public void TestSort_IAtomContainerSet()
{
// Create some IAtomContainers
var cycloPentane = builder.NewRing(5, "C");
var cycloHexane = builder.NewRing(6, "C");
var hexaneNitrogen = builder.NewRing(6, "N");
hexaneNitrogen.Bonds.RemoveAt(0);
var cycloHexaneNitrogen = builder.NewRing(6, "N");
var cycloHexeneNitrogen = builder.NewRing(6, "N");
cycloHexeneNitrogen.Bonds[0].Order = BondOrder.Double;
// Add them to a IAtomContainerSet
var atomContainerSet = builder.NewAtomContainerSet();
atomContainerSet.Add(cycloHexane);
atomContainerSet.Add(cycloHexeneNitrogen);
atomContainerSet.Add(cycloPentane);
atomContainerSet.Add(hexaneNitrogen);
atomContainerSet.Add(cycloHexaneNitrogen);
// Sort the IAtomContainerSet
AtomContainerSetManipulator.Sort(atomContainerSet);
// Assert.assert the correct order
Assert.AreSame(cycloPentane, atomContainerSet[0], "first order: cycloPentane");
Assert.AreSame(cycloHexane, atomContainerSet[1], "second order: cycloHexane");
Assert.AreSame(hexaneNitrogen, atomContainerSet[2], "third order: hexaneNitrogen");
Assert.AreSame(cycloHexaneNitrogen, atomContainerSet[3], "forth order: cycloHexaneNitrogen");
Assert.AreSame(cycloHexeneNitrogen, atomContainerSet[4], "firth order: cycloHexeneNitrogen");
}
/// <summary>
/// Get the expected set of molecules.
/// TODO:reaction. Set the products
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
setOfProducts.Add(null);
return(setOfProducts);
}
public void TestAssignrPiMarsilliFactors_IAtomContainerSet()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("F"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
foreach (var atom in molecule.Atoms)
{
atom.Charge = 0;
}
var set = builder.NewAtomContainerSet();
set.Add(molecule);
set.Add(molecule);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
Assert.IsNotNull(peoe.AssignrPiMarsilliFactors(set));
}
/// <summary>
/// Get the expected set of molecules. [C-]-C = C
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms[0].FormalCharge = -1;
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Double);
try
{
AddExplicitHydrogens(molecule);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfProducts.Add(molecule);
return(setOfProducts);
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("O"));
molecule.Atoms[0].FormalCharge = 1;
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[3], BondOrder.Single);
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[4], BondOrder.Single);
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[5], BondOrder.Single);
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[6], BondOrder.Single);
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[7], BondOrder.Single);
try
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
}
catch (CDKException e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfProducts.Add(molecule);
return(setOfProducts);
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
var molecule1 = builder.NewAtomContainer();
molecule1.Atoms.Add(builder.NewAtom("O"));
molecule1.Atoms.Add(builder.NewAtom("C"));
molecule1.AddBond(molecule1.Atoms[0], molecule1.Atoms[1], BondOrder.Double);
molecule1.Atoms.Add(builder.NewAtom("H"));
molecule1.AddBond(molecule1.Atoms[1], molecule1.Atoms[2], BondOrder.Single);
molecule1.Atoms.Add(builder.NewAtom("H"));
molecule1.AddBond(molecule1.Atoms[1], molecule1.Atoms[3], BondOrder.Single);
molecule1.Atoms[0].FormalCharge = 1;
molecule1.Atoms.Add(builder.NewAtom("H"));
molecule1.AddBond(molecule1.Atoms[0], molecule1.Atoms[4], BondOrder.Single);
setOfProducts.Add(molecule1);
var molecule2 = builder.NewAtomContainer();
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.Atoms.Add(builder.NewAtom("H"));
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[1], BondOrder.Single);
molecule2.Atoms.Add(builder.NewAtom("H"));
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[2], BondOrder.Single);
molecule2.Atoms.Add(builder.NewAtom("H"));
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[3], BondOrder.Single);
molecule2.SingleElectrons.Add(CDK.Builder.NewSingleElectron(molecule2.Atoms[0]));
setOfProducts.Add(molecule2);
return(setOfProducts);
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
//[O+]=C-[C-]-C
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("O"));
molecule.Atoms[0].FormalCharge = +1;
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms[2].FormalCharge = -1;
molecule.LonePairs.Add(CDK.Builder.NewLonePair(molecule.Atoms[0]));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[3], BondOrder.Single);
try
{
