public void TestCalculateCharges_IAtomContainer()
{
double[] testResult = { 0.07915, -0.25264, 0.05783, 0.05783, 0.05783 };
var peoe = new GasteigerMarsiliPartialCharges();
var 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);
peoe.CalculateCharges(molecule);
for (int i = 0; i < molecule.Atoms.Count; i++)
{
Assert.AreEqual(testResult[i], molecule.Atoms[i].Charge.Value, 0.01);
}
}
public void TestUndefinedPartialCharge()
{
var filename = "NCDK.Data.MDL.burden_undefined.sdf";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var content = reader.Read(builder.NewChemFile());
reader.Close();
var cList = ChemFileManipulator.GetAllAtomContainers(content);
var ac = cList.First();
Assert.IsNotNull(ac);
AddExplicitHydrogens(ac);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(ac);
Aromaticity.CDKLegacy.Apply(ac);
AddExplicitHydrogens(ac);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(ac);
CDK.LonePairElectronChecker.Saturate(ac);
var peoe = new GasteigerMarsiliPartialCharges();
peoe.CalculateCharges(ac);
}