public void TestAromaticAndNonAromatic()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
string smiles1 = "c1ccccc1";
string smiles2 = "C1=CC=CC=C1";
var sp = CDK.SmilesParser;
var mol1 = sp.ParseSmiles(smiles1);
var mol2 = sp.ParseSmiles(smiles2);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
Aromaticity.CDKLegacy.Apply(mol1);
Aromaticity.CDKLegacy.Apply(mol2);
AddExplicitHydrogens(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
CDK.LonePairElectronChecker.Saturate(mol1);
AddExplicitHydrogens(mol2);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol2);
CDK.LonePairElectronChecker.Saturate(mol2);
peoe.CalculateCharges(mol1);
peoe.CalculateCharges(mol2);
for (int i = 0; i < mol1.Atoms.Count; i++)
{
Assert.AreEqual(mol1.Atoms[i].Charge.Value, mol2.Atoms[i].Charge.Value, 0.01, "charge on atom " + i + " does not match");
}
}
public void TestAromaticBondOrders()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
string smiles1 = "c1ccccc1";
var sp = CDK.SmilesParser;
var mol1 = sp.ParseSmiles(smiles1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
Aromaticity.CDKLegacy.Apply(mol1);
AddExplicitHydrogens(mol1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol1);
CDK.LonePairElectronChecker.Saturate(mol1);
List <bool> oldBondOrders = new List <bool>();
for (int i = 0; i < mol1.Bonds.Count; i++)
{
oldBondOrders.Add(mol1.Bonds[i].IsAromatic);
}
peoe.CalculateCharges(mol1);
List <bool> newBondOrders = new List <bool>();
for (int i = 0; i < mol1.Bonds.Count; i++)
{
newBondOrders.Add(mol1.Bonds[i].IsAromatic);
}
for (int i = 0; i < oldBondOrders.Count; i++)
{
Assert.AreEqual(oldBondOrders[i], newBondOrders[i], "bond " + i + " does not match");
}
}
public void TestCalculateCharges_IAtomContainer()
{
double[] testResult = { 0.0, 0.0, 0.0, 0.0, 0.0 };
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);
peoe.CalculateCharges(molecule);
for (int i = 0; i < molecule.Atoms.Count; i++)
{
//Debug.WriteLine("Charge for atom:"+i+" S:"+mol.GetAtomAt(i).Symbol+" Charge:"+mol.GetAtomAt(i).Charge);
Assert.AreEqual(testResult[i], molecule.Atoms[i].Charge.Value, 0.01);
}
}