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfProducts.Add(molecule);
return(setOfProducts);
}
public void TestNewMoleculeSet()
{
IChemObjectBuilder builder = RootObject.Builder;
var set = builder.NewAtomContainerSet();
Assert.IsNotNull(set);
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
IAtomContainer molecule1 = builder.NewAtomContainer();//CreateFromSmiles("[C+]");
IAtom carb = builder.NewAtom("C");
carb.FormalCharge = 1;
molecule1.Atoms.Add(carb);
molecule1.Atoms.Add(builder.NewAtom("H"));
molecule1.AddBond(molecule1.Atoms[0], molecule1.Atoms[1], BondOrder.Single);
molecule1.Atoms.Add(builder.NewAtom("H"));
molecule1.AddBond(molecule1.Atoms[0], molecule1.Atoms[2], BondOrder.Single);
molecule1.Atoms.Add(builder.NewAtom("H"));
molecule1.AddBond(molecule1.Atoms[0], molecule1.Atoms[3], BondOrder.Single);
IAtomContainer molecule2 = builder.NewAtomContainer();//CreateFromSmiles("[C-]#[O+]");
carb = builder.NewAtom("C");
carb.FormalCharge = -1;
molecule2.LonePairs.Add(new LonePair(carb));
molecule2.Atoms.Add(carb);
IAtom oxy = builder.NewAtom("O");
oxy.FormalCharge = 1;
molecule2.Atoms.Add(oxy);
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[1], BondOrder.Triple);
setOfProducts.Add(molecule1);
setOfProducts.Add(molecule2);
return(setOfProducts);
}
public static void CleanDataSet(string dataFile)
{
var som = builder.NewAtomContainerSet();
try
{
Console.Out.WriteLine("Start clean dataset...");
using (var fin = new StreamReader(dataFile))
using (var imdl = new EnumerableSDFReader(fin, builder))
{
Console.Out.WriteLine("READY");
int c = 0;
foreach (var m in imdl)
{
c++;
if (c % 1000 == 0)
{
Console.Out.WriteLine("...");
}
if (m.Atoms.Count > 2)
{
if (m.Atoms[0].Point3D != null)
{
som.Add(m);
}
}
}
}
Console.Out.Write("Read File in..");
}
catch (Exception exc)
{
Console.Out.WriteLine($"Could not read Molecules from file {dataFile} due to: {exc.Message}");
}
Console.Out.WriteLine($"{som.Count} Templates are read in");
WriteChemModel(som, dataFile, "_CLEAN");
}
public void TestWrite_IAtomContainerSet()
{
StringWriter writer = new StringWriter();
IChemObjectSet <IAtomContainer> molSet = builder.NewAtomContainerSet();
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molSet.Add(molecule);
SDFWriter sdfWriter = new SDFWriter(writer);
sdfWriter.Write(molSet);
sdfWriter.Close();
Assert.AreNotSame(0, writer.ToString().Length);
}
public void badSmilesLine()
{
IChemObjectBuilder bldr = CDK.Builder;
string input = "C\nn1cccc1\nc1ccccc1\n";
DefaultChemObjectReader cor = new SMILESReader(new StringReader(input));
IChemObjectSet <IAtomContainer> mols = cor.Read(bldr.NewAtomContainerSet());
Assert.AreEqual(3, mols.Count);
Assert.AreEqual(1, mols[0].Atoms.Count);
Assert.IsNull(mols[0].GetProperty <string>(EnumerableSMILESReader.BadSmilesInput));
Assert.AreEqual(0, mols[1].Atoms.Count);
Assert.IsNotNull(mols[1].GetProperty <string>(EnumerableSMILESReader.BadSmilesInput));
Assert.AreEqual(6, mols[2].Atoms.Count);
Assert.IsNull(mols[2].GetProperty <string>(EnumerableSMILESReader.BadSmilesInput));
}
public void TestGetAllMolecules_IReactionScheme_IAtomContainerSet()
{
IReactionScheme reactionScheme = builder.NewReactionScheme();
IReaction reaction1 = builder.NewReaction();
reaction1.Products.Add(builder.NewAtomContainer());
IReaction reaction2 = builder.NewReaction();
reaction2.Products.Add(builder.NewAtomContainer());
reactionScheme.Add(reaction1); // 1
reactionScheme.Add(reaction2); // 2
Assert.AreEqual(
2,
ReactionSchemeManipulator.GetAllAtomContainers(reactionScheme,
builder.NewAtomContainerSet()).Count);
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
var molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms[0].FormalCharge = 1;
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[3], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[3], molecule.Atoms[4], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[4], molecule.Atoms[5], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[4], molecule.Atoms[6], BondOrder.Single);
try
{
AddExplicitHydrogens(molecule);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
molecule.Atoms[0].FormalCharge = 0;
molecule.SingleElectrons.Add(CDK.Builder.NewSingleElectron(molecule.Atoms[0]));
try
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
MakeSureAtomTypesAreRecognized(molecule);
}
catch (CDKException e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfProducts.Add(molecule);
return(setOfProducts);
}
/// <summary>
/// Get the expected set of molecules. 2-methylnaphthalene.
