public void TestFerrocene()
{
IAtomContainer ferrocene = builder.NewAtomContainer();
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms[4].FormalCharge = -1;
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms.Add(builder.NewAtom("C"));
ferrocene.Atoms[9].FormalCharge = -1;
ferrocene.Atoms.Add(builder.NewAtom("Fe"));
ferrocene.Atoms[10].FormalCharge = +2;
ferrocene.AddBond(ferrocene.Atoms[0], ferrocene.Atoms[1], BondOrder.Double);
ferrocene.AddBond(ferrocene.Atoms[1], ferrocene.Atoms[2], BondOrder.Single);
ferrocene.AddBond(ferrocene.Atoms[2], ferrocene.Atoms[3], BondOrder.Double);
ferrocene.AddBond(ferrocene.Atoms[3], ferrocene.Atoms[4], BondOrder.Single);
ferrocene.AddBond(ferrocene.Atoms[4], ferrocene.Atoms[0], BondOrder.Single);
ferrocene.AddBond(ferrocene.Atoms[5], ferrocene.Atoms[6], BondOrder.Double);
ferrocene.AddBond(ferrocene.Atoms[6], ferrocene.Atoms[7], BondOrder.Single);
ferrocene.AddBond(ferrocene.Atoms[7], ferrocene.Atoms[8], BondOrder.Double);
ferrocene.AddBond(ferrocene.Atoms[8], ferrocene.Atoms[9], BondOrder.Single);
ferrocene.AddBond(ferrocene.Atoms[9], ferrocene.Atoms[5], BondOrder.Single);
var expectedTypes = new string[] { "C.2", "C.2", "C.2", "C.2", "Any", "C.2", "C.2", "C.2", "C.2", "Any", "Fe" };
AssertAtomTypes(testedAtomTypes, expectedTypes, ferrocene);
}
/// <summary>
/// Get the expected set of molecules. [C-]-C = C
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
IAtomContainer 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 molecule 1: [C-]-[C+] - C
/// </summary>
private IChemObjectSet <IAtomContainer> GetExampleReactants()
{
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms[0].FormalCharge = -1;
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms[1].FormalCharge = +1;
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);
try
{
AddExplicitHydrogens(molecule);
MakeSureAtomTypesAreRecognized(molecule);
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfReactants.Add(molecule);
return(setOfReactants);
}
/// <summary>
/// Get the Ethene structure.
/// </summary>
/// <returns>The IAtomContainer</returns>
/// <exception cref="CDKException"></exception>
private IChemObjectSet <IAtomContainer> GetExampleReactants()
{
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
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.Double);
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[0], molecule.Atoms[2], BondOrder.Single);
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[3], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[4], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[5], BondOrder.Single);
try
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
}
catch (CDKException e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfReactants.Add(molecule);
return(setOfReactants);
}
/// <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 void MethyleneCyclopropeneTest()
{
IAtomContainer mol = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(mol, 4);
AbstractSignatureTest.AddHydrogens(mol, 1, 2);
AbstractSignatureTest.AddHydrogens(mol, 2, 1);
AbstractSignatureTest.AddHydrogens(mol, 3, 1);
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Double);
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[3], BondOrder.Single);
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Double);
MoleculeSignature molSig = new MoleculeSignature(mol);
string sigFor2Height1 = molSig.SignatureStringForVertex(2, 1);
string sigFor3Height1 = molSig.SignatureStringForVertex(3, 1);
Assert.IsTrue(
sigFor2Height1.Equals(sigFor3Height1),
"Height 1 signatures for atoms 2 and 3" + " should be the same");
string sigFor2Height2 = molSig.SignatureStringForVertex(2, 1);
string sigFor3Height2 = molSig.SignatureStringForVertex(3, 1);
Assert.IsTrue(
sigFor2Height2.Equals(sigFor3Height2),
"Height 2 signatures for atoms 2 and 3" + " should be the same");
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
IAtomContainer 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);
IAtomContainer 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(new SingleElectron(molecule2.Atoms[0]));
setOfProducts.Add(molecule2);
return(setOfProducts);
}
/// <summary>
/// Get the example set of molecules.
