public void TestReactionCustomization()
{
var writer = new StringWriter();
var reaction = builder.NewReaction();
reaction.Id = "reaction1";
IAtomContainer reactant = reaction.Builder.NewAtomContainer();
reactant.Id = "react";
IAtomContainer product = reaction.Builder.NewAtomContainer();
product.Id = "product";
IAtomContainer agent = reaction.Builder.NewAtomContainer();
agent.Id = "agent";
reaction.Reactants.Add(reactant);
reaction.Products.Add(product);
reaction.Agents.Add(agent);
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(reaction);
cmlWriter.Close();
string cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"reaction1") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"react") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"product") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"agent") != -1);
}
public void TestStabilityAfterRoundtrip()
{
var filename = "NCDK.Data.MDL.bug1014344-1.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLReader(ins, ChemObjectReaderMode.Strict);
var mol1 = reader.Read(builder.NewAtomContainer());
AddImplicitHydrogens(mol1);
var output = new StringWriter();
var cmlWriter = new CMLWriter(output);
cmlWriter.Write(mol1);
var cmlreader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(output.ToString())));
var mol2 = ((IChemFile)cmlreader.Read(builder.NewChemFile()))[0][0].MoleculeSet[0];
AddImplicitHydrogens(mol2);
labeler.CanonLabel(mol1);
labeler.CanonLabel(mol2);
var atoms1 = mol1.Atoms.GetEnumerator();
var atoms2 = mol2.Atoms.GetEnumerator();
while (atoms1.MoveNext())
{
atoms2.MoveNext();
var atom1 = atoms1.Current;
var atom2 = atoms2.Current;
Assert.AreEqual(atom1.GetProperty <long>(InvPair.CanonicalLabelPropertyKey), atom2.GetProperty <long>(InvPair.CanonicalLabelPropertyKey));
}
}
public void TestReactionSchemeWithFormula()
{
var writer = new StringWriter();
var scheme1 = builder.NewReactionScheme();
scheme1.Id = "rs0";
var reaction = builder.NewReaction();
reaction.Id = "r1";
var moleculeA = reaction.Builder.NewAtomContainer();
moleculeA.Id = "A";
var formula = new MolecularFormula();
formula.Add(reaction.Builder.NewIsotope("C"), 10);
formula.Add(reaction.Builder.NewIsotope("H"), 15);
formula.Add(reaction.Builder.NewIsotope("N"), 2);
formula.Add(reaction.Builder.NewIsotope("O"), 1);
moleculeA.SetProperty(CDKPropertyName.Formula, formula);
var moleculeB = reaction.Builder.NewAtomContainer();
moleculeB.Id = "B";
reaction.Reactants.Add(moleculeA);
reaction.Products.Add(moleculeB);
scheme1.Add(reaction);
var reaction2 = reaction.Builder.NewReaction();
reaction2.Id = "r2";
var moleculeC = reaction.Builder.NewAtomContainer();
moleculeC.Id = "C";
reaction2.Reactants.Add(moleculeB);
reaction2.Products.Add(moleculeC);
scheme1.Add(reaction2);
using (var cmlWriter = new CMLWriter(writer))
{
cmlWriter.Write(scheme1);
}
var cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<reactionScheme id=\"rs0") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"r1") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"r2") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"A") != -1);
Assert.IsTrue(cmlContent.IndexOf("<formula concise=") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"B") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"C") != -1);
}
public void TestReactionScheme1()
{
var writer = new StringWriter();
var scheme1 = builder.NewReactionScheme();
scheme1.Id = "rs0";
var scheme2 = scheme1.Builder.NewReactionScheme();
scheme2.Id = "rs1";
scheme1.Add(scheme2);
var reaction = scheme1.Builder.NewReaction();
reaction.Id = "r1";
var moleculeA = reaction.Builder.NewAtomContainer();
moleculeA.Id = "A";
var moleculeB = reaction.Builder.NewAtomContainer();
moleculeB.Id = "B";
reaction.Reactants.Add(moleculeA);
reaction.Products.Add(moleculeB);
scheme2.Add(reaction);
var reaction2 = reaction.Builder.NewReaction();
reaction2.Id = "r2";
var moleculeC = reaction.Builder.NewAtomContainer();
moleculeC.Id = "C";
reaction2.Reactants.Add(moleculeB);
reaction2.Products.Add(moleculeC);
scheme1.Add(reaction2);
using (var cmlWriter = new CMLWriter(writer))
{
cmlWriter.Write(scheme1);
}
var cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<reactionScheme id=\"rs0") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reactionScheme id=\"rs1") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"r1") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"r2") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"A") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"B") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"C") != -1);
}
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 TestReactionSchemeWithFormula2()
{
var writer = new StringWriter();
var scheme1 = builder.NewReactionScheme();
scheme1.Id = "rs0";
var reaction = builder.NewReaction();
reaction.Id = "r1";
var moleculeA = reaction.Builder.NewAtomContainer();
moleculeA.Id = "A";
moleculeA.SetProperty(CDKPropertyName.Formula, "C 10 H 15 N 2 O 1");
var moleculeB = reaction.Builder.NewAtomContainer();
moleculeB.Id = "B";
reaction.Reactants.Add(moleculeA);
reaction.Products.Add(moleculeB);
scheme1.Add(reaction);
var reaction2 = reaction.Builder.NewReaction();
reaction2.Id = "r2";
var moleculeC = reaction.Builder.NewAtomContainer();
moleculeC.Id = "C";
reaction2.Reactants.Add(moleculeB);
reaction2.Products.Add(moleculeC);
scheme1.Add(reaction2);
using (var cmlWriter = new CMLWriter(writer))
{
cmlWriter.Write(scheme1);
}
var cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<reactionScheme id=\"rs0") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"r1") != -1);
Assert.IsTrue(cmlContent.IndexOf("<reaction id=\"r2") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"A") != -1);
Assert.IsTrue(cmlContent.IndexOf("<scalar dictRef=\"cdk:molecularProperty") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"B") != -1);
Assert.IsTrue(cmlContent.IndexOf("<molecule id=\"C") != -1);
}
public void TestNullFormalCharge()
{
var writer = new StringWriter();
IAtomContainer molecule = builder.NewAtomContainer(); // methane
molecule.Atoms.Add(molecule.Builder.NewAtom(ChemicalElement.C));
molecule.Atoms[0].FormalCharge = null;
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(molecule);
cmlWriter.Close();
Debug.WriteLine("****************************** TestNullFormalCharge()");
Debug.WriteLine(writer.ToString());
Debug.WriteLine("******************************");
Assert.IsFalse(writer.ToString().Contains("formalCharge"));
}
public void TestHydrogenCount()
{
var writer = new StringWriter();
IAtomContainer molecule = builder.NewAtomContainer(); // methane
molecule.Atoms.Add(molecule.Builder.NewAtom(ChemicalElement.C));
molecule.Atoms[0].ImplicitHydrogenCount = 4;
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(molecule);
cmlWriter.Close();
Debug.WriteLine("****************************** TestHydrogenCount()");
Debug.WriteLine(writer.ToString());
Debug.WriteLine("******************************");
Assert.IsTrue(writer.ToString().IndexOf("hydrogenCount=\"4\"") != -1);
}
public void TestCMLWriterBenzene()
{
var writer = new StringWriter();
IAtomContainer molecule = TestMoleculeFactory.MakeBenzene();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
Aromaticity.CDKLegacy.Apply(molecule);
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(molecule);
cmlWriter.Close();
Debug.WriteLine("****************************** TestCMLWriterBenzene()");
Debug.WriteLine(writer.ToString());
Debug.WriteLine("******************************");
Assert.IsTrue(writer.ToString().IndexOf("</molecule>") != -1);
}
public void TestMassNumber()
{
var writer = new StringWriter();
var mol = builder.NewAtomContainer();
var atom = builder.NewAtom("C");
atom.MassNumber = 12;
mol.Atoms.Add(atom);
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(mol);
cmlWriter.Close();
Debug.WriteLine("****************************** TestMAssNumber()");
Debug.WriteLine(writer.ToString());
Debug.WriteLine("******************************");
Assert.IsTrue(writer.ToString().IndexOf("isotopeNumber=\"12\"") != -1);
}
public void TestReactionProperty()
{
var writer = new StringWriter();
var reaction = builder.NewReaction();
reaction.Id = "r1";
reaction.SetProperty("blabla", "blabla2");
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(reaction);
cmlWriter.Close();
string cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<scalar dictRef=\"cdk:reactionProperty") != -1);
