public void TestExampleFile_SupportColumns()
{
var filename = "NCDK.Data.MoSS.TKO.mossoutput";
var ins = ResourceLoader.GetAsStream(filename);
MoSSOutputReader reader = new MoSSOutputReader(ins);
var moleculeSet = new ChemObjectSet <IAtomContainer>();
moleculeSet = reader.Read(moleculeSet);
Assert.AreEqual(5.06, double.Parse(moleculeSet[0].GetProperty <string>("focusSupport").ToString()), 0.01);
Assert.AreEqual(1.74, double.Parse(moleculeSet[0].GetProperty <string>("complementSupport").ToString()), 0.01);
}
public void TestCallingTwice()
{
var molSet = new ChemObjectSet <IAtomContainer>();
var mol = new AtomContainer();
Atom atom0 = new Atom("C")
{
Id = "a1"
};
Atom atom2 = new Atom("C");
mol.Atoms.Add(atom2);
mol.Atoms.Add(atom0);
molSet.Add(mol);
IDCreator.CreateIDs(molSet);
var ids = MoleculeSetManipulator.GetAllIDs(molSet);
Assert.AreEqual(4, ids.Count());
mol = new AtomContainer();
Atom atom1 = new Atom("C")
{
Id = "a2"
};
atom2 = new Atom("C");
mol.Atoms.Add(atom2);
mol.Atoms.Add(atom1);
molSet.Add(mol);
IDCreator.CreateIDs(molSet);
ids = MoleculeSetManipulator.GetAllIDs(molSet);
Assert.AreEqual(7, ids.Count());
mol = new AtomContainer();
atom1 = new Atom("C");
atom2 = new Atom("C");
mol.Atoms.Add(atom2);
mol.Atoms.Add(atom1);
molSet.Add(mol);
atom0.Id = "atomX";
ids = MoleculeSetManipulator.GetAllIDs(molSet);
Assert.IsFalse(ids.Contains("a1"));
IDCreator.CreateIDs(molSet);
var idsAfter = MoleculeSetManipulator.GetAllIDs(molSet);
Assert.IsTrue(idsAfter.Contains("a1"));
Assert.AreEqual(10, idsAfter.Count());
}
public void TestWrite_IAtomContainerSet_SingleMolecule()
{
StringWriter writer = new StringWriter();
IChemObjectSet <IAtomContainer> molSet = new ChemObjectSet <IAtomContainer>();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molSet.Add(molecule);
SDFWriter sdfWriter = new SDFWriter(writer);
sdfWriter.Write(molSet);
sdfWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf("$$$$") != -1);
}
public void TestExampleFile_MolReading()
{
var filename = "NCDK.Data.MoSS.TKO.mossoutput";
var ins = ResourceLoader.GetAsStream(filename);
MoSSOutputReader reader = new MoSSOutputReader(ins);
var moleculeSet = new ChemObjectSet <IAtomContainer>();
moleculeSet = reader.Read(moleculeSet);
Assert.AreEqual(19, moleculeSet.Count);
foreach (var mol in moleculeSet)
{
Assert.AreEqual(int.Parse(mol.GetProperty <string>("atomCount").ToString()), mol.Atoms.Count);
Assert.AreEqual(int.Parse(mol.GetProperty <string>("bondCount").ToString()), mol.Bonds.Count);
}
}
public void TestWrite_IAtomContainerSet_CDKProperties()
{
StringWriter writer = new StringWriter();
IChemObjectSet <IAtomContainer> molSet = new ChemObjectSet <IAtomContainer>();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty(InvPair.CanonicalLabelPropertyKey, "bar");
molSet.Add(molecule);
SDFWriter sdfWriter = new SDFWriter(writer);
sdfWriter.Write(molSet);
sdfWriter.Close();
Assert.IsTrue(writer.ToString().IndexOf(InvPair.CanonicalLabelPropertyKey) == -1);
}
public void TestRemoveElectronContainer_IAtomContainerSet_IElectronContainer()
{