/// </summary>
private IChemObjectSet <IAtomContainer> GetExampleReactants()
{
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
IAtomContainer molecule = builder.NewAtomContainer();//CreateFromSmiles("C-C#[O+]")
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[2], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[3], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[4], BondOrder.Single);
IAtom oxy = builder.NewAtom("O");
oxy.FormalCharge = 1;
molecule.Atoms.Add(oxy);
molecule.AddBond(molecule.Atoms[4], molecule.Atoms[5], BondOrder.Triple);
try
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
MakeSureAtomTypesAreRecognized(molecule);
}
catch (CDKException e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfReactants.Add(molecule);
return(setOfReactants);
}
public void TestAutomatic_Set_Active_Bond()
{
/* ionize all possible double bonds */
IAtomContainer reactant = builder.NewAtomContainer();//Miles("C=CC")
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.Atoms.Add(builder.NewAtom("C"));
reactant.AddBond(reactant.Atoms[0], reactant.Atoms[1], BondOrder.Double);
reactant.AddBond(reactant.Atoms[1], reactant.Atoms[2], BondOrder.Single);
AddExplicitHydrogens(reactant);
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
setOfReactants.Add(reactant);
/* initiate */
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(reactant);
MakeSureAtomTypesAreRecognized(reactant);
IReactionProcess type = new ElectronImpactPDBReaction();
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(2, setOfReactions.Count);
IAtomContainer molecule = setOfReactions[0].Products[0];
Assert.AreEqual(1, molecule.Atoms[0].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[1]).Count());
molecule = setOfReactions[1].Products[0];
Assert.AreEqual(1, molecule.Atoms[1].FormalCharge.Value);
Assert.AreEqual(1, molecule.GetConnectedSingleElectrons(molecule.Atoms[0]).Count());
}
/// <inheritdoc/>
public override void MakeEdge(int vertexIndex1, int vertexIndex2, string vertexSymbol1, string vertexSymbol2, string edgeLabel)
{
switch (edgeLabel)
{
case "":
container.AddBond(container.Atoms[vertexIndex1], container.Atoms[vertexIndex2], BondOrder.Single);
break;
case "=":
container.AddBond(container.Atoms[vertexIndex1], container.Atoms[vertexIndex2], BondOrder.Double);
break;
case "#":
container.AddBond(container.Atoms[vertexIndex1], container.Atoms[vertexIndex2], BondOrder.Triple);
break;
case "p":
IBond bond = builder.NewBond(container.Atoms[vertexIndex1], container.Atoms[vertexIndex2], BondOrder.Single);
bond.IsAromatic = true;
container.Bonds.Add(bond);
break;
default:
break;
}
}
public void TestM25()
{
//CreateFromSmiles("C[O*]")
IAtomContainer expected1 = builder.NewAtomContainer();
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.Atoms.Add(builder.NewAtom("O"));
expected1.SingleElectrons.Add(builder.NewSingleElectron(expected1.Atoms[1]));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[1], BondOrder.Single);
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[2], BondOrder.Single);
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[3], BondOrder.Single);
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[4], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected1);
string[] expectedTypes = { "C.sp3", "O.sp3.radical", "H", "H", "H" };
Assert.AreEqual(expectedTypes.Length, expected1.Atoms.Count);
for (int i = 0; i < expectedTypes.Length; i++)
{
IAtom nextAtom = expected1.Atoms[i];
IAtomType perceivedType = matcher.FindMatchingAtomType(expected1, nextAtom);
Assert.IsNotNull(perceivedType, "Missing atom type for: " + nextAtom + " " + i + " expected: " + expectedTypes[i]);
Assert.AreEqual(expectedTypes[i], perceivedType.AtomTypeName, "Incorrect atom type perceived for: " + nextAtom);
}
}
public void TestM19()
{
//CreateFromSmiles("C=[N*+]")
IAtomContainer expected1 = builder.NewAtomContainer();
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.Atoms.Add(builder.NewAtom("N"));
expected1.Atoms[1].FormalCharge = 1;
expected1.SingleElectrons.Add(builder.NewSingleElectron(expected1.Atoms[1]));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[1], BondOrder.Double);
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[2], BondOrder.Single);
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[3], BondOrder.Single);
