitHydrogenCount);
}
}
public void TestCMLSchemeMoleculeSet()
{
var filename = "NCDK.Data.CML.reactionSchemeMoleculeSet.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
// test reaction
Assert.AreEqual(1, model.ReactionSet.Count);
string[] idReaction = { "react_1" };
string[] idReactants = { "A" };
string[] idProducts = { "B", "C" };
IReaction reaction = model.ReactionSet[0];
Assert.AreEqual(idReaction[0], reaction.Id);
// test molecule
Assert.AreEqual(2, reaction.Products.Count());
Assert.AreEqual(idProducts[0], reaction.Products[0].Id);
Assert.AreEqual("C 9 H 20 N 1",
reaction.Products[0].GetProperty <IList <string> >(CDKPropertyName.Formula)[0]);
Assert.AreEqual(idProducts[1], reaction.Products[1].Id);
Assert.AreEqual(1, reaction.Reactants.Count());
Assert.AreEqual(idReactants[0], reaction.Reactants[0].Id);
Assert.AreEqual("C 28 H 60 N 1",
reaction.Reactants[0].GetProperty <IList <string> >(CDKPropertyName.Formula)[0]);
}
public void TestCOONa()
{
var filename = "NCDK.Data.CML.COONa.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, 1);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(model.MoleculeSet.Count(), 1);
// test the molecule
var mol = model.MoleculeSet[0];
Assert.IsNotNull(mol);
Assert.AreEqual(4, mol.Atoms.Count);
Assert.AreEqual(2, mol.Bonds.Count);
Assert.IsTrue(GeometryUtil.Has3DCoordinates(mol));
Assert.IsTrue(!GeometryUtil.Has2DCoordinates(mol));
foreach (var atom in mol.Atoms)
{
if (atom.Symbol.Equals("Na"))
{
Assert.AreEqual(+1, atom.FormalCharge.Value);
}
}
}
public void TestFile3()
{
var filename = "NCDK.Data.CML.3.cml";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
var mol = ChemFileManipulator.GetAllAtomContainers(chemFile).First();
for (int i = 0; i <= 3; i++)
{
Assert.IsFalse(mol.Bonds[i].IsAromatic, "Bond " + (i + 1) + " is not aromatic in the file");
}
for (int i = 4; i <= 9; i++)
{
Assert.IsTrue(mol.Bonds[i].IsAromatic, "Bond " + (i + 1) + " is aromatic in the file");
}
}
public void TestCMLStepList()
{
var filename = "NCDK.Data.CML.reactionStepList.1.cml";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
var reader = new CMLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
// test the resulting ChemFile content
Assert.IsNotNull(chemFile);
Assert.AreEqual(chemFile.Count, 1);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
// test reaction
Assert.AreEqual(3, model.ReactionSet.Count);
string[] idReaction = { "r1", "r2", "r3" };
string[] idReactants = { "A", "B", "C" };
string[] idProducts = { "B", "C", "D" };
for (int i = 0; i < idReaction.Length; i++)
{
IReaction reaction = model.ReactionSet[i];
Assert.AreEqual(idReaction[i], reaction.Id);
// test molecule
Assert.AreEqual(1, reaction.Products.Count());
Assert.AreEqual(idProducts[i], reaction.Products[0].Id);
Assert.AreEqual(1, reaction.Reactants.Count());
Assert.AreEqual(idReactants[i], reaction.Reactants[0].Id);
}
}
public void TestMDMoleculeCustomizationRoundtripping()
{
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new MDMoleculeCustomizer());
MDMolecule molecule = MakeMDBenzene();
cmlWriter.Write(molecule);
cmlWriter.Close();
string serializedMol = writer.ToString();
Debug.WriteLine("****************************** TestMDMoleculeCustomizationRoundtripping()");
Debug.WriteLine(serializedMol);
Debug.WriteLine("******************************");
Debug.WriteLine("****************************** testMDMoleculeCustomization Write first");
Debug.WriteLine(serializedMol);
Debug.WriteLine("******************************");
CMLReader reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(serializedMol)));
reader.RegisterConvention("md:mdMolecule", new MDMoleculeConvention(builder.NewChemFile()));
IChemFile file = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
var containers = ChemFileManipulator.GetAllAtomContainers(file).ToReadOnlyList();
Assert.AreEqual(1, containers.Count);
var molecule2 = containers[0];
Assert.IsTrue(molecule2 is MDMolecule);
MDMolecule mdMol = (MDMolecule)molecule2;
Assert.AreEqual(6, mdMol.Atoms.Count);
Assert.AreEqual(6, mdMol.Bonds.Count);
var residues = mdMol.GetResidues();
Assert.AreEqual(2, residues.Count);
Assert.AreEqual(3, ((Residue)residues[0]).Atoms.Count);
Assert.AreEqual(3, ((Residue)residues[1]).Atoms.Count);
Assert.AreEqual("myResidue1", ((Residue)residues[0]).Name);
Assert.AreEqual("myResidue2", ((Residue)residues[1]).Name);
Assert.AreEqual(0, ((Residue)residues[0]).GetNumber());
Assert.AreEqual(1, ((Residue)residues[1]).GetNumber());
var chargeGroup = mdMol.GetChargeGroups();
Assert.AreEqual(2, chargeGroup.Count);
Assert.AreEqual(2, ((ChargeGroup)chargeGroup[0]).Atoms.Count);
Assert.AreEqual(4, ((ChargeGroup)chargeGroup[1]).Atoms.Count);
Assert.IsNotNull(((ChargeGroup)chargeGroup[0]).GetSwitchingAtom());
Assert.AreEqual("a2", ((ChargeGroup)chargeGroup[0]).GetSwitchingAtom().Id);
Assert.IsNotNull(((ChargeGroup)chargeGroup[1]).GetSwitchingAtom());
Assert.AreEqual("a5", ((ChargeGroup)chargeGroup[1]).GetSwitchingAtom().Id);
Assert.AreEqual(2, ((ChargeGroup)chargeGroup[0]).GetNumber());
Assert.AreEqual(3, ((ChargeGroup)chargeGroup[1]).GetNumber());
writer = new StringWriter();
cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new MDMoleculeCustomizer());
cmlWriter.Write(mdMol);
cmlWriter.Close();
string serializedMDMol = writer.ToString();
Debug.WriteLine("****************************** TestMDMoleculeCustomizationRoundtripping()");
Debug.WriteLine(serializedMol);
Debug.WriteLine("******************************");
Debug.WriteLine("****************************** testMDMoleculeCustomization Write second");
Debug.WriteLine(serializedMDMol);
Debug.WriteLine("******************************");
Assert.AreEqual(serializedMol, serializedMDMol);
}
