public void RadicalCanon()
{
var builder = CDK.Builder;
IAtomContainer mola = builder.NewAtomContainer();
mola.Atoms.Add(builder.NewAtom("CH3"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH1"));
mola.Atoms.Add(builder.NewAtom("CH3"));
mola.AddBond(mola.Atoms[1], mola.Atoms[2], BondOrder.Single);
mola.AddBond(mola.Atoms[2], mola.Atoms[3], BondOrder.Single);
mola.AddBond(mola.Atoms[3], mola.Atoms[4], BondOrder.Single);
mola.AddBond(mola.Atoms[4], mola.Atoms[5], BondOrder.Single);
mola.AddBond(mola.Atoms[5], mola.Atoms[6], BondOrder.Single);
mola.AddBond(mola.Atoms[0], mola.Atoms[5], BondOrder.Single);
mola.AddSingleElectronTo(mola.Atoms[1]);
SmilesParser smipar = new SmilesParser(builder);
var molb = smipar.ParseSmiles("CC(CCC[CH2])C |^1:5|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.Canonical | SmiFlavors.CxRadical);
Assert.AreEqual(smigen.Create(molb), smigen.Create(mola));
}
public void TestCompareIonized()
{
var molA = CDK.Builder.NewAtomContainer();
molA.Atoms.Add(CDK.Builder.NewAtom("C"));
molA.Atoms.Add(CDK.Builder.NewAtom("C"));
molA.AddBond(molA.Atoms[0], molA.Atoms[1], BondOrder.Single);
molA.Atoms.Add(CDK.Builder.NewAtom("C"));
molA.AddBond(molA.Atoms[1], molA.Atoms[2], BondOrder.Single);
molA.Atoms.Add(CDK.Builder.NewAtom("Cl"));
molA.AddBond(molA.Atoms[2], molA.Atoms[3], BondOrder.Single);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molA);
AddExplicitHydrogens(molA);
CDK.LonePairElectronChecker.Saturate(molA);
PiElectronegativityDescriptor descriptor;
descriptor = CreateDescriptor(molA);
var resultA = descriptor.Calculate(molA.Atoms[3]).Value;
IAtomContainer molB = CDK.Builder.NewAtomContainer();
molB.Atoms.Add(CDK.Builder.NewAtom("C"));
molB.Atoms.Add(CDK.Builder.NewAtom("C"));
molB.AddBond(molB.Atoms[0], molB.Atoms[1], BondOrder.Single);
molB.Atoms.Add(CDK.Builder.NewAtom("C"));
molB.AddBond(molB.Atoms[1], molB.Atoms[2], BondOrder.Single);
molB.Atoms.Add(CDK.Builder.NewAtom("Cl"));
molB.Atoms[3].FormalCharge = 1;
molB.AddSingleElectronTo(molB.Atoms[3]);
molB.AddLonePairTo(molB.Atoms[3]);
molB.AddLonePairTo(molB.Atoms[3]);
molB.AddBond(molB.Atoms[2], molB.Atoms[3], BondOrder.Single);
AddExplicitHydrogens(molB);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molB);
CDK.LonePairElectronChecker.Saturate(molB);
Assert.AreEqual(1, molB.Atoms[3].FormalCharge.Value, 0.00001);
Assert.AreEqual(1, molB.SingleElectrons.Count, 0.00001);
Assert.AreEqual(2, molB.LonePairs.Count, 0.00001);
descriptor = CreateDescriptor(molB);
var resultB = descriptor.Calculate(molB.Atoms[3]).Value;
Assert.AreEqual(resultA, resultB, 0.00001);
}