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 TestAssignrPiMarsilliFactors_IAtomContainerSet()
{
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);
foreach (var atom in molecule.Atoms)
{
atom.Charge = 0;
}
var set = builder.NewAtomContainerSet();
set.Add(molecule);
set.Add(molecule);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
Assert.IsNotNull(peoe.AssignrPiMarsilliFactors(set));
}
/// <summary>
/// Constructor for the Electronegativity object.
/// </summary>
/// <param name="maxIterations">The maximal number of Iteration</param>
/// <param name="maxResonStruc">The maximal number of Resonance Structures</param>
public PiElectronegativity(int maxIterations, int maxResonStruc)
{
peoe = new GasteigerMarsiliPartialCharges();
pepe = new GasteigerPEPEPartialCharges();
MaxIterations = maxIterations;
MaxResonanceStructures = maxResonStruc;
}
public void TestSetStepSize()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
int StepSize = 22;
peoe.StepSize = StepSize;
Assert.AreEqual(StepSize, peoe.StepSize);
}
public void TestSetMaxResoStruc_Int()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
int MX_RESON = 1;
peoe.MaxResonanceStructures = MX_RESON;
Assert.AreEqual(MX_RESON, peoe.MaxResonanceStructures);
}
public void TestSetMaxGasteigerIters_Double()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
int MX_ITERATIONS = 10;
peoe.MaxGasteigerIterations = MX_ITERATIONS;
Assert.AreEqual(MX_ITERATIONS, peoe.MaxGasteigerIterations);
}
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);
}
}
public void TestGetStepSize()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
Assert.AreEqual(5, peoe.StepSize);
}
public void TestGetMaxResoStruc()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
Assert.AreEqual(50, peoe.MaxResonanceStructures);
}
public void TestGetMaxGasteigerIters()
{
GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
Assert.AreEqual(8, peoe.MaxGasteigerIterations);
}