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[4], BondOrder.Single);
string[] expectedTypes = { "C.sp2", "N.plus.sp2.radical", "H", "H", "H" };
Assert.AreEqual(expectedTypes.Length, expected1.Atoms.Count);
for (int i = 0; i < expectedTypes.Length; i++)
{
IAtom nextAtom = expected1.Atoms[i];
IAtomType perceivedType = matcher.FindMatchingAtomType(expected1, nextAtom);
Assert.IsNotNull(perceivedType, "Missing atom type for: " + nextAtom + " " + i + " expected: " + expectedTypes[i]);
Assert.AreEqual(expectedTypes[i], perceivedType.AtomTypeName, "Incorrect atom type perceived for: " + nextAtom);
}
}
public void TestCalculatePositive_IAtomContainer_IAtom()
{
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[1].FormalCharge = +1;
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.Double);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
for (int i = 0; i < molecule.Atoms.Count; i++)
{
if (i == 1)
{
Assert.AreNotSame(0.0, StabilizationCharges.CalculatePositive(molecule, molecule.Atoms[i]));
}
else
{
Assert.AreEqual(0.0, StabilizationCharges.CalculatePositive(molecule, molecule.Atoms[i]), 0.001);
}
}
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
/// <returns>The IAtomContainerSet</returns>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
//C[C+]O|
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms[1].FormalCharge = 1;
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("O"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], 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 Test12DimethylBenzene()
{
var builder = CDK.Builder;
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Double);
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[3], BondOrder.Single);
molecule.AddBond(molecule.Atoms[3], molecule.Atoms[4], BondOrder.Double);
molecule.AddBond(molecule.Atoms[4], molecule.Atoms[5], BondOrder.Single);
molecule.AddBond(molecule.Atoms[5], molecule.Atoms[0], BondOrder.Double);
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[6], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[7], BondOrder.Single);
// 2,3-dimethyl-1,3-butadiene matches
IAtomContainer query1 = builder.NewAtomContainer();
query1.Atoms.Add(builder.NewAtom("C"));
query1.Atoms.Add(builder.NewAtom("C"));
query1.Atoms.Add(builder.NewAtom("C"));
query1.Atoms.Add(builder.NewAtom("C"));
query1.Atoms.Add(builder.NewAtom("C"));
query1.Atoms.Add(builder.NewAtom("C"));
query1.AddBond(query1.Atoms[0], query1.Atoms[1], BondOrder.Single);
query1.AddBond(query1.Atoms[1], query1.Atoms[2], BondOrder.Double);
query1.AddBond(query1.Atoms[3], query1.Atoms[0], BondOrder.Double);
query1.AddBond(query1.Atoms[0], query1.Atoms[4], BondOrder.Single);
query1.AddBond(query1.Atoms[1], query1.Atoms[5], BondOrder.Single);
QueryAtomContainer queryContainer1 = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(query1);
Assert.IsTrue(new UniversalIsomorphismTester().IsSubgraph(molecule, queryContainer1));
// 2,3-dimethyl-2-butene does not match
IAtomContainer query2 = builder.NewAtomContainer();
query2.Atoms.Add(builder.NewAtom("C"));
query2.Atoms.Add(builder.NewAtom("C"));
query2.Atoms.Add(builder.NewAtom("C"));
query2.Atoms.Add(builder.NewAtom("C"));
query2.Atoms.Add(builder.NewAtom("C"));
query2.Atoms.Add(builder.NewAtom("C"));
query2.AddBond(query2.Atoms[0], query2.Atoms[1], BondOrder.Double);
query2.AddBond(query2.Atoms[1], query2.Atoms[2], BondOrder.Single);
query2.AddBond(query2.Atoms[3], query2.Atoms[0], BondOrder.Single);
query2.AddBond(query2.Atoms[0], query2.Atoms[4], BondOrder.Single);
query2.AddBond(query2.Atoms[1], query2.Atoms[5], BondOrder.Single);
QueryAtomContainer queryContainer2 = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(query2);
Assert.IsFalse(new UniversalIsomorphismTester().IsSubgraph(molecule, queryContainer2));
}
public void TestOspDoubleB()
{
//CreateFromSmiles("O=C")
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("O"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Double);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[3], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
molecule.Atoms[0].IsReactiveCenter = true;
molecule.Atoms[1].IsReactiveCenter = true;
molecule.Bonds[0].IsReactiveCenter = true;
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
setOfReactants.Add(molecule);
IReactionProcess type = new HeterolyticCleavagePBReaction();