}
public void TestMoleculeSetID()
{
var writer = new StringWriter();
var moleculeSet = builder.NewChemObjectSet <IAtomContainer>();
moleculeSet.Id = "ms0";
var cmlWriter = new CMLWriter(writer);
cmlWriter.Write(moleculeSet);
cmlWriter.Close();
string cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestReactionCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<moleculeList convention=\"cdk:moleculeSet\" id=\"ms0") != -1);
}
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 void TestHydrogenCount_2()
{
var writer = new StringWriter();
var molecule = builder.NewAtomContainer(); // methane
molecule.Atoms.Add(molecule.Builder.NewAtom(ChemicalElement.C));
molecule.Atoms.Add(molecule.Builder.NewAtom(ChemicalElement.H));
molecule.Atoms[0].ImplicitHydrogenCount = 3;
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
using (var cmlWriter = new CMLWriter(writer))
{
cmlWriter.Write(molecule);
}
Debug.WriteLine("****************************** TestHydrogenCount_2()");
Debug.WriteLine(writer.ToString());
Debug.WriteLine("******************************");
Assert.IsTrue(writer.ToString().IndexOf("hydrogenCount=\"4\"") != -1);
}
public void TestMDMoleculeCustomization()
{
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new MDMoleculeCustomizer());
try
{
IAtomContainer molecule = MakeMDBenzene();
cmlWriter.Write(molecule);
cmlWriter.Close();
}
catch (Exception exception)
{
if (!(exception is CDKException || exception is IOException))
{
throw;
}
{
Trace.TraceError($"Error while creating an CML2 file: {exception.Message}");
Debug.WriteLine(exception);
Assert.Fail(exception.Message);
}
}
string cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestMDMoleculeCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
// Console.Out.WriteLine("****************************** TestMDMoleculeCustomization()");
// Console.Out.WriteLine(cmlContent);
// Console.Out.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("xmlns:md") != -1);
Assert.IsTrue(cmlContent.IndexOf("md:residue\"") != -1);
Assert.IsTrue(cmlContent.IndexOf("md:resNumber\"") != -1);
Assert.IsTrue(cmlContent.IndexOf("md:chargeGroup\"") != -1);
Assert.IsTrue(cmlContent.IndexOf("md:cgNumber\"") != -1);
Assert.IsTrue(cmlContent.IndexOf("md:switchingAtom\"") != -1);
}
public void TestPDBAtomCustomization()
{
StringWriter writer = new StringWriter();
var molecule = builder.NewAtomContainer();
IPDBAtom atom = builder.NewPDBAtom("C");
atom.Name = "CA";
atom.ResName = "PHE";
molecule.Atoms.Add(atom);
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(molecule);
cmlWriter.Close();
string cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestPDBAtomCustomization()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("<scalar dictRef=\"pdb:resName") != -1);
}
public void TestCMLCrystal()
{
var writer = new StringWriter();
var crystal = builder.NewCrystal();
var silicon = builder.NewAtom("Si");
silicon.FractionalPoint3D = new Vector3(0, 0, 0);
crystal.Atoms.Add(silicon);
crystal.A = (new Vector3(1.5, 0.0, 0.0));
crystal.B = (new Vector3(0.0, 2.0, 0.0));
crystal.C = (new Vector3(0.0, 0.0, 1.5));
using (var cmlWriter = new CMLWriter(writer))
{
cmlWriter.Write(crystal);
}
var cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestCMLCrystal()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("</crystal>") != -1); // the cystal info has to be present
Assert.IsTrue(cmlContent.IndexOf("<atom") != -1); // an Atom has to be present
}
static void Main(string[] args)
{
var container = Builder.NewAtomContainer();
container.Add(Builder.NewAtom("C"));
container.Add(Builder.NewAtom("C"));
container.Add(Builder.NewBond(container.Atoms[0], container.Atoms[1], BondOrder.Unset));
using (var file = new FileStream("./cml.cml", FileMode.Create, FileAccess.Write))
{
using (var writer = new CMLWriter(file))
{
writer.Write(container);
}
}
using (var cmlFile = new FileStream("./cml.cml", FileMode.Open, FileAccess.Read))
{
var reader = new CMLReader(cmlFile);
var chemFile = reader.Read(Builder.NewChemFile());
Console.WriteLine(chemFile[0][0].MoleculeSet[0].Bonds[0].Order);
}
}
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);
}
