public void TestDetectNaphtalene()
{
Trace.TraceInformation("Entering testDetectNaphtalene.");
IAtomContainer mol = null;
var filename = "NCDK.Data.CML.naphtalene.cml";
mol = ReadCMLMolecule(filename);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
var acSet = ConjugatedPiSystemsDetector.Detect(mol);
Assert.AreEqual(1, acSet.Count);
IAtomContainer ac = acSet[0];
Assert.AreEqual(10, ac.Atoms.Count);
Assert.AreEqual(11, ac.Bonds.Count);
for (int i = 0; i < ac.Atoms.Count; i++)
{
Assert.IsTrue(mol.Contains(ac.Atoms[i]));
}
for (int i = 0; i < ac.Bonds.Count; i++)
{
Assert.IsTrue(mol.Contains(ac.Bonds[i]));
}
}
public void TestCyanoallene()
{
IAtomContainer mol = null;
mol = CDK.SmilesParser.ParseSmiles("C=C=CC#N");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
AddImplicitHydrogens(mol);
CDK.LonePairElectronChecker.Saturate(mol);
Aromaticity.CDKLegacy.Apply(mol);
var acSet = ConjugatedPiSystemsDetector.Detect(mol);
Assert.AreEqual(1, acSet.Count);
IAtomContainer ac1 = acSet[0];
Assert.AreEqual(4, ac1.Atoms.Count);
Assert.AreEqual(3, ac1.Bonds.Count);
for (int i = 0; i < ac1.Atoms.Count; i++)
{
Assert.IsTrue(mol.Contains(ac1.Atoms[i]));
}
for (int i = 0; i < ac1.Bonds.Count; i++)
{
Assert.IsTrue(mol.Contains(ac1.Bonds[i]));
}
}
public void TestChargeWithProtonImplicit()
{
var sp = CDK.SmilesParser;
var mol = sp.ParseSmiles("C=C[C+]");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
CDK.LonePairElectronChecker.Saturate(mol);
Aromaticity.CDKLegacy.Apply(mol);
var acSet = ConjugatedPiSystemsDetector.Detect(mol);
Assert.AreEqual(1, acSet.Count);
IAtomContainer ac1 = acSet[0];
Assert.AreEqual(3, ac1.Atoms.Count);
Assert.AreEqual(2, ac1.Bonds.Count);
for (int i = 0; i < ac1.Atoms.Count; i++)
{
Assert.IsTrue(mol.Contains(ac1.Atoms[i]));
}
for (int i = 0; i < ac1.Bonds.Count; i++)
{
Assert.IsTrue(mol.Contains(ac1.Bonds[i]));
}
}
public static void Main(string[] args)
{
{
var mol = new AtomContainer();
#region Detect
Atom a0 = new Atom("C"); mol.Atoms.Add(a0);
Atom a1 = new Atom("C"); mol.Atoms.Add(a1);
Atom a2 = new Atom("C"); mol.Atoms.Add(a2);
Atom h1 = new Atom("H"); mol.Atoms.Add(h1);
Atom h2 = new Atom("H"); mol.Atoms.Add(h2);
Atom h3 = new Atom("H"); mol.Atoms.Add(h3);
Atom h4 = new Atom("H"); mol.Atoms.Add(h4);
Atom h5 = new Atom("H"); mol.Atoms.Add(h5);
mol.AddBond(a0, a1, BondOrder.Double);
mol.AddBond(a1, a2, BondOrder.Single);
mol.AddBond(a0, h1, BondOrder.Single);
mol.AddBond(a0, h2, BondOrder.Single);
mol.AddBond(a1, h3, BondOrder.Single);
mol.AddBond(a2, h4, BondOrder.Single);
mol.AddBond(a2, h5, BondOrder.Single);
SingleElectron se = new SingleElectron(a2);
mol.Add(se);
var pi_systems = ConjugatedPiSystemsDetector.Detect(mol);
#endregion
}
}
public void TestPiSystemWithCarbokation()
{
Trace.TraceInformation("Entering testPiSystemWithCarbokation.");
IAtomContainer mol = null;
var filename = "NCDK.Data.MDL.piSystemWithCarbokation.mol";
var ins = ResourceLoader.GetAsStream(filename);
MDLReader reader = new MDLReader(ins);