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter();
param.IsSetParameter = true;
paramList.Add(param);
type.ParameterList = paramList;
/* initiate */
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(1, setOfReactions.Count);
// expected products
//CreateFromSmiles("[O-][C+]")
IAtomContainer expected1 = builder.NewAtomContainer();
expected1.Atoms.Add(builder.NewAtom("O"));
expected1.Atoms[0].FormalCharge = -1;
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.Atoms[1].FormalCharge = +1;
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[1], BondOrder.Single);
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[2], BondOrder.Single);
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[3], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected1);
CDK.LonePairElectronChecker.Saturate(expected1);
IAtomContainer product1 = setOfReactions[0].Products[0];
QueryAtomContainer queryAtom = QueryAtomContainerCreator.CreateSymbolAndChargeQueryContainer(expected1);
Assert.IsTrue(uiTester.IsIsomorph(product1, queryAtom));
}
public static IAtomContainer MakeSandwich(int ringSize, bool hasMethyl)
{
IAtomContainer mol = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(mol, (ringSize * 2));
mol.Atoms.Add(builder.NewAtom("Fe"));
int center = ringSize * 2;
// face A
for (int i = 0; i < ringSize - 1; i++)
{
mol.AddBond(mol.Atoms[i], mol.Atoms[i + 1], BondOrder.Single);
mol.AddBond(mol.Atoms[i], mol.Atoms[center], BondOrder.Single);
}
mol.AddBond(mol.Atoms[ringSize - 1], mol.Atoms[0], BondOrder.Single);
mol.AddBond(mol.Atoms[ringSize - 1], mol.Atoms[center], BondOrder.Single);
// // face B
for (int i = 0; i < ringSize - 1; i++)
{
mol.AddBond(mol.Atoms[ringSize + 1], mol.Atoms[i + ringSize + 1], BondOrder.Single);
mol.AddBond(mol.Atoms[ringSize + 1], mol.Atoms[center], BondOrder.Single);
}
mol.AddBond(mol.Atoms[(2 * ringSize) - 1], mol.Atoms[ringSize], BondOrder.Single);
mol.AddBond(mol.Atoms[(2 * ringSize) - 1], mol.Atoms[center], BondOrder.Single);
if (hasMethyl)
{
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[0], mol.Atoms.Last(), BondOrder.Single);
}
return(mol);
}
public override void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
IReactionProcess type = new HyperconjugationReaction();
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
/* [C+]CC */
IAtomContainer 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);
AddExplicitHydrogens(molecule);
setOfReactants.Add(molecule);
/* automatic search of the center active */
var paramList = new List <IParameterReaction>();
var param = new SetReactionCenter();
param.IsSetParameter = false;
paramList.Add(param);
type.ParameterList = paramList;
/* initiate */
MakeSureAtomTypesAreRecognized(molecule);
var setOfReactions = type.Initiate(setOfReactants, null);
Assert.AreEqual(2, setOfReactions.Count);
Assert.AreEqual(2, setOfReactions[0].Products.Count);
IAtomContainer product = setOfReactions[0].Products[0];
/* C=CC */
IAtomContainer molecule2 = builder.NewAtomContainer();
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.AddBond(molecule2.Atoms[0], molecule2.Atoms[1], BondOrder.Double);
molecule2.Atoms.Add(builder.NewAtom("C"));
molecule2.AddBond(molecule2.Atoms[1], molecule2.Atoms[2], BondOrder.Single);
AddExplicitHydrogens(molecule2);
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, product));
product = setOfReactions[0].Products[1];
/* [H+] */
molecule2 = builder.NewAtomContainer();
molecule2.Atoms.Add(builder.NewAtom("H"));
molecule2.Atoms[0].FormalCharge = 1;
Assert.IsTrue(new UniversalIsomorphismTester().IsIsomorph(molecule2, product));
}
public IAtomContainer MakeCCC()
{
IAtomContainer container = builder.NewAtomContainer();
container.Atoms.Add(builder.NewAtom("C", new Vector2(-1, -1)));
container.Atoms.Add(builder.NewAtom("C", new Vector2(0, 0)));
container.Atoms.Add(builder.NewAtom("C", new Vector2(1, -1)));
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
container.AddBond(container.Atoms[1], container.Atoms[2], BondOrder.Single);
return(container);
}
public static IAtomContainer MakeCyclobutane()
{
IAtomContainer mol = builder.NewAtomContainer();
AddCarbons(mol, 4);
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[3], BondOrder.Single);
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single);
return(mol);
}
/// <summary>
/// This method creates <i>E</i>-but-2-ene.