IChemObjectSet <IAtomContainer> ms = new ChemObjectSet <IAtomContainer>();
var mol = new AtomContainer();
mol.Atoms.Add(new Atom("O"));
mol.Atoms.Add(new Atom("O"));
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Double);
IBond bond = mol.Bonds[0];
ms.Add(mol);
IBond otherBond = new Bond(new Atom(), new Atom());
MoleculeSetManipulator.RemoveElectronContainer(ms, otherBond);
Assert.AreEqual(1, MoleculeSetManipulator.GetBondCount(ms));
MoleculeSetManipulator.RemoveElectronContainer(ms, bond);
Assert.AreEqual(0, MoleculeSetManipulator.GetBondCount(ms));
}
public void TestMoleculeSet()
{
var list = new ChemObjectSet <IAtomContainer>
{
new AtomContainer(),
new AtomContainer()
};
var model = new ChemModel {
MoleculeSet = list
};
IChemModel roundTripped = CMLRoundTripTool.RoundTripChemModel(convertor, model);
var newList = roundTripped.MoleculeSet;
Assert.IsNotNull(newList);
Assert.AreEqual(2, newList.Count());
Assert.IsNotNull(newList[0]);
Assert.IsNotNull(newList[1]);
}
public void TestRemoveAtomAndConnectedElectronContainers_IAtomContainerSet_IAtom()
{
IChemObjectSet <IAtomContainer> ms = new ChemObjectSet <IAtomContainer>();
var mol = new AtomContainer();
mol.Atoms.Add(new Atom("O"));
mol.Atoms.Add(new Atom("O"));
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Double);
IAtom atom = mol.Atoms[0];
ms.Add(mol);
IAtom otherAtom = new Atom("O");
MoleculeSetManipulator.RemoveAtomAndConnectedElectronContainers(ms, otherAtom);
Assert.AreEqual(1, MoleculeSetManipulator.GetBondCount(ms));
Assert.AreEqual(2, MoleculeSetManipulator.GetAtomCount(ms));
MoleculeSetManipulator.RemoveAtomAndConnectedElectronContainers(ms, atom);
Assert.AreEqual(0, MoleculeSetManipulator.GetBondCount(ms));
Assert.AreEqual(1, MoleculeSetManipulator.GetAtomCount(ms));
}
public void TestChemModel()
{
ChemModel model = new ChemModel();
var moleculeSet = new ChemObjectSet <IAtomContainer>();
var mol = new AtomContainer();
PseudoAtom atom = new PseudoAtom("N");
mol.Atoms.Add(atom);
moleculeSet.Add(mol);
model.MoleculeSet = moleculeSet;
IChemModel roundTrippedModel = CMLRoundTripTool.RoundTripChemModel(convertor, model);
var roundTrippedMolSet = roundTrippedModel.MoleculeSet;
Assert.IsNotNull(roundTrippedMolSet);
Assert.AreEqual(1, roundTrippedMolSet.Count);
IAtomContainer roundTrippedMolecule = roundTrippedMolSet[0];
Assert.IsNotNull(roundTrippedMolecule);
Assert.AreEqual(1, roundTrippedMolecule.Atoms.Count);
}
public void TestWrite_IAtomContainerSet_Properties_Off()
{
StringWriter writer = new StringWriter();
IChemObjectSet <IAtomContainer> molSet = new ChemObjectSet <IAtomContainer>();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.SetProperty("foo", "bar");
molSet.Add(molecule);
SDFWriter sdfWriter = new SDFWriter(writer);
var sdfWriterProps = new NameValueCollection();
sdfWriterProps["writeProperties"] = "false";
sdfWriter.Listeners.Add(new PropertiesListener(sdfWriterProps));
sdfWriter.CustomizeJob();
sdfWriter.Write(molSet);
sdfWriter.Close();
string result = writer.ToString();
Assert.IsFalse(result.Contains("<foo>"));
}