/// C=1C=CC2=CC(=CC=C2(C=1))C
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
//C=1C=CC2=CC(=CC=C2(C=1))C
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[3], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[3], molecule.Atoms[4], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[4], molecule.Atoms[5], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[5], molecule.Atoms[6], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[6], molecule.Atoms[7], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[7], molecule.Atoms[8], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[8], molecule.Atoms[9], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[9], molecule.Atoms[10], BondOrder.Double);
molecule.AddBond(molecule.Atoms[10], molecule.Atoms[1], BondOrder.Single);
molecule.AddBond(molecule.Atoms[9], molecule.Atoms[4], BondOrder.Single);
try
{
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
MakeSureAtomTypesAreRecognized(molecule);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfProducts.Add(molecule);
return(setOfProducts);
}
public IChemObjectSet <IAtomContainer> ParseCompoundsBlock(XElement parser)
{
var set = builder.NewAtomContainerSet();
// assume the current element is PC-Compounds
if (!parser.Name.Equals(Name_EL_PCCOMPOUNDS))
{
return(null);
}
foreach (var elm in parser.Elements(Name_EL_PCCOMPOUND))
{
IAtomContainer molecule = ParseMolecule(elm, builder);
if (molecule.Atoms.Count > 0)
{
// skip empty PC-Compound's
set.Add(molecule);
}
}
return(set);
}
public void TestIsEmpty_MoleculeSet()
{
IChemModel chemModel = (IChemModel)NewChemObject();
IChemObjectBuilder builder = chemModel.Builder;
Assert.IsNotNull(chemModel);
Assert.IsTrue(chemModel.IsEmpty());
IAtom atom = builder.NewAtom();
IAtomContainer mol = builder.NewAtomContainer();
IChemObjectSet<IAtomContainer> mset = builder.NewAtomContainerSet();
mol.Atoms.Add(atom);
mset.Add(mol);
chemModel.MoleculeSet = mset;
Assert.IsFalse(chemModel.IsEmpty(), "chem model with a molecule set should not be empty");
mol.Atoms.Remove(atom);
Assert.IsFalse(chemModel.IsEmpty(), "chem model with a (empty) molecule set should not be empty");
chemModel.MoleculeSet = null;
Assert.IsTrue(chemModel.IsEmpty(), "chemo model with no molecule set should be empty");
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
/// <returns>The IAtomContainerSet</returns>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
//CreateFromSmiles("[C+](H)(H)-[O-]");
IAtomContainer molecule = builder.NewAtomContainer();
IAtom carbon = builder.NewAtom("C");
carbon.FormalCharge = 1;
molecule.Atoms.Add(carbon);
IAtom oxyg = builder.NewAtom("O");
oxyg.FormalCharge = -1;
molecule.Atoms.Add(oxyg);
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.Atoms.Add(new Atom("H"));
molecule.Atoms.Add(new Atom("H"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[2], BondOrder.Single);
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[3], BondOrder.Single);
setOfProducts.Add(molecule);
return(setOfProducts);
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
/* C=C */
var molecule1 = builder.NewAtomContainer();
molecule1.Atoms.Add(builder.NewAtom("C"));
molecule1.Atoms.Add(builder.NewAtom("C"));
molecule1.AddBond(molecule1.Atoms[0], molecule1.Atoms[1], BondOrder.Double);
try
{
AddExplicitHydrogens(molecule1);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
/* [C*] */
var molecule2 = builder.NewAtomContainer();
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.Atoms.Add(builder.NewAtom("H"));
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[1], BondOrder.Single);
molecule2.Atoms.Add(builder.NewAtom("H"));
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[2], BondOrder.Single);
molecule2.Atoms.Add(builder.NewAtom("H"));
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[3], BondOrder.Single);
IAtom atom = molecule2.Atoms[0];
molecule2.SingleElectrons.Add(CDK.Builder.NewSingleElectron(atom));
setOfProducts.Add(molecule1);
setOfProducts.Add(molecule2);
return(setOfProducts);
}