/// </summary>
static DoubleBondStereochemistryTest()
{
molecule = new AtomContainer();
molecule.Atoms.Add(new Atom("C"));
molecule.Atoms.Add(new Atom("C"));
molecule.Atoms.Add(new Atom("C"));
molecule.Atoms.Add(new Atom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Double);
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[3], BondOrder.Single);
ligands = new IBond[] { molecule.Bonds[0], molecule.Bonds[2] };
}
static IAtomContainer But2ene()
{
IAtomContainer container = CDK.Builder.NewAtomContainer();
container.Atoms.Add(Atom("C", 1));
container.Atoms.Add(Atom("C", 1));
container.Atoms.Add(Atom("C", 3));
container.Atoms.Add(Atom("C", 3));
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Double);
container.AddBond(container.Atoms[0], container.Atoms[2], BondOrder.Single);
container.AddBond(container.Atoms[1], container.Atoms[3], BondOrder.Single);
return(container);
}
static TetrahedralChiralityTest()
{
molecule = new AtomContainer();
molecule.Atoms.Add(new Atom("Cl"));
molecule.Atoms.Add(new Atom("C"));
molecule.Atoms.Add(new Atom("Br"));
molecule.Atoms.Add(new Atom("I"));
molecule.Atoms.Add(new Atom("H"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[2], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[3], BondOrder.Single);
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[4], BondOrder.Single);
ligands = new IAtom[] { molecule.Atoms[4], molecule.Atoms[3], molecule.Atoms[2], molecule.Atoms[0] };
}
private IChemObjectSet <IAtomContainer> GetExampleReactants()
{
var setOfReactants = ChemObjectBuilder.Instance.NewAtomContainerSet();
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("O"));
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("H"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[3], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[1], molecule.Atoms[4], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[5], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[6], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[2], molecule.Atoms[7], BondOrder.Single);
molecule.Atoms.Add(builder.NewAtom("H"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[8], BondOrder.Single);
IAtom atom = molecule.Atoms[0];
atom.FormalCharge = 1;
molecule.SingleElectrons.Add(new SingleElectron(atom));
setOfReactants.Add(molecule);
return(setOfReactants);
}
/// <summary>
/// Get the expected set of molecules.
