public override void StartDocument()
{
ChemFile = builder.NewChemFile();
chemSequence = builder.NewChemSequence();
chemModel = builder.NewChemModel();
setOfMolecules = builder.NewChemObjectSet <IAtomContainer>();
}
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 TestRemoveElectronContainer_IAtomContainerSet_IElectronContainer()
{
var ms = builder.NewChemObjectSet <IAtomContainer>();
var mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("O"));
mol.Atoms.Add(builder.NewAtom("O"));
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Double);
var bond = mol.Bonds[0];
ms.Add(mol);
var otherBond = builder.NewBond(builder.NewAtom(), builder.NewAtom());
AtomContainerSetManipulator.RemoveElectronContainer(ms, otherBond);
Assert.AreEqual(1, AtomContainerSetManipulator.GetBondCount(ms));
AtomContainerSetManipulator.RemoveElectronContainer(ms, bond);
Assert.AreEqual(0, AtomContainerSetManipulator.GetBondCount(ms));
}
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);
}