var chemFile = reader.Read(builder.NewChemFile());
mol = chemFile[0][0].MoleculeSet[0];
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
var acSet = ConjugatedPiSystemsDetector.Detect(mol);
Assert.AreEqual(2, acSet.Count);
IAtomContainer ac1 = acSet[0];
Assert.AreEqual(4, ac1.Atoms.Count);
Assert.AreEqual(3, ac1.Bonds.Count);
for (int i = 0; i < ac1.Atoms.Count; i++)
{
Assert.IsTrue(mol.Contains(ac1.Atoms[i]));
}
for (int i = 0; i < ac1.Bonds.Count; i++)
{
Assert.IsTrue(mol.Contains(ac1.Bonds[i]));
}
IAtomContainer ac2 = acSet[0];
Assert.AreEqual(4, ac2.Atoms.Count);
Assert.AreEqual(3, ac2.Bonds.Count);
for (int i = 0; i < ac2.Atoms.Count; i++)
{
Assert.IsTrue(mol.Contains(ac2.Atoms[i]));
}
for (int i = 0; i < ac2.Bonds.Count; i++)
{
Assert.IsTrue(mol.Contains(ac2.Bonds[i]));
}
}
public void Test1_fluorobutadienene()
{
IAtomContainer mol = CDK.SmilesParser.ParseSmiles("FC=CC=C");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
AddImplicitHydrogens(mol);
CDK.LonePairElectronChecker.Saturate(mol);
Aromaticity.CDKLegacy.Apply(mol);
var acSet = ConjugatedPiSystemsDetector.Detect(mol);
Assert.AreEqual(1, acSet.Count);
IAtomContainer ac1 = acSet[0];
Assert.AreEqual(5, ac1.Atoms.Count);
Assert.AreEqual(4, ac1.Bonds.Count);
}
public void Test3Aminomethane_cation()
{
var builder = CDK.Builder;
var mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("N"));
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[0], mol.Atoms[3], BondOrder.Single);
mol.Atoms[3].FormalCharge = +1;
mol.Atoms.Add(builder.NewAtom("N"));
mol.AddBond(mol.Atoms[3], mol.Atoms[4], BondOrder.Single);
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[4], mol.Atoms[5], BondOrder.Single);
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[4], mol.Atoms[6], BondOrder.Single);
mol.Atoms.Add(builder.NewAtom("N"));
mol.AddBond(mol.Atoms[3], mol.Atoms[7], BondOrder.Single);
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[7], mol.Atoms[8], BondOrder.Single);
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[7], mol.Atoms[8], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
AddImplicitHydrogens(mol);
CDK.LonePairElectronChecker.Saturate(mol);
Aromaticity.CDKLegacy.Apply(mol);
var acSet = ConjugatedPiSystemsDetector.Detect(mol);
Assert.AreEqual(1, acSet.Count);
IAtomContainer ac1 = acSet[0];
Assert.AreEqual(4, ac1.Atoms.Count);
Assert.AreEqual(3, ac1.Bonds.Count);
}
public void TestNN_dimethylaniline_cation()
{
IAtomContainer mol = null;
var filename = "NCDK.Data.MDL.NN_dimethylaniline.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
mol = chemFile[0][0].MoleculeSet[0];
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
AddImplicitHydrogens(mol);
CDK.LonePairElectronChecker.Saturate(mol);
Aromaticity.CDKLegacy.Apply(mol);
var acSet = ConjugatedPiSystemsDetector.Detect(mol);
Assert.AreEqual(1, acSet.Count);
IAtomContainer ac1 = acSet[0];
Assert.AreEqual(6, ac1.Atoms.Count);
Assert.AreEqual(5, ac1.Bonds.Count);
}