/// </summary>
/// <returns>The IAtomContainerSet</returns>
private IChemObjectSet <IAtomContainer> GetExpectedProducts()
{
var setOfProducts = builder.NewAtomContainerSet();
IAtomContainer expected1 = builder.NewAtomContainer();
expected1.Atoms.Add(builder.NewAtom("C"));
expected1.Atoms.Add(builder.NewAtom("O"));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[1], BondOrder.Single);
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.Atoms.Add(builder.NewAtom("H"));
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[2], BondOrder.Single);
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[3], BondOrder.Single);
expected1.AddBond(expected1.Atoms[0], expected1.Atoms[4], BondOrder.Single);
expected1.AddBond(expected1.Atoms[1], expected1.Atoms[5], BondOrder.Single);
try
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected1);
CDK.LonePairElectronChecker.Saturate(expected1);
}
catch (CDKException e)
{
Console.Out.WriteLine(e.StackTrace);
}
IAtomContainer expected2 = builder.NewAtomContainer();
expected2.Atoms.Add(builder.NewAtom("C"));
expected2.Atoms[0].FormalCharge = +1;
expected2.Atoms.Add(builder.NewAtom("H"));
expected2.Atoms.Add(builder.NewAtom("H"));
expected2.Atoms.Add(builder.NewAtom("H"));
expected2.AddBond(expected2.Atoms[0], expected2.Atoms[1], BondOrder.Single);
expected2.AddBond(expected2.Atoms[0], expected2.Atoms[2], BondOrder.Single);
expected2.AddBond(expected2.Atoms[0], expected2.Atoms[3], BondOrder.Single);
try
{
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(expected2);
}
catch (CDKException e)
{
Console.Out.WriteLine(e.StackTrace);
}
setOfProducts.Add(expected1);
setOfProducts.Add(expected2);
return(setOfProducts);
}
/// <summary>
/// Make a square with four different elements, to test things like atom color.
/// </summary>
/// <returns>an unlikely S-N-O-P square</returns>
public IAtomContainer MakeSNOPSquare()
{
IAtomContainer container = builder.NewAtomContainer();
container.Atoms.Add(builder.NewAtom("S", new Vector2(-1, -1)));
container.Atoms.Add(builder.NewAtom("N", new Vector2(1, -1)));
container.Atoms.Add(builder.NewAtom("O", new Vector2(1, 1)));
container.Atoms.Add(builder.NewAtom("P", new Vector2(-1, 1)));
container.AddBond(container.Atoms[0], container.Atoms[1], BondOrder.Single);
container.AddBond(container.Atoms[0], container.Atoms[3], BondOrder.Single);
container.AddBond(container.Atoms[1], container.Atoms[2], BondOrder.Single);
container.AddBond(container.Atoms[2], container.Atoms[3], BondOrder.Single);
return(container);
}
public static IAtomContainer GetIsobutane(IChemObjectBuilder builder)
{
IAtomContainer mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("C"));
mol.Atoms.Add(builder.NewAtom("C"));
mol.Atoms.Add(builder.NewAtom("C"));
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[3], BondOrder.Single);
return(mol);
}
public static void AddRing(int atomToAttachTo, int ringSize, IAtomContainer mol)
{
int numberOfAtoms = mol.Atoms.Count;
int previous = atomToAttachTo;
for (int i = 0; i < ringSize; i++)
{
mol.Atoms.Add(builder.NewAtom("C"));
int current = numberOfAtoms + i;
mol.AddBond(mol.Atoms[previous], mol.Atoms[current], BondOrder.Single);
previous = current;
}
mol.AddBond(mol.Atoms[numberOfAtoms], mol.Atoms[numberOfAtoms + (ringSize - 1)], BondOrder.Single);
}
public IAtomContainer MakeRing(int ringSize)
{
IAtomContainer ring = builder.NewAtomContainer();
for (int i = 0; i < ringSize; i++)
{
ring.Atoms.Add(builder.NewAtom("C"));
if (i > 0)
{
ring.AddBond(ring.Atoms[i - 1], ring.Atoms[i], BondOrder.Single);
}
}
ring.AddBond(ring.Atoms[0], ring.Atoms[ringSize - 1], BondOrder.Single);
return(ring);
}
public IAtomContainer MakeSquare()
{
IAtomContainer square = builder.NewAtomContainer();
square.Atoms.Add(builder.NewAtom("C"));
square.Atoms.Add(builder.NewAtom("C"));
square.Atoms.Add(builder.NewAtom("C"));
square.Atoms.Add(builder.NewAtom("C"));
square.AddBond(square.Atoms[0], square.Atoms[1], BondOrder.Single);
square.AddBond(square.Atoms[0], square.Atoms[3], BondOrder.Single);
square.AddBond(square.Atoms[1], square.Atoms[2], BondOrder.Single);
square.AddBond(square.Atoms[2], square.Atoms[3], BondOrder.Single);
return(Layout